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1. Can GPT-3.5 Generate and Code Discharge Summaries?

Author

Falis, Matúš, Gema, Aryo Pradipta, Dong, Hang, Daines, Luke, Basetti, Siddharth, Holder, Michael, Penfold, Rose S, Birch, Alexandra, and Alex, Beatrice

Subjects
Computer Science - Computation and Language
Abstract

Objective: To investigate GPT-3.5 in generating and coding medical documents with ICD-10 codes for data augmentation on low-resources labels. Materials and Methods: Employing GPT-3.5 we generated and coded 9,606 discharge summaries based on lists of ICD-10 code descriptions of patients with infrequent (generation) codes within the MIMIC-IV dataset. Combined with the baseline training set, this formed an augmented training set. Neural coding models were trained on baseline and augmented data and evaluated on a MIMIC-IV test set. We report micro- and macro-F1 scores on the full codeset, generation codes, and their families. Weak Hierarchical Confusion Matrices were employed to determine within-family and outside-of-family coding errors in the latter codesets. The coding performance of GPT-3.5 was evaluated both on prompt-guided self-generated data and real MIMIC-IV data. Clinical professionals evaluated the clinical acceptability of the generated documents. Results: Augmentation slightly hinders the overall performance of the models but improves performance for the generation candidate codes and their families, including one unseen in the baseline training data. Augmented models display lower out-of-family error rates. GPT-3.5 can identify ICD-10 codes by the prompted descriptions, but performs poorly on real data. Evaluators note the correctness of generated concepts while suffering in variety, supporting information, and narrative. Discussion and Conclusion: GPT-3.5 alone is unsuitable for ICD-10 coding. Augmentation positively affects generation code families but mainly benefits codes with existing examples. Augmentation reduces out-of-family errors. Discharge summaries generated by GPT-3.5 state prompted concepts correctly but lack variety, and authenticity in narratives. They are unsuitable for clinical practice., Comment: 15 pages; 250 words in abstract; 4,152 words in main body; 4 figures (1 black and white, 3 colour); 4 tables; 34 references; Accepted and published by the Journal of the American Medical Informatics Association

Published
2024
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2. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus

Author

Hawes Alicia C, Dinh Huyen H, Buhay Christian J, Blyth Peter R, Dugan Shannon, Ding Yan, Hemphill Lisa, Muzny Donna M, Cardenas Ana, Fox George E, Uzman Akif, Tirumalai Madhan, Petrosino Joseph, Igboeli Okezie, Liu Yamei, Fortunov Régine M, Williams Tiffany M, Shang Yue, Mason Edward O, Yerrapragada Shailaja, Jiang Huaiyang, Qin Xiang, Hultén Kristina G, Highlander Sarah K, Holder Michael, Kovar Christie L, Lee Sandra L, Liu Wen, Nazareth Lynne V, Wang Qiaoyan, Zhou Jianling, Kaplan Sheldon L, and Weinstock George M

Subjects
Microbiology, QR1-502
Abstract

Abstract Background Community acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) increasingly causes disease worldwide. USA300 has emerged as the predominant clone causing superficial and invasive infections in children and adults in the USA. Epidemiological studies suggest that USA300 is more virulent than other CA-MRSA. The genetic determinants that render virulence and dominance to USA300 remain unclear. Results We sequenced the genomes of two pediatric USA300 isolates: one CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at Texas Children's Hospital in Houston. DNA sequencing was performed by Sanger dideoxy whole genome shotgun (WGS) and 454 Life Sciences pyrosequencing strategies. The sequence of the USA300 MRSA strain was rigorously annotated. In USA300-MRSA 2658 chromosomal open reading frames were predicted and 3.1 and 27 kilobase (kb) plasmids were identified. USA300-MSSA contained a 20 kb plasmid with some homology to the 27 kb plasmid found in USA300-MRSA. Two regions found in US300-MRSA were absent in USA300-MSSA. One of these carried the arginine deiminase operon that appears to have been acquired from S. epidermidis. The USA300 sequence was aligned with other sequenced S. aureus genomes and regions unique to USA300 MRSA were identified. Conclusion USA300-MRSA is highly similar to other MRSA strains based on whole genome alignments and gene content, indicating that the differences in pathogenesis are due to subtle changes rather than to large-scale acquisition of virulence factor genes. The USA300 Houston isolate differs from another sequenced USA300 strain isolate, derived from a patient in San Francisco, in plasmid content and a number of sequence polymorphisms. Such differences will provide new insights into the evolution of pathogens.

Published
2007
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3. Hemichordate genomes and deuterostome origins.

Author

Simakov, Oleg, Kawashima, Takeshi, Marlétaz, Ferdinand, Jenkins, Jerry, Koyanagi, Ryo, Mitros, Therese, Hisata, Kanako, Bredeson, Jessen, Shoguchi, Eiichi, Gyoja, Fuki, Yue, Jia-Xing, Chen, Yi-Chih, Freeman, Robert M, Sasaki, Akane, Hikosaka-Katayama, Tomoe, Sato, Atsuko, Fujie, Manabu, Baughman, Kenneth W, Levine, Judith, Gonzalez, Paul, Cameron, Christopher, Fritzenwanker, Jens H, Pani, Ariel M, Goto, Hiroki, Kanda, Miyuki, Arakaki, Nana, Yamasaki, Shinichi, Qu, Jiaxin, Cree, Andrew, Ding, Yan, Dinh, Huyen H, Dugan, Shannon, Holder, Michael, Jhangiani, Shalini N, Kovar, Christie L, Lee, Sandra L, Lewis, Lora R, Morton, Donna, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Chen, Rui, Richards, Stephen, Muzny, Donna M, Gillis, Andrew, Peshkin, Leonid, Wu, Michael, Humphreys, Tom, Su, Yi-Hsien, Putnam, Nicholas H, Schmutz, Jeremy, Fujiyama, Asao, Yu, Jr-Kai, Tagawa, Kunifumi, Worley, Kim C, Gibbs, Richard A, Kirschner, Marc W, Lowe, Christopher J, Satoh, Noriyuki, Rokhsar, Daniel S, and Gerhart, John

Subjects
Animals, Chordata, Nonvertebrate, Echinodermata, Transforming Growth Factor beta, Evolution, Molecular, Phylogeny, Signal Transduction, Conserved Sequence, Synteny, Multigene Family, Genome, Chordata, Nonvertebrate, Evolution, Molecular, General Science & Technology
Abstract

Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Published
2015

4. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

Author

Chipman, Ariel D, Ferrier, David EK, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel ST, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer CJ, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis JP, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome HL, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, and Zou, Xiaoyan

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Prevention, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Arthropods, Circadian Rhythm Signaling Peptides and Proteins, DNA Methylation, Evolution, Molecular, Female, Genome, Genome, Mitochondrial, Hormones, Male, Multigene Family, Phylogeny, Polymorphism, Genetic, Protein Kinases, RNA, Untranslated, Receptors, Odorant, Selenoproteins, Sex Chromosomes, Synteny, Transcription Factors, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.

Published
2014

6. Functional Genomics of Gastrointestinal Escherichia coli Isolated from Patients with Cancer and Diarrhea

Author

Carter, Hannah, Clark, Justin, Carlin, Lily G., Vaughan, Ellen, Rajan, Anubama, Olvera, Adilene, Yu, Xiaomin, Zeng, Xi-Lei, Kambal, Amal, Holder, Michael, Qin, Xiang, Gibbs, Richard A., Petrosino, Joseph F., Muzny, Donna M., Doddapaneni, Harsha, Menon, Vipin K., Hoffman, Kristi L., Meng, Qingchang, Ross, Matthew C., Javornik Cregeen, Sara J., Metcalf, Ginger, Jenq, Robert, Blutt, Sarah, Estes, Mary K., Maresso, Anthony, and Okhuysen, Pablo C.

Subjects
Article
Abstract

We describe the epidemiology and clinical characteristics of 29 patients with cancer and diarrhea in whom Enteroaggregative Escherichia coli (EAEC) was initially identified by GI BioFire panel multiplex. E. coli strains were successfully isolated from fecal cultures in 14 of 29 patients. Six of the 14 strains were identified as EAEC and 8 belonged to other diverse E. coli groups of unknown pathogenesis. We investigated these strains by their adherence to human intestinal organoids, cytotoxic responses, antibiotic resistance profile, full sequencing of their genomes, and annotation of their functional virulome. Interestingly, we discovered novel and enhanced adherence and aggregative patterns for several diarrheagenic pathotypes that were not previously seen when co-cultured with immortalized cell lines. EAEC isolates displayed exceptional adherence and aggregation to human colonoids compared not only to diverse GI E. coli , but also compared to prototype strains of other diarrheagenic E. coli . Some of the diverse E. coli strains that could not be classified as a conventional pathotype also showed an enhanced aggregative and cytotoxic response. Notably, we found a high carriage rate of antibiotic resistance genes in both EAEC strains and diverse GI E. coli isolates and observed a positive correlation between adherence to colonoids and the number of metal acquisition genes carried in both EAEC and the diverse E. coli strains. This work indicates that E. coli from cancer patients constitute strains of remarkable pathotypic and genomic divergence, including strains of unknown disease etiology with unique virulomes. Future studies will allow for the opportunity to re-define E. coli pathotypes with greater diagnostic accuracy and into more clinically relevant groupings.

Published
2023

7. LAOCOON.

Author

HOLDER, MICHAEL

Subjects
SUFFERING, EMOTIONS, GREEK tragedy, COURAGE, HEROES
Abstract

The article focuses on the debate between regarding the portrayal of suffering in art, questioning whether explicit depictions of pain can coexist with the requirement that art represents beauty. Topics explored include the tension between art's need to express strong emotions and the limits of taste, as well as the contrasting views on suffering in Greek tragedy versus Nordic notions of heroism.

Published
2023

8. Sequence type 1 group B Streptococcus , an emerging cause of invasive disease in adults, evolves by small genetic changes

Author

Flores, Anthony R., Galloway-Peña, Jessica, Sahasrabhojane, Pranoti, Saldaña, Miguel, Yao, Hui, Su, Xiaoping, Ajami, Nadim J., Holder, Michael E., Petrosino, Joseph F., Thompson, Erika, Margarit Y Ros, Immaculada, Rosini, Roberto, Grandi, Guido, Horstmann, Nicola, Teatero, Sarah, McGeer, Allison, Fittipaldi, Nahuel, Rappuoli, Rino, Baker, Carol J., and Shelburne, Samuel A.

Published
2015

9. The sheep genome illuminates biology of the rumen and lipid metabolism

Author

Jiang, Yu, Xie, Min, Chen, Wenbin, Talbot, Richard, Maddox, Jillian F., Faraut, Thomas, Wu, Chunhua, Muzny, Donna M., Li, Yuxiang, Zhang, Wenguang, Stanton, Jo-Ann, Brauning, Rudiger, Barris, Wesley C., Hourlier, Thibaut, Aken, Bronwen L., Searle, Stephen M. J., Adelson, David L., Bian, Chao, Cam, Graham R., Chen, Yulin, Cheng, Shifeng, DeSilva, Udaya, Dixen, Karen, Dong, Yang, Fan, Guangyi, Franklin, Ian R., Fu, Shaoyin, Fuentes-Utrilla, Pablo, Guan, Rui, Highland, Margaret A., Holder, Michael E., Huang, Guodong, Ingham, Aaron B., Jhangiani, Shalini N., Kalra, Divya, Kovar, Christie L., Lee, Sandra L., Liu, Weiqing, Liu, Xin, Lu, Changxin, Lv, Tian, Mathew, Tittu, McWilliam, Sean, Menzies, Moira, Pan, Shengkai, Robelin, David, Servin, Bertrand, Townley, David, Wang, Wenliang, Wei, Bin, White, Stephen N., Yang, Xinhua, Ye, Chen, Yue, Yaojing, Zeng, Peng, Zhou, Qing, Hansen, Jacob B., Kristiansen, Karsten, Gibbs, Richard A., Flicek, Paul, Warkup, Christopher C., Jones, Huw E., Oddy, V. Hutton, Nicholas, Frank W., McEwan, John C., Kijas, James W., Wang, Jun, Worley, Kim C., Archibald, Alan L., Cockett, Noelle, Xu, Xun, Wang, Wen, and Dalrymple, Brian P.

Published
2014

11. Impact of Trauma Resuscitation Emergency Care Nurse Deployment in Trauma Activations in a Rural Trauma Center.

Author

Holder, Michael W., Leonard, Matthew A., Collins, Hannah W., Brogan, Allison A., and Burns, J. Bracken

Subjects
WOUND nursing, WOUND care, OCCUPATIONAL roles, TIME, TRAUMA centers, BLOOD transfusion, RETROSPECTIVE studies, ACQUISITION of data, PATIENTS, PRE-tests & post-tests, T-test (Statistics), HOSPITAL admission & discharge, NURSES, QUALITY assurance, GLASGOW Coma Scale, TRAUMA severity indices, CHI-squared test, DESCRIPTIVE statistics, MEDICAL records, EMERGENCY medical services, HOSPITAL care, RESUSCITATION, DATA analysis software, COMPUTED tomography, WOUNDS & injuries, NURSING interventions, RURAL health clinics
Abstract

BACKGROUND: Although the role of a dedicated trauma nurse has been implemented in an urban setting, it has not been studied in the rural trauma setting. We instituted a trauma resuscitation emergency care (TREC) nurse role to respond to trauma activations at our rural trauma center. OBJECTIVE: This study aims to determine the impact of TREC nurse deployment on the timeliness of resuscitation interventions in trauma activations. METHODS: This pre- and postintervention study at a rural Level I trauma center compared the time to resuscitation interventions before (August 2018 to July 2019) and after (August 2019 to July 2020) deploying TREC nurses to trauma activations. RESULTS: A total of 2,593 participants were studied, of which 1,153 (44%) were in the pre-TREC group and 1,440 (56%) in the post-TREC group. After TREC deployment, the median (interquartile range [IQR]) emergency department times within the first hour decreased from 45 (31.23–53) to 35 (16–51) min (p =.013). The median (IQR) time to the operating room within the first hour decreased from 46 (37–52) to 29 (12–46) min (p =.001), and within the first 2 hr, decreased from 59 (43.8–86) to 48 (23–72) min (p =.014). CONCLUSION: Our study found that TREC nurse deployment improved resuscitation intervention timeliness during the first 2 hr (early phase) of trauma activations. [ABSTRACT FROM AUTHOR]

Published
2023
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15. Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia

Author

Morrison, Hilary G., McArthur, Andrew G., Gillin, Frances D., Aley, Stephen B., Adam, Rodney D., Olsen, Gary J., Best, Aaron A., Cande, W. Zacheus, Chen, Feng, Cipriano, Michael J., Davids, Barbara J., Dawson, Scott C., Elmendorf, Heidi G., Hehl, Adrian B., Holder, Michael E., Huse, Susan M., Kim, Ulandt U., Lasek-Nesselquist, Erica, Manning, Gerard, Nigam, Anuranjini, Nixon, Julie E. J., Palm, Daniel, Passamaneck, Nora E., Prabhu, Anjali, Reich, Claudia I., Reiner, David S., Samuelson, John, Svard, Staffan G., and Sogin, Mitchell L.

Published
2007
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16. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

Author

Bellott, Daniel W., Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Cho, Ting-Jan, Koutseva, Natalia, Zaghlul, Sara, Graves, Tina, Rock, Susie, Kremitzki, Colin, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Morton, Donna, Khan, Ziad, Lewis, Lora, Buhay, Christian, Wang, Qiaoyan, Watt, Jennifer, Holder, Michael, Lee, Sandy, Nazareth, Lynne, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., Wilson, Richard K., and Page, David C.

Subjects
Spermatogenesis -- Research, Evolutionary biology -- Research, X chromosome -- Physiological aspects -- Research, Y chromosome -- Physiological aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human X and Y chromosomes evolved from an ordinary pair of autosomes, but millions of years ago genetic decay ravaged the Y chromosome, and only three per cent of its ancestral genes survived. We reconstructed the evolution of the Y chromosome across eight mammals to identify biases in gene content and the selective pressures that preserved the surviving ancestral genes. Our findings indicate that survival was nonrandom, and in two cases, convergent across placental and marsupial mammals. We conclude that the gene content of the Y chromosome became specialized through selection to maintain the ancestral dosage of homologous X-Ygene pairs that function as broadly expressed regulators of transcription, translation and protein stability. We propose that beyond its roles in testis determination and spermatogenesis, the Y chromosome is essential for male viability, and has unappreciated roles in Turner's syndrome and in phenotypic differences between the sexes in health and disease., The human X and Y chromosomes evolved from autosomes over the past 300 million years (1). Only 3% of ancestral genes survive on the human Y chromosome (2,3), compared to [...]

Published
2014
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19. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

Author

Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Graves, Tina, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Buhay, Christian J., Kremitzki, Colin, Wang, Qiaoyan, Shen, Hua, Holder, Michael, Villasana, Donna, Nazareth, Lynne V., Cree, Andrew, Courtney, Laura, Veizer, Joelle, Kotkiewicz, Holland, Cho, Ting-Jan, Koutseva, Natalia, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., Wilson, Richard K., and Page, David C.

Subjects
Rhesus monkey -- Genetic aspects, Chimpanzees -- Genetic aspects, Human genetics -- Research, Human chromosomes -- Properties, Y chromosome -- Properties, Evolutionary genetics -- Research, Chromosome mapping -- Methods, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200-300 million years (1-3). The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes' genes owing to genetic decay (4,5). This evolutionary decay was driven by a series of five 'stratification' events. Each event suppressed X-Y crossing over within a chromosome segment or 'stratum', incorporated that segment into the MSY and subjected its genes to the erosive forces that attend the absence of crossing over (2,6). The last of these events occurred 30 million years ago, 5 million years before the human and Old World monkey lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome (7-10), remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage. To investigate this question, we sequenced the MSY of the rhesus macaque, an Old World monkey, and compared it to the human MSY. We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. In the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 million years ago. Likewise, the rhesus MSY has not lost any older genes (from strata 1-4) during the past 25 million years, despite its major structural differences to the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection., The human Y chromosome no longer engages in crossing over with its once-identical partner, the X chromosome, except in its pseudoautosomal regions. During evolution, X-Y crossing over was suppressed in [...]

Published
2012
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20. A type VII secretion system of Streptococcus gallolyticus subsp. gallolyticus contributes to gut colonization and the development of colon tumors

Author

Taylor, John Culver, primary, Gao, Xinsheng, additional, Xu, Juan, additional, Holder, Michael, additional, Petrosino, Joseph, additional, Kumar, Ritesh, additional, Liu, Wen, additional, Höök, Magnus, additional, Mackenzie, Chris, additional, Hillhouse, Andrew, additional, Brashear, Wesley, additional, Nunez, Maria Patricia, additional, and Xu, Yi, additional

Published
2021
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23. A framework for human microbiome research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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24. Structure, function and diversity of the healthy human microbiome

Author

Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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27. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Author

Elsik, Christine G., Tellam, Ross L., Worley, Kim C., Gibbs, Richard A., Elsik, Christine G., Tellam, Ross L, Gibbs, Richard A., Muzny, Donna M., Weinstock, George M., Adelson, David L, Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Guigó, Roderic, Hamernik, Debora L., Kappes, Steve M., Lewin, Harris A, Lynn, David J., Nicholas, Frank W., Reymond, Alexandre, Rijnkels, Monique, Skow, Loren C., Tellam, Ross L, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., Kappes, Steve M., Schook, Lawrence, Skow, Loren C., Weinstock, George M., Womack, James, Alioto, Tyler, Antonarakis, Stylianos E., Astashyn, Alex, Chapple, Charles E., Chen, Hsiu-Chuan, Chrast, Jacqueline, Câmara, Francisco, Elsik, Christine G., Ermolaeva, Olga, Guigó, Roderic, Henrichsen, Charlotte N., Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Kokocinski, Felix, Landrum, Melissa, Maglott, Donna, Pruitt, Kim, Reymond, Alexandre, Sapojnikov, Victor, Searle, Stephen M., Solovyev, Victor, Souvorov, Alexandre, Ucla, Catherine, Weinstock, George M., Wyss, Carine, Alioto, Tyler, Antonarakis, Stylianos E., Chapple, Charles E., Chrast, Jacqueline, Câmara, Francisco, Guigó, Roderic, Henrichsen, Charlotte N., Reymond, Alexandre, Ucla, Catherine, Wyss, Carine, Anzola, Juan M., Gerlach, Daniel, Zdobnov, Evgeny M., Elhaik, Eran, Elsik, Christine G., Graur, Dan, Reese, Justin T., Adelson, David L., Edgar, Robert C., McEwan, John C., Payne, Gemma M., Raison, Joy M., Junier, Thomas, Kriventseva, Evgenia V., Zdobnov, Evgeny M., Chrast, Jacqueline, Eyras, Eduardo, Henrichsen, Charlotte N., Plass, Mireya, Reymond, Alexandre, Donthu, Ravikiran, Larkin, Denis M., Lewin, Harris A., Nicholas, Frank W., Elnitski, Laura, Larkin, Denis M., Lewin, Harris A., Reecy, James, Yang, Mary Q., Adelson, David L, Chen, Lin, Cheng, Ze, Chitko-McKown, Carol G., Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Liu, George E., Matukumalli, Lakshmi K., Song, Jiuzhou, Zhu, Bin, Elsik, Christine G., Lynn, David J., Reese, Justin T., Bradley, Daniel G., Brinkman, Fiona S.L, Lau, Lilian P.L., Lynn, David J., Whiteside, Matthew D., Tellam, Ross L, Walker, Angela, Wheeler, Thomas T., Casey, Theresa, German, Bruce J., Lemay, Danielle G., Lynn, David J., Maqbool, Nauman J., Molenaar, Adrian J., Rijnkels, Monique, Lewin, Harris A., Seo, Seongwon, Stothard, Paul, Baldwin, Cynthia L., Baxter, Rebecca, Brinkmeyer-Langford, Candice L., Brown, Wendy C., Childers, Christopher P., Connelley, Timothy, Ellis, Shirley A., Fritz, Krista, Glass, Elizabeth J., Herzig, Carolyn T.A., livanainen, Antti, Lahmers, Kevin K., Skow, Loren C., Bennett, Anna K., Childers, Christopher P., Dickens, Michael C., Elsik, Christine G., Gilbert, James G.R., Hagen, Darren E., Reese, Justin T., Salih, Hanni, Aerts, Jan, Caetano, Alexandre R., Dalrymple, Brian, Elsik, Christine G., Fernando Garcia, Jose, Gibbs, Richard A., Gill, Clare A., Hamernik, Debora L, Hiendleder, Stefan G., Memili, Erdogan, Nicholas, Frank W., Reecy, James, Rijnkels, Monique, Skow, Loren C., Spurlock, Diane, Stothard, Paul, Tellam, Ross L, Weinstock, George M., Williams, John L, Worley, Kim C., Alexander, Lee, Brownstein, Michael J., Guan, Leluo, Holt, Robert A., Jones, Steven J.M., Marra, Marco A., Moore, Richard, Moore, Stephen S., Roberts, Andy, Taniguchi, Masaaki, Waterman, Richard C., Chacko, Joseph, Chandrabose, Mimi M., Cree, Andy, Diep Dao, Marvin, Dinh, Huyen H., Ayiesha Gabisi, Ramatu, Hines, Sandra, Hume, Jennifer, Jhangiani, Shalini N., Joshi, Vandita, Kovar, Christie L., Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Muzny, Donna M., Bich Nguyen, Ngoc, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Buhay, Christian, Ding, Yan, Dugan-Rocha, Shannon, Herdandez, Judith, Holder, Michael, Sabo, Aniko, Egan, Amy, Goodell, Jason, Wilczek-Boney, Katarzyna, Fowler, Gerald R., Edward Hitchens, Matthew, Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Chiu, Readman, Jones, Steven J.M., Marra, Marco A., Schein, Jacqueline E., James Durbin, K., Havlak, Paul, Jiang, Huaiyang, Liu, Yue, Qin, Xiang, Ren, Yanru, Shen, Yufeng, Song, Henry, Weinstock, George M., Worley, Kim C., Nicole Bell, Stephanie, Davis, Clay, Jolivet Johnson, Angela, Lee, Sandra, Nazareth, Lynne V., Patel, Bella Mayurkumar, Pu, Ling-Ling, Vattathil, Selina, Williams, Rex Lee, Jr., Curry, Stacey, Hamilton, Cerissa, Sodergren, Erica, Nazareth, Lynne V., Wheeler, David A., Adelson, David L, Aerts, Jan, Barris, Wes, Bennett, Gary L, Dalrymple, Brian, Eggen, André, Gill, Clare A., Green, Ronnie D., Harhay, Gregory P., Hobbs, Matthew, Jann, Oliver, Kappes, Steve M., Keele, John W., Kent, Matthew P., Larkin, Denis M., Lewin, Harris A., Lien, Sigbjørn, McEwan, John C., McKay, Stephanie D., McWilliam, Sean, Moore, Stephen S., Nicholas, Frank W., Payne, Gemma M., Ratnakumar, Abhirami, Salih, Hanni, Schnabel, Robert D., Smith, Timothy, Snelling, Warren M., Sonstegard, Tad S., Stone, Roger T., Sugimoto, Yoshikazu, Takasuga, Akiko, Taylor, Jeremy F., Tellam, Ross L., Van Tassell, Curtis P., Williams, John L, MacNeil, Michael D., Abatepaulo, Antonio R.R., Abbey, Colette A., Aerts, Jan, Ahola, Virpi, Almeida, Iassudara G., Amadio, Ariel F., Anatriello, Elen, Bahadue, Suria M., Baldwin, Cynthia L., Baxter, Rebecca, Bennett, Anna K., Biase, Fernando H., Boldt, Clayton R., Brinkmeyer-Langford, Candice L, Brown, Wendy C., Caetano, Alexandre R., Carroll, Jeffery A., Carvalho, Wanessa A, Casey, Theresa, Cervelatti, Eliane P., Chacko, Elsa, Chapin, Jennifer E., Cheng, Ye, Childers, Christopher P., Choi, Jungwoo, Colley, Adam J., Connelley, Timothy, de Campos, Tatiana A., De Donato, Marcos, de Miranda Santos, Isabel K.F., de Oliveira, Carlo J.F., Deobald, Heather, Devinoy, Eve, Dickens, Michael C., Donohue, Kaitlin E., Dovc, Peter, Eberlein, Annett, Ellis, Shirley A., Fitzsimmons, Carolyn J., Franzin, Alessandra M., Fritz, Krista, Garcia, Gustavo R., Fernando Garcia, Jose, Genini, Sem, German, Bruce J., Gilbert, James G.R., Gill, Clare A., Gladney, Cody J., Glass, Elizabeth J., Grant, Jason R., Greaser, Marion L., Green, Jonathan A., Hadsell, Darryl L., Hagen, Darren E., Hakimov, Hatam A., Halgren, Rob, Harrow, Jennifer L, Hart, Elizabeth A., Hastings, Nicola, Hernandez, Marta, Herzig, Carolyn T.A., Hiendleder, Stefan G., Hobbs, Matthew, Hu, Zhi-Liang, livanainen, Antti, Ingham, Aaron, Iso-Touru, Terhi, Jamis, Catherine, Jann, Oliver, Jensen, Kirsty, Kapetis, Dimos, Kerr, Tovah, Khalil, Sari S., Khatib, Hasan, Kolbehdari, Davood, Kumar, Charu G., Kumar, Dinesh, Leach, Richard, Lee, Justin C-M, Lemay, Danielle G., Li, Changxi, Liu, George E., Logan, Krystin M., Malinverni, Roberto, Maqbool, Nauman J., Marques, Elisa, Martin, William F., Martins, Natalia F., Maruyama, Sandra R., Mazza, Raffaele, McLean, Kim L, Medrano, Juan F., Memili, Erdogan, Molenaar, Adrian J., Moreno, Barbara T., Moré, Daniela D., Muntean, Carl T., Nandakumar, Hari P., Nogueira, Marcelo F.G., Olsaker, Ingrid, Pant, Sameer D., Panzitta, Francesca, Pastor, Rosemeire C.P., Poli, Mario A., Poslusny, Nathan, Rachagani, Satyanarayana, Ranganathan, Shoba, Razpet, Andrej, Reecy, James, Riggs, Penny K., Rijnkels, Monique, Rincon, Gonzalo, Rodriguez-Osorio, Nelida, Rodriguez-Zas, Sandra L., Romero, Natasha E., Rosenwald, Anne, Sando, Lillian, Schmutz, Sheila M., Seo, Seongwon, Shen, Libing, Sherman, Laura, Skow, Loren C., Southey, Bruce R., Spurlock, Diane, Strandberg Lutzow, Ylva, Sweedler, Jonathan V., Tammen, Imke, Taniguchi, Masaaki, Tellam, Ross L, Telugu, Bhanu Prakash V.L, Urbanski, Jennifer M., Utsunomiya, Yuri T., Verschoor, Chris P., Waardenberg, Ashley J., Walker, Angela, Wang, Zhiquan, Ward, Robert, Weikard, Rosemarie, Welsh, Thomas H., Jr., Wheeler, Thomas T., White, Stephen N., Williams, John L, Wilming, Laurens G., Wunderlich, Kris R., Yang, Jianqi, and Zhao, Feng-Qi

Published
2009

29. Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia Iamblia

Author

Morrison, Hilary G., McArthur, Andrew G., Gillin, Frances D., Aley, Stephen B., Adam, Rodney D., Olsen, Gary J., Best, Aaron A., Cande, W. Zacheus, Chen, Feng, Cipriano, Michael J., Davids, Barbara J., Dawson, Scott C., Elmendorf, Heidi G., Hehl, Adrian B., Holder, Michael E., Huse, Susan M., Kim, Ulandt U., Lasek-Nesselquist, Erica, Manning, Gerard, Nigam, Anuranjini, Nixon, Julie E. J., Palm, Daniel, Passamaneck, Nora E., Prabhu, Anjali, Reich, Claudia I., Reiner, David S., Samuelson, John, Svard, Staffan G., and Sogin, Mitchell L.

Published
2007
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30. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

Author

Massachusetts Institute of Technology. Department of Biology, Bellott, Daniel W., Page, David C, Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Cho, Ting-Jan, Koutseva, Natalia, Zaghlul, Sara, Graves, Tina, Rock, Susie, Kremitzki, Colin, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Morton, Donna, Khan, Ziad, Lewis, Lora, Buhay, Christian, Wang, Qiaoyan, Watt, Jennifer, Holder, Michael, Lee, Sandy, Nazareth, Lynne, Alföldi, Jessica, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., Wilson, Richard K., Massachusetts Institute of Technology. Department of Biology, Bellott, Daniel W., Page, David C, Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Cho, Ting-Jan, Koutseva, Natalia, Zaghlul, Sara, Graves, Tina, Rock, Susie, Kremitzki, Colin, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Morton, Donna, Khan, Ziad, Lewis, Lora, Buhay, Christian, Wang, Qiaoyan, Watt, Jennifer, Holder, Michael, Lee, Sandy, Nazareth, Lynne, Alföldi, Jessica, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., and Wilson, Richard K.

Abstract

The human X and Y chromosomes evolved from an ordinary pair of autosomes, but millions of years ago genetic decay ravaged the Y chromosome, and only three per cent of its ancestral genes survived. We reconstructed the evolution of the Y chromosome across eight mammals to identify biases in gene content and the selective pressures that preserved the surviving ancestral genes. Our findings indicate that survival was nonrandom, and in two cases, convergent across placental and marsupial mammals. We conclude that the gene content of the Y chromosome became specialized through selection to maintain the ancestral dosage of homologous X-Y gene pairs that function as broadly expressed regulators of transcription, translation and protein stability. We propose that beyond its roles in testis determination and spermatogenesis, the Y chromosome is essential for male viability, and has unappreciated roles in Turner (tm) s syndrome and in phenotypic differences between the sexes in health and disease.

Published
2018

32. Banality

Author

Holder, Michael

Published
1974

33. Complete Genome Sequence of Vibrio gazogenes ATCC 43942

Author

Gummadidala, Phani M., primary, Holder, Michael E., additional, O’Brien, Jacqueline L., additional, Ajami, Nadim J., additional, Petrosino, Joseph F., additional, Mitra, Chandrani, additional, Chen, Yung Pin, additional, Decho, Alan W., additional, and Chanda, Anindya, additional

Published
2017
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36. Street lighting program benefits residents and astronomers

Author

Holder, Michael D.

Subjects
Street lighting -- Management, Light pollution -- Prevention, Government, Political science
Abstract

Concern over the adverse effects of light pollution has prompted citizens of Tuczon, AZ, to adopt policies restricting the use of outdoor lighting. With its many astronomical observatories, Tuczon was concerned over the reduced effectiveness of optical telescopes as a result of the illumination which clouds the night sky. Low pressure sodium (LPS) lights were used for residential streets, while high pressure sodium lights were tapped for arterial streets. Controversy has been raised over the merits of LPS for residential street lighting in terms of cost effectiveness and illumination., STREET LIGHTING has greatly changed our living habits in that it has increased our time for various activities while providing some measure of security and safety. Unfortunately this same light [...]

Published
1994

37. Finding the Missing Honey Bee Genes: Lessons Learned From a Genome Upgrade

Author

Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, HGSC production teams, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin FA, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Van Vaerenbergh, Matthias, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A

Subjects
Apis mellifera, GC content, Gene annotation, Gene prediction, Genome assembly, Genome improvement, Genome sequencing, Repetitive DNA, Transcriptome, fungi
Abstract

Background The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Published
2014

39. The genomes of two key bumblebee species with primitive eusocial organization

Author

Sadd, Ben M., Barribeau, Seth M., Bloch, Guy, de Graaf, Dirk C., Dearden, Peter, Elsik, Christine G., Gadau, Jürgen, Grimmelikhuijzen, Cornelis J. P., Hasselmann, Martin, Lozier, Jeffrey D., Robertson, Hugh M., Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M., Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K., Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V., Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M. G., Blaxter, Mark L., Bourke, Andrew F. G., Brown, Mark J. F., Buechel, Severine D., Cameron, Rossanah, Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Ciborowski, Kate L., Clarke, David F., Colgan, Thomas J., Collins, David H., Cridge, Andrew G., Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C. P., Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C., Irvine, Frano, Jermiin, Lars S., Johnson, Claire E., Johnson, Reed M., Jones, Andrew K., Kadowaki, Tatsuhiko, Kidner, Jonathan H., Koch, Vasco, Köhler, Arian, Kraus, F. Bernhard, Lattorff, H. Michael G., Leask, Megan, Lockett, Gabrielle A., Mallon, Eamonn B., Antonio, David S. Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F. A., Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M. F., Oakeshott, John G., Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G., Rossié, Nina, Rueppell, Olav, Santos, Carolina G., Schmid-Hempel, Regula, Schmitt, Björn D., Schulte, Christina, Simões, Zilá L. P., Soares, Michelle P. M., Swevers, Luc, Winnebeck, Eva C., Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M., Aqrawi, Peshtewani K., Blankenburg, Kerstin P., Coyle, Marcus, Francisco, Liezl, Hernandez, Alvaro G., Holder, Michael, Hudson, Matthew E., Jackson, LaRonda, Jayaseelan, Joy, Joshi, Vandita, Kovar, Christie, Lee, Sandra L., Mata, Robert, Mathew, Tittu, Newsham, Irene F., Ngo, Robin, Okwuonu, Geoffrey, Pham, Christopher, Pu, Ling-Ling, Saada, Nehad, Santibanez, Jireh, Simmons, DeNard, Thornton, Rebecca, Venkat, Aarti, Walden, Kimberly Ko, Wu, Yuan-Qing, Debyser, Griet, Devreese, Bart, Asher, Claire, Blommaert, Julie, Chipman, Ariel D., Chittka, Lars, Fouks, Bertrand, Liu, Jisheng, O'Neill, Meaghan P., Sumner, Seirian, Puiu, Daniela, Qu, Jiaxin, Salzberg, Steven L., Scherer, Steven E., Muzny, Donna M., Richards, Stephen, Robinson, Gene E., Gibbs, Richard A., Schmid-Hempel, Paul, Worley, Kim C., Sadd, Ben M., Barribeau, Seth M., Bloch, Guy, de Graaf, Dirk C., Dearden, Peter, Elsik, Christine G., Gadau, Jürgen, Grimmelikhuijzen, Cornelis J. P., Hasselmann, Martin, Lozier, Jeffrey D., Robertson, Hugh M., Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M., Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K., Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V., Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M. G., Blaxter, Mark L., Bourke, Andrew F. G., Brown, Mark J. F., Buechel, Severine D., Cameron, Rossanah, Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Ciborowski, Kate L., Clarke, David F., Colgan, Thomas J., Collins, David H., Cridge, Andrew G., Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C. P., Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C., Irvine, Frano, Jermiin, Lars S., Johnson, Claire E., Johnson, Reed M., Jones, Andrew K., Kadowaki, Tatsuhiko, Kidner, Jonathan H., Koch, Vasco, Köhler, Arian, Kraus, F. Bernhard, Lattorff, H. Michael G., Leask, Megan, Lockett, Gabrielle A., Mallon, Eamonn B., Antonio, David S. Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F. A., Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M. F., Oakeshott, John G., Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G., Rossié, Nina, Rueppell, Olav, Santos, Carolina G., Schmid-Hempel, Regula, Schmitt, Björn D., Schulte, Christina, Simões, Zilá L. P., Soares, Michelle P. M., Swevers, Luc, Winnebeck, Eva C., Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M., Aqrawi, Peshtewani K., Blankenburg, Kerstin P., Coyle, Marcus, Francisco, Liezl, Hernandez, Alvaro G., Holder, Michael, Hudson, Matthew E., Jackson, LaRonda, Jayaseelan, Joy, Joshi, Vandita, Kovar, Christie, Lee, Sandra L., Mata, Robert, Mathew, Tittu, Newsham, Irene F., Ngo, Robin, Okwuonu, Geoffrey, Pham, Christopher, Pu, Ling-Ling, Saada, Nehad, Santibanez, Jireh, Simmons, DeNard, Thornton, Rebecca, Venkat, Aarti, Walden, Kimberly Ko, Wu, Yuan-Qing, Debyser, Griet, Devreese, Bart, Asher, Claire, Blommaert, Julie, Chipman, Ariel D., Chittka, Lars, Fouks, Bertrand, Liu, Jisheng, O'Neill, Meaghan P., Sumner, Seirian, Puiu, Daniela, Qu, Jiaxin, Salzberg, Steven L., Scherer, Steven E., Muzny, Donna M., Richards, Stephen, Robinson, Gene E., Gibbs, Richard A., Schmid-Hempel, Paul, and Worley, Kim C.

Abstract

BACKGROUND: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. RESULTS: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. CONCLUSIONS: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.

Published
2015
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40. Hemichordate genomes and deuterostome origins.

Author

Hisata, Kanako, Hisata, Kanako, Bredeson, Jessen, Shoguchi, Eiichi, Gyoja, Fuki, Yue, Jia-Xing, Chen, Yi-Chih, Freeman, Robert, Sasaki, Akane, Hikosaka-Katayama, Tomoe, Sato, Atsuko, Fujie, Manabu, Baughman, Kenneth, Levine, Judith, Gonzalez, Paul, Cameron, Christopher, Fritzenwanker, Jens, Pani, Ariel, Goto, Hiroki, Kanda, Miyuki, Arakaki, Nana, Yamasaki, Shinichi, Qu, Jiaxin, Cree, Andrew, Ding, Yan, Dinh, Huyen, Dugan, Shannon, Holder, Michael, Jhangiani, Shalini, Kovar, Christie, Lee, Sandra, Lewis, Lora, Morton, Donna, Nazareth, Lynne, Okwuonu, Geoffrey, Santibanez, Jireh, Chen, Rui, Richards, Stephen, Muzny, Donna, Gillis, Andrew, Peshkin, Leonid, Wu, Michael, Humphreys, Tom, Su, Yi-Hsien, Putnam, Nicholas, Schmutz, Jeremy, Fujiyama, Asao, Yu, Jr-Kai, Tagawa, Kunifumi, Simakov, Oleg, Kawashima, Takeshi, Marlétaz, Ferdinand, Jenkins, Jerry, Koyanagi, Ryo, Worley, Kim, Gibbs, Richard, Kirschner, Marc, Lowe, Christopher, Satoh, Noriyuki, Gerhart, John, Rokhsar, Daniel, Mitros, Therese, Hisata, Kanako, Hisata, Kanako, Bredeson, Jessen, Shoguchi, Eiichi, Gyoja, Fuki, Yue, Jia-Xing, Chen, Yi-Chih, Freeman, Robert, Sasaki, Akane, Hikosaka-Katayama, Tomoe, Sato, Atsuko, Fujie, Manabu, Baughman, Kenneth, Levine, Judith, Gonzalez, Paul, Cameron, Christopher, Fritzenwanker, Jens, Pani, Ariel, Goto, Hiroki, Kanda, Miyuki, Arakaki, Nana, Yamasaki, Shinichi, Qu, Jiaxin, Cree, Andrew, Ding, Yan, Dinh, Huyen, Dugan, Shannon, Holder, Michael, Jhangiani, Shalini, Kovar, Christie, Lee, Sandra, Lewis, Lora, Morton, Donna, Nazareth, Lynne, Okwuonu, Geoffrey, Santibanez, Jireh, Chen, Rui, Richards, Stephen, Muzny, Donna, Gillis, Andrew, Peshkin, Leonid, Wu, Michael, Humphreys, Tom, Su, Yi-Hsien, Putnam, Nicholas, Schmutz, Jeremy, Fujiyama, Asao, Yu, Jr-Kai, Tagawa, Kunifumi, Simakov, Oleg, Kawashima, Takeshi, Marlétaz, Ferdinand, Jenkins, Jerry, Koyanagi, Ryo, Worley, Kim, Gibbs, Richard, Kirschner, Marc, Lowe, Christopher, Satoh, Noriyuki, Gerhart, John, Rokhsar, Daniel, and Mitros, Therese

Abstract

Acorn worms, also known as enteropneust (literally, gut-breathing) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal gill slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Published
2015

41. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

Author

Zhao, Chaoyang, Escalante, Lucio Navarro, Chen, Hang, Benatti, Thiago R., Qu, Jiaxin, Chellapilla, Sanjay, Waterhouse, Robert M., Wheeler, David, Andersson, Martin N., Bao, Riyue, Batterton, Matthew, Behura, Susanta K., Blankenburg, Kerstin P., Caragea, Doina, Carolan, James C., Coyle, Marcus, El-Bouhssini, Mustapha, Francisco, Liezl, Friedrich, Markus, Gill, Navdeep, Grace, Tony, Grimmelikhuijzen, Cornelis J.P., Han, Yi, Hauser, Frank, Herndon, Nicolae, Holder, Michael, Ioannidis, Panagiotis, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N., Johnson, Alisha J., Kalra, Divya, Korchina, Viktoriya, Kovar, Christie, Lara, Fremiet, Lee, Sandra L., Liu, Xuming, Löfstedt, Christer, Mata, Robert, Mathew, Tittu, Muzny, Donna M., Nagar, Swapnil, Nazareth, Lynne V., Okwuonu, Geoffrey, Ongeri, Fiona, Perales, Lora, Peterson, Brittany F., Pu, Ling-Ling, Robertson, Hugh M., Schemerhorn, Brandon J., Scherer, Steven E., Shreve, Jacob T., Simmons, DeNard, Subramanyam, Subhashree, Thornton, Rebecca, Xue, Kun, Weissenberger, George M., Williams, Christie E., Worley, Kim C., Zhu, Dianhui, Zhu, Yiming, Harris, Marion O., Shukle, Richard H., Weren, John H., Zdobnov, Evgeny M., Chen, Ming-Shun, Brown, Susan J., Stuart, Jeffery J., Richards, Stephen, Zhao, Chaoyang, Escalante, Lucio Navarro, Chen, Hang, Benatti, Thiago R., Qu, Jiaxin, Chellapilla, Sanjay, Waterhouse, Robert M., Wheeler, David, Andersson, Martin N., Bao, Riyue, Batterton, Matthew, Behura, Susanta K., Blankenburg, Kerstin P., Caragea, Doina, Carolan, James C., Coyle, Marcus, El-Bouhssini, Mustapha, Francisco, Liezl, Friedrich, Markus, Gill, Navdeep, Grace, Tony, Grimmelikhuijzen, Cornelis J.P., Han, Yi, Hauser, Frank, Herndon, Nicolae, Holder, Michael, Ioannidis, Panagiotis, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N., Johnson, Alisha J., Kalra, Divya, Korchina, Viktoriya, Kovar, Christie, Lara, Fremiet, Lee, Sandra L., Liu, Xuming, Löfstedt, Christer, Mata, Robert, Mathew, Tittu, Muzny, Donna M., Nagar, Swapnil, Nazareth, Lynne V., Okwuonu, Geoffrey, Ongeri, Fiona, Perales, Lora, Peterson, Brittany F., Pu, Ling-Ling, Robertson, Hugh M., Schemerhorn, Brandon J., Scherer, Steven E., Shreve, Jacob T., Simmons, DeNard, Subramanyam, Subhashree, Thornton, Rebecca, Xue, Kun, Weissenberger, George M., Williams, Christie E., Worley, Kim C., Zhu, Dianhui, Zhu, Yiming, Harris, Marion O., Shukle, Richard H., Weren, John H., Zdobnov, Evgeny M., Chen, Ming-Shun, Brown, Susan J., Stuart, Jeffery J., and Richards, Stephen

Abstract

Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticum spp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M. destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.

Published
2015

43. The genomes of two key bumblebee species with primitive eusocial organization

Author

Sadd, Ben M, primary, Barribeau, Seth M, additional, Bloch, Guy, additional, de Graaf, Dirk C, additional, Dearden, Peter, additional, Elsik, Christine G, additional, Gadau, Jürgen, additional, Grimmelikhuijzen, Cornelis JP, additional, Hasselmann, Martin, additional, Lozier, Jeffrey D, additional, Robertson, Hugh M, additional, Smagghe, Guy, additional, Stolle, Eckart, additional, Van Vaerenbergh, Matthias, additional, Waterhouse, Robert M, additional, Bornberg-Bauer, Erich, additional, Klasberg, Steffen, additional, Bennett, Anna K, additional, Câmara, Francisco, additional, Guigó, Roderic, additional, Hoff, Katharina, additional, Mariotti, Marco, additional, Munoz-Torres, Monica, additional, Murphy, Terence, additional, Santesmasses, Didac, additional, Amdam, Gro V, additional, Beckers, Matthew, additional, Beye, Martin, additional, Biewer, Matthias, additional, Bitondi, Márcia MG, additional, Blaxter, Mark L, additional, Bourke, Andrew FG, additional, Brown, Mark JF, additional, Buechel, Severine D, additional, Cameron, Rossanah, additional, Cappelle, Kaat, additional, Carolan, James C, additional, Christiaens, Olivier, additional, Ciborowski, Kate L, additional, Clarke, David F, additional, Colgan, Thomas J, additional, Collins, David H, additional, Cridge, Andrew G, additional, Dalmay, Tamas, additional, Dreier, Stephanie, additional, du Plessis, Louis, additional, Duncan, Elizabeth, additional, Erler, Silvio, additional, Evans, Jay, additional, Falcon, Tiago, additional, Flores, Kevin, additional, Freitas, Flávia CP, additional, Fuchikawa, Taro, additional, Gempe, Tanja, additional, Hartfelder, Klaus, additional, Hauser, Frank, additional, Helbing, Sophie, additional, Humann, Fernanda C, additional, Irvine, Frano, additional, Jermiin, Lars S, additional, Johnson, Claire E, additional, Johnson, Reed M, additional, Jones, Andrew K, additional, Kadowaki, Tatsuhiko, additional, Kidner, Jonathan H, additional, Koch, Vasco, additional, Köhler, Arian, additional, Kraus, F Bernhard, additional, Lattorff, H Michael G, additional, Leask, Megan, additional, Lockett, Gabrielle A, additional, Mallon, Eamonn B, additional, Antonio, David S Marco, additional, Marxer, Monika, additional, Meeus, Ivan, additional, Moritz, Robin FA, additional, Nair, Ajay, additional, Näpflin, Kathrin, additional, Nissen, Inga, additional, Niu, Jinzhi, additional, Nunes, Francis MF, additional, Oakeshott, John G, additional, Osborne, Amy, additional, Otte, Marianne, additional, Pinheiro, Daniel G, additional, Rossié, Nina, additional, Rueppell, Olav, additional, Santos, Carolina G, additional, Schmid-Hempel, Regula, additional, Schmitt, Björn D, additional, Schulte, Christina, additional, Simões, Zilá LP, additional, Soares, Michelle PM, additional, Swevers, Luc, additional, Winnebeck, Eva C, additional, Wolschin, Florian, additional, Yu, Na, additional, Zdobnov, Evgeny M, additional, Aqrawi, Peshtewani K, additional, Blankenburg, Kerstin P, additional, Coyle, Marcus, additional, Francisco, Liezl, additional, Hernandez, Alvaro G, additional, Holder, Michael, additional, Hudson, Matthew E, additional, Jackson, LaRonda, additional, Jayaseelan, Joy, additional, Joshi, Vandita, additional, Kovar, Christie, additional, Lee, Sandra L, additional, Mata, Robert, additional, Mathew, Tittu, additional, Newsham, Irene F, additional, Ngo, Robin, additional, Okwuonu, Geoffrey, additional, Pham, Christopher, additional, Pu, Ling-Ling, additional, Saada, Nehad, additional, Santibanez, Jireh, additional, Simmons, DeNard, additional, Thornton, Rebecca, additional, Venkat, Aarti, additional, Walden, Kimberly KO, additional, Wu, Yuan-Qing, additional, Debyser, Griet, additional, Devreese, Bart, additional, Asher, Claire, additional, Blommaert, Julie, additional, Chipman, Ariel D, additional, Chittka, Lars, additional, Fouks, Bertrand, additional, Liu, Jisheng, additional, O’Neill, Meaghan P, additional, Sumner, Seirian, additional, Puiu, Daniela, additional, Qu, Jiaxin, additional, Salzberg, Steven L, additional, Scherer, Steven E, additional, Muzny, Donna M, additional, Richards, Stephen, additional, Robinson, Gene E, additional, Gibbs, Richard A, additional, Schmid-Hempel, Paul, additional, and Worley, Kim C, additional

Published
2015
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44. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

Author

Zhao, Chaoyang, primary, Escalante, Lucio Navarro, additional, Chen, Hang, additional, Benatti, Thiago R., additional, Qu, Jiaxin, additional, Chellapilla, Sanjay, additional, Waterhouse, Robert M., additional, Wheeler, David, additional, Andersson, Martin N., additional, Bao, Riyue, additional, Batterton, Matthew, additional, Behura, Susanta K., additional, Blankenburg, Kerstin P., additional, Caragea, Doina, additional, Carolan, James C., additional, Coyle, Marcus, additional, El-Bouhssini, Mustapha, additional, Francisco, Liezl, additional, Friedrich, Markus, additional, Gill, Navdeep, additional, Grace, Tony, additional, Grimmelikhuijzen, Cornelis J.P., additional, Han, Yi, additional, Hauser, Frank, additional, Herndon, Nicolae, additional, Holder, Michael, additional, Ioannidis, Panagiotis, additional, Jackson, LaRonda, additional, Javaid, Mehwish, additional, Jhangiani, Shalini N., additional, Johnson, Alisha J., additional, Kalra, Divya, additional, Korchina, Viktoriya, additional, Kovar, Christie L., additional, Lara, Fremiet, additional, Lee, Sandra L., additional, Liu, Xuming, additional, Löfstedt, Christer, additional, Mata, Robert, additional, Mathew, Tittu, additional, Muzny, Donna M., additional, Nagar, Swapnil, additional, Nazareth, Lynne V., additional, Okwuonu, Geoffrey, additional, Ongeri, Fiona, additional, Perales, Lora, additional, Peterson, Brittany F., additional, Pu, Ling-Ling, additional, Robertson, Hugh M., additional, Schemerhorn, Brandon J., additional, Scherer, Steven E., additional, Shreve, Jacob T., additional, Simmons, DeNard, additional, Subramanyam, Subhashree, additional, Thornton, Rebecca L., additional, Xue, Kun, additional, Weissenberger, George M., additional, Williams, Christie E., additional, Worley, Kim C., additional, Zhu, Dianhui, additional, Zhu, Yiming, additional, Harris, Marion O., additional, Shukle, Richard H., additional, Werren, John H., additional, Zdobnov, Evgeny M., additional, Chen, Ming-Shun, additional, Brown, Susan J., additional, Stuart, Jeffery J., additional, and Richards, Stephen, additional

Published
2015
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45. Finding the missing honey bee genes: lessons learned from a genome upgrade

Author

Elsik, Christine G., Worley, Kim C., Bennett, Anna K., Beye, Martin, Camara, Francisco, Childers, Christopher P., de Graaf, Dirk C., Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D., Foster, Leonard J., Graur, Dan, Guigo, Roderic, Hoff, Katharina J., Holder, Michael E., Hudson, Matthew E., Hunt, Greg J., Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L., Ma, Jian, Maleszka, Ryszard, Moritz, Robin F. A., Munoz-Torres, Monica C., Murphy, Terence D., Muzny, Donna M., Newsham, Irene F., Reese, Justin T., Robertson, Hugh M., Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M., Vaerenbergh, Matthias V., Waterhouse, Robert M., Weaver, Daniel B., Whitfield, Charles W., Wu, Yuanqing, Zdobnov, Evgeny M., Zhang, Lan, Zhu, Dianhui, Gibbs, Richard A., Elsik, Christine G., Worley, Kim C., Bennett, Anna K., Beye, Martin, Camara, Francisco, Childers, Christopher P., de Graaf, Dirk C., Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D., Foster, Leonard J., Graur, Dan, Guigo, Roderic, Hoff, Katharina J., Holder, Michael E., Hudson, Matthew E., Hunt, Greg J., Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L., Ma, Jian, Maleszka, Ryszard, Moritz, Robin F. A., Munoz-Torres, Monica C., Murphy, Terence D., Muzny, Donna M., Newsham, Irene F., Reese, Justin T., Robertson, Hugh M., Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M., Vaerenbergh, Matthias V., Waterhouse, Robert M., Weaver, Daniel B., Whitfield, Charles W., Wu, Yuanqing, Zdobnov, Evgeny M., Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A.

Abstract

BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Published
2014

46. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

Author

Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen, Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, and Richards, Stephen

Abstract

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific l

Published
2014

47. 879

Author

Tirodker, Urmila, primary, Kahlenberg, Lindsay, additional, Watson, Lindsay, additional, Patterson, Mary, additional, Wachsberger, Don, additional, Gothard, Michael, additional, and Holder, Michael G., additional

Published
2014
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49. Erratum: Corrigendum: Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

Author

Bellott, Daniel W., primary, Hughes, Jennifer F., additional, Skaletsky, Helen, additional, Brown, Laura G., additional, Pyntikova, Tatyana, additional, Cho, Ting-Jan, additional, Koutseva, Natalia, additional, Zaghlul, Sara, additional, Graves, Tina, additional, Rock, Susie, additional, Kremitzki, Colin, additional, Fulton, Robert S., additional, Dugan, Shannon, additional, Ding, Yan, additional, Morton, Donna, additional, Khan, Ziad, additional, Lewis, Lora, additional, Buhay, Christian, additional, Wang, Qiaoyan, additional, Watt, Jennifer, additional, Holder, Michael, additional, Lee, Sandy, additional, Nazareth, Lynne, additional, Alföldi, Jessica, additional, Rozen, Steve, additional, Muzny, Donna M., additional, Warren, Wesley C., additional, Gibbs, Richard A., additional, Wilson, Richard K., additional, and Page, David C., additional

Published
2014
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