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2. The Ruminant Telomere-to-Telomere (RT2T) Consortium

Author

Kalbfleisch, Theodore S., McKay, Stephanie D., Murdoch, Brenda M., Adelson, David L., Almansa-Villa, Diego, Becker, Gabrielle, Beckett, Linda M., Benítez-Galeano, María José, Biase, Fernando, Casey, Theresa, Chuong, Edward, Clark, Emily, Clarke, Shannon, Cockett, Noelle, Couldrey, Christine, Davis, Brian W., Elsik, Christine G., Faraut, Thomas, Gao, Yahui, Genet, Carine, Grady, Patrick, Green, Jonathan, Green, Richard, Guan, Dailu, Hagen, Darren, Hartley, Gabrielle A., Heaton, Mike, Hoyt, Savannah J., Huang, Wen, Jarvis, Erich, Kalleberg, Jenna, Khatib, Hasan, Koepfi, Klaus-Peter, Koltes, James, Koren, Sergey, Kuehn, Christa, Leeb, Tosso, Leonard, Alexander, Liu, George E., Low, Wai Yee, McConnell, Hunter, McRae, Kathryn, Miga, Karen, Mousel, Michelle, Neibergs, Holly, Olagunju, Temitayo, Pennell, Matt, Petry, Bruna, Pewsner, Mirjam, Phillippy, Adam M., Pickett, Brandon D., Pineda, Paulene, Potapova, Tamara, Rachagani, Satyanarayana, Rhie, Arang, Rijnkels, Monique, Robic, Annie, Rodriguez Osorio, Nelida, Safonova, Yana, Schettini, Gustavo, Schnabel, Robert D., Sirpu Natesh, Nagabhishek, Stegemiller, Morgan, Storer, Jessica, Stothard, Paul, Stull, Caleb, Tosser-Klopp, Gwenola, Traglia, Germán M., Tuggle, Christopher K., Van Tassell, Curtis P., Watson, Corey, Weikard, Rosemarie, Wimmers, Klaus, Xie, Shangqian, Yang, Liu, Smith, Timothy P. L., O’Neill, Rachel J., and Rosen, Benjamin D.

Published
2024
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12. The tuatara genome reveals ancient features of amniote evolution

Author

Gemmell, Neil J., Rutherford, Kim, Prost, Stefan, Tollis, Marc, Winter, David, Macey, J. Robert, Adelson, David L., Suh, Alexander, Bertozzi, Terry, Grau, José H., Organ, Chris, Gardner, Paul P., Muffato, Matthieu, Patricio, Mateus, Billis, Konstantinos, Martin, Fergal J., Flicek, Paul, Petersen, Bent, Kang, Lin, Michalak, Pawel, Buckley, Thomas R., Wilson, Melissa, Cheng, Yuanyuan, Miller, Hilary, Schott, Ryan K., Jordan, Melissa D., Newcomb, Richard D., Arroyo, José Ignacio, Valenzuela, Nicole, Hore, Tim A., Renart, Jaime, Peona, Valentina, Peart, Claire R., Warmuth, Vera M., Zeng, Lu, Kortschak, R. Daniel, Raison, Joy M., Zapata, Valeria Velásquez, Wu, Zhiqiang, Santesmasses, Didac, Mariotti, Marco, Guigó, Roderic, Rupp, Shawn M., Twort, Victoria G., Dussex, Nicolas, Taylor, Helen, Abe, Hideaki, Bond, Donna M., Paterson, James M., Mulcahy, Daniel G., Gonzalez, Vanessa L., Barbieri, Charles G., DeMeo, Dustin P., Pabinger, Stephan, Van Stijn, Tracey, Clarke, Shannon, Ryder, Oliver, Edwards, Scott V., Salzberg, Steven L., Anderson, Lindsay, Nelson, Nicola, and Stone, Clive

Published
2020
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14. RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia

Author

Kalbfleisch, Ted, primary, McKay, Stephanie, additional, Murdoch, Brenda, additional, Adelson, David L., additional, Almansa, Diego, additional, Becker, Gabrielle, additional, Beckett, Linda M., additional, Benítez-Galeano, María José, additional, Biase, Fernando, additional, Casey, Theresa, additional, Chuong, Edward, additional, Clark, Emily, additional, Clarke, Shannon, additional, Cockett, Noelle, additional, Couldrey, Christine, additional, Davis, Brian W., additional, Elsik, Christine G., additional, Faraut, Thomas, additional, Gao, Yahui, additional, Genet, Carine, additional, Grady, Patrick, additional, Green, Jonathan, additional, Green, Richard, additional, Guan, Dailu, additional, Hagen, Darren, additional, Hartley, Gabrielle A., additional, Heaton, Mike, additional, Hoyt, Savannah J., additional, Huang, Wen, additional, Jarvis, Erich, additional, Kalleberg, Jenna, additional, Khatib, Hasan, additional, Koepfi, Klaus-Peter, additional, Koltes, James, additional, Koren, Sergey, additional, Kuehn, Christa, additional, Leeb, Tosso, additional, Leonard, Alexander, additional, Liu, George E., additional, Low, Wai Yee, additional, McConnell, Hunter, additional, McRae, Kathryn, additional, Miga, Karen, additional, Mousel, Michelle, additional, Neibergs, Holly, additional, O'Neill, Rachel, additional, Olagunju, Temitayo, additional, Pennell, Matt, additional, Petry, Bruna, additional, Pewsner, Mirjam, additional, Phillippy, Adam M., additional, Pickett, Brandon D., additional, Pineda, Paulene, additional, Potapova, Tamara, additional, Rachagani, Satyanarayana, additional, Rhie, Arang, additional, Rijnkels, Monique, additional, Robic, Annie, additional, Osorio, Nelida Rodriguez, additional, Safonova, Yana, additional, Schettini, Gustavo, additional, Schnabel, Robert D., additional, Natesh, Nagabhishek Sirpu, additional, Stegemiller, Morgan, additional, Storer, Jessica, additional, Stothard, Paul, additional, Stull, Caleb, additional, Tosser-Klopp, Gwenola, additional, Traglia, Germán M., additional, Tuggle, Chris, additional, Tassell, Curtis P. Van, additional, Watson, Corey, additional, Weikard, Rosemarie, additional, Wimmers, Klaus, additional, Xie, Shangqian, additional, Yang, Liu, additional, Smith, Tim, additional, and Rosen, Ben, additional

Published
2024
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15. Efficacy and safety of pharmacogenomic-guided antidepressant prescribing in patients with depression: an umbrella review and updated meta-analysis.

Author

Tesfamicael, Kiflu G., Lijun Zhao, Fernández-Rodríguez, Rubén, Adelson, David L., Musker, Michael, Polasek, Thomas M., and Lewis, Martin David

Subjects
MENTAL depression, DRUG prescribing, RANDOMIZED controlled trials, ANTIDEPRESSANTS, PHARMACOGENOMICS
Abstract

Aim: To determine the efficacy and safety of pharmacogenomics (PGx)-guided antidepressant prescribing in patients with depression through an umbrella review and updated meta-analysis. Methods: A comprehensive systematic search was conducted on PsycINFO, PubMed, Embase and the Cochrane databases. The pooled effect sizes of randomized controlled trials (RCTs) were expressed as mean differences for continuous data and risk ratios for noncontinuous data. Results: Patients who received PGx-guided medications were 41% to 78% more likely to achieve remission and 20% to 49% more likely to respond to antidepressants than patients receiving treatment-as-usual (TAU). Conclusion: PGx-guided antidepressant prescribing improves the treatment of depression. However, the significance and magnitude of the benefit varies widely between studies and different PGx testing panels. [ABSTRACT FROM AUTHOR]

Published
2024
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16. A comprehensive genomic history of extinct and living elephants

Author

Palkopoulou, Eleftheria, Lipson, Mark, Mallick, Swapan, Nielsen, Svend, Rohland, Nadin, Baleka, Sina, Karpinski, Emil, Ivancevic, Atma M., To, Thu-Hien, Kortschak, R. Daniel, Raison, Joy M., Qu, Zhipeng, Chin, Tat-Jun, Alt, Kurt W., Claesson, Stefan, Dalén, Love, MacPhee, Ross D. E., Meller, Harald, Roca, Alfred L., Ryder, Oliver A., Heiman, David, Young, Sarah, Breen, Matthew, Williams, Christina, Aken, Bronwen L., Ruffier, Magali, Karlsson, Elinor, Johnson, Jeremy, Di Palma, Federica, Alfoldi, Jessica, Adelson, David L., Mailund, Thomas, Munch, Kasper, Lindblad-Toh, Kerstin, Hofreiter, Michael, Poinar, Hendrik, and Reich, David

Published
2018

17. Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse.

Author

Bellone, Rebecca R, Holl, Heather, Setaluri, Vijayasaradhi, Devi, Sulochana, Maddodi, Nityanand, Archer, Sheila, Sandmeyer, Lynne, Ludwig, Arne, Foerster, Daniel, Pruvost, Melanie, Reissmann, Monika, Bortfeldt, Ralf, Adelson, David L, Lim, Sim Lin, Nelson, Janelle, Haase, Bianca, Engensteiner, Martina, Leeb, Tosso, Forsyth, George, Mienaltowski, Michael J, Mahadevan, Padmanabhan, Hofreiter, Michael, Paijmans, Johanna LA, Gonzalez-Fortes, Gloria, Grahn, Bruce, and Brooks, Samantha A

Subjects
Animals, Horses, Retroviridae, Night Blindness, Horse Diseases, Retroelements, Skin Pigmentation, Mutagenesis, Insertional, Female, Male, TRPM Cation Channels, Mutagenesis, Insertional, General Science & Technology
Abstract

Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ(2)=1022.00, p<

Published
2013

24. Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis.

Author

Baer, Lachlan, Barthelson, Karissa, Postlethwait, John H., Adelson, David L., Pederson, Stephen M., and Lardelli, Michael

Subjects
LOCUS (Genetics), GENE expression, BIOLOGICAL systems, HOMOZYGOSITY, CHROMOSOMES, ORYZIAS latipes
Abstract

In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when the effects of homozygosity for recessive mutations are studied in non-isogenic backgrounds, genes located proximal to the mutation on the same chromosome often appear over-represented among those genes identified as differentially expressed (DE). One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect functional responses to the mutation but, instead, result from an unequal distribution of expression quantitative trait loci (eQTLs) between sample groups of mutant or wild-type genotypes. This is problematic because eQTL expression differences are difficult to distinguish from genes that are DE due to functional responses to a mutation. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) are also observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between those sample groups subjected to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting-based approaches. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. Our method for DAR analysis requires only RNA-sequencing data, facilitating its application across new and existing datasets. Author summary: Many human-relevant diseases result from genetic mutations that disrupt cellular functions. We can model these mutations in other organisms (e.g. mouse, zebrafish) and employ gene expression analysis (transcriptomics) to determine how mutations directly affect cells and how cells adjust expression of their genes to compensate for these mutations. In our transcriptome analyses of dominant disease-causative mutations in zebrafish, we identified an interesting phenomenon where a disproportionate number of differentially expressed genes reside on the same chromosome as a mutated gene. Here, we provide strong evidence supporting that the differential expression of some of these chromosomally co-located genes is not due to the mutation but is due to differential segregation of gene alleles with innately different expression levels (i.e. expression quantitative trait loci, eQTLs). We have developed a procedure to measure the likelihood of differential gene expression being due to an eQTL. This allows us to compensate for the presence of such eQTLs in bioinformatic analyses. Our procedure, Differential Allelic Representation (DAR) analysis, revealed evidence for aggregation of genes with related functions on the same chromosome over evolutionary timescales. DAR analysis allows disentanglement of eQTLs from mutation-dependent gene expression responses, thereby permitting more comprehensive investigation of transcriptome data. [ABSTRACT FROM AUTHOR]

Published
2024
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27. Additional file 1 of Transient Polycomb activity represses developmental genes in growing oocytes

Author

Jarred, Ellen G., Qu, Zhipeng, Tsai, Tesha, Oberin, Ruby, Petautschnig, Sigrid, Bildsoe, Heidi, Pederson, Stephen, Zhang, Qing-hua, Stringer, Jessica M., Carroll, John, Gardner, David K., Van den Buuse, Maarten, Sims, Natalie A., Gibson, William T., Adelson, David L., and Western, Patrick S.

Abstract

Additional file 1: Fig. S1: Zp3Cre-mediated Eed deletion results in loss of EED in oocytes from the primary follicle stage in Eed-hom females. Representative images of EED (red) immunofluorescence analysis in primary (top), secondary (middle) and antral (bottom) follicles in females producing Eed-wt and Eed-hom oocytes. a. shows widefield follicle images and b. shows magnified images of the area inside the white squares containing the oocyte nucleus. Lamin B1 (green) marks the nuclear lamina and delineates the edge of the oocyte nucleus in b. DAPI (blue) shows DNA in somatic cells. Images are representative of two ovaries from three biological replicates. Scale bars: 20 μm. Fig. S2: Deletion of Eed in oocytes moderately increased the rate of Surrounded Nucleolus (SN) GV oocytes compared to Non-Surrounded Nucleolus (NSN) GV oocytes. Percentage of SN (left) and NSN (right) GV oocytes obtained from Eed-wt, Eed-het, and Eed-hom females during oocyte collections. *P < 0.05, one-way ANOVA plus Tukey’s multiple comparisons test, N = 7 Eed-wt, 5 Eed-het and 7 Eed-hom females. Error bars represent mean ± standard deviation. Fig. S3: Loss of Eed in growing oocytes did not impact the transcription of genes encoding other core PRC2 subunits, PRC1 core components or DNMTs. Expression of core (a) PRC2 and (b) PRC1 components, and (c) DNMTs in Eed-wt, Eed-het and Eed-hom oocytes. Data represent the mean transcripts per million reads (TPM) for each gene from N = 5 Eed-wt, 4 Eed-het and 6 Eed-hom females. FDR < 0.05 for Eed only, error bars represent mean ± standard deviation. Fig. S4: Eed deletion results in up-regulation of a subset of imprinted and X-linked genes in Eed-hom GV oocytes. Expression of core (a) putative H3K27me3-imprinted (b) classically imprinted, and (c) X-linked Eed oocyte DEGs in Eed-het and Eed-hom oocytes. Data represent the mean transcripts per million reads (TPM) for each gene from N = 5 Eed-wt, 4 Eed-het and 6 Eed-hom females. For classically imprinted and X-linked genes, expression levels were highly varied across some genes and have therefore been graphed for genes with low (TPM < 1), medium (TPM 1 to 5) or high (TPM > 5) expression. For all genes FDR < 0.05 in Eed-hom vs Eed-het oocytes, Error bars represent mean ± standard deviation. Fig. S5: Loss of Eed in growing oocytes did not impact expression of LINE-1 transposons. (a) Percentages of total input reads which aligned to a LINE-1 (L1) element. (b) Number of reads which map to unique and multiple L1s. (c) Proportions of reads according to the number of sites mapped to per read, to a maximum of 20. For (a-c), data represent individual replicates from Eed-wt (n = 5), Eed-wt Cre (n = 2), Eed-het (n = 4) and Eed-hom (n = 6) females. Fig. S6: Eed oocyte DEGs were not dysregulated in pre-implantation embryos. Venn Diagram comparing Eed oocyte DEGs against DEGs identified in Eed maternal null morula and blastocyst embryos. Six genes (Plxnd1, Tceal8, Rap2c, Bbx, Xlr3c and Trm2b) were common in oocytes and morula embryos, five genes (Chrdl1, Lonrf2, Trim6, Cyp1b1 and Ccbe1) were common in oocytes and blastocyst embryos, and two genes (Tspan6 and Gk) were common in morula and blastocyst embryos. For full DEG lists see Tables S1, S6 and S7. Morula and Blastocyst data sets were generated by analysis of published raw data sets (Manuscript References [33, 34).

Published
2023
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28. 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

31. Mammalian genome evolution as a result of epigenetic regulation of transposable elements

Author

Buckley Reuben M. and Adelson David L.

Subjects
epigenetics, genome evolution, mammals, transposable elements, Biology (General), QH301-705.5
Abstract

Transposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming – an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.

Published
2014
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33. Transient Polycomb activity represses developmental genes in growing oocytes

Author

Jarred, Ellen G., primary, Qu, Zhipeng, additional, Tsai, Tesha, additional, Oberin, Ruby, additional, Petautschnig, Sigrid, additional, Bildsoe, Heidi, additional, Pederson, Stephen, additional, Zhang, Qing-hua, additional, Stringer, Jessica M., additional, Carroll, John, additional, Gardner, David K., additional, van den Buuse, Maarten, additional, Sims, Natalie A., additional, Gibson, William T., additional, Adelson, David L., additional, and Western, Patrick S., additional

Published
2022
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36. Loss of EED in the oocyte causes initial fetal growth restriction followed by placental hyperplasia and offspring overgrowth

Author

Oberin, Ruby, primary, Petautschnig, Sigrid, additional, Tsai, Tesha, additional, Jarred, Ellen G., additional, Qu, Zhipeng, additional, Youngson, Neil A., additional, Bildsoe, Heidi, additional, Truong, Thi T., additional, Fernando, Dilini, additional, van den Buuse, Maarten, additional, Gardner, David K., additional, Sims, Natalie A., additional, Adelson, David L., additional, and Western, Patrick S., additional

Published
2022
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38. Corrigendum to “Future directions for the discovery of natural product-derived immunomodulating drugs: An IUPHAR positional review” [Pharmacol. Res. 177 (2022) 106076]

Author

Wainwright, Cherry L., primary, Teixeira, Mauro M., additional, Adelson, David L., additional, Buenz, Eric J., additional, David, Bruno, additional, Glaser, Keith B., additional, Harata-Lee, Yuka, additional, Howes, Melanie-Jayne R., additional, Izzo, Angelo A., additional, Maffia, Pasquale, additional, Mayer, Alejandro M.S., additional, Mazars, Claire, additional, Newman, David J., additional, Lughadha, Eimear Nic, additional, Pimenta, Adriano M.C., additional, Parra, John A.A., additional, Qu, Zhipeng, additional, Shen, Hanyuan, additional, Spedding, Michael, additional, and Wolfender, Jean-Luc, additional

Published
2022
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40. Future directions for the discovery of natural product-derived immunomodulating drugs

Author

Wainwright, Cherry L., Teixeira, Mauro M., Adelson, David L., Buenz, Eric J., David, Bruno, Glaser, Keith B., Harata-Lee, Yuka, Howes, Melanie-Jayne R., Izzo, Angelo A., Maffia, Pasquale, Mayer, Alejandro M.S., Mazars, Claire, Newman, David J., Nic Lughadha, Eimear, Pimenta, Adriano M.C., Parra, John A.A., Qu, Zhipeng, Shen, Hanyan, Spedding, Michael, and Wolfender, Jean-Luc

Abstract

Drug discovery from natural sources is going through a renaissance, having spent many decades in the shadow of synthetic molecule drug discovery, despite the fact that natural product-derived compounds occupy a much greater chemical space than those created through synthetic chemistry methods. With this new era comes new possibilities, not least the novel targets that have emerged in recent times and the development of state-of-the-art technologies that can be applied to drug discovery from natural sources. Although progress has been made with some immunomodulating drugs, there remains a pressing need for new agents that can be used to treat the wide variety of conditions that arise from disruption, or over-activation, of the immune system; natural products may therefore be key in filling this gap. Recognising that, at present, there is no authoritative article that details the current state-of-the-art of the immunomodulatory activity of natural products, this in-depth review has arisen from a joint effort between the International Union of Basic and Clinical Pharmacology (IUPHAR) Natural Products and Immunopharmacology, with contributions from a Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation number of world-leading researchers in the field of natural product drug discovery, to provide a “position statement” on what natural products has to offer in the search for new immunomodulatory argents. To this end, we provide a historical look at previous discoveries of naturally occurring immunomodulators, present a picture of the current status of the field and provide insight into the future opportunities and challenges for the discovery of new drugs to treat immune-related diseases.

Published
2022

42. Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes

Author

Galbraith, James D., Ludington, Alastair J., Sanders, Kate L., Amos, Timothy G., Thomson, Vicki A., Tuipulotu, Daniel Enosi, Dunstan, Nathan, Edwards, Richard J., Suh, Alexander, Adelson, David L., Galbraith, James D., Ludington, Alastair J., Sanders, Kate L., Amos, Timothy G., Thomson, Vicki A., Tuipulotu, Daniel Enosi, Dunstan, Nathan, Edwards, Richard J., Suh, Alexander, and Adelson, David L.

Abstract

Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids similar to 30 Mya and have since rapidly diversified into six amphibious, similar to 60 marine and similar to 100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.

Published
2022
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43. Genome stability is in the eye of the beholder: CR1 retrotransposon activity varies significantly across avian diversity

Author

Galbraith, James D., Kortschak, R. Daniel, Suh, Alexander, and Adelson, David L.

Subjects
AcademicSubjects/SCI01140, Mammals, Evolutionary Biology, Genome, Retroelements, AcademicSubjects/SCI01130, food and beverages, transposable element, genome evolution, Genomic Instability, Evolution, Molecular, Evolutionsbiologi, birds, DNA Transposable Elements, Genetics, Animals, Genetik, Chickens, Phylogeny, Ecology, Evolution, Behavior and Systematics, Research Article
Abstract

Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.

Published
2021

49. 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, 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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

50. ARMC5 Mutations Are Common in Familial Bilateral Macronodular Adrenal Hyperplasia

Author

Gagliardi, Lucia, Schreiber, Andreas W., Hahn, Christopher N., Feng, Jinghua, Cranston, Treena, Boon, Hannah, Hotu, Cheri, Oftedal, Bergithe E., Cutfield, Richard, Adelson, David L., Braund, Wilton J., Gordon, Richard D., Rees, D. Aled, Grossman, Ashley B., Torpy, David J., and Scott, Hamish S.

Published
2014

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