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1. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea

Author

Khan, Aamir W., Garg, Vanika, Sun, Shuai, Gupta, Saurabh, Dudchenko, Olga, Roorkiwal, Manish, Chitikineni, Annapurna, Bayer, Philipp E., Shi, Chengcheng, Upadhyaya, Hari D., Bohra, Abhishek, Bharadwaj, Chellapilla, Mir, Reyazul Rouf, Baruch, Kobi, Yang, Bicheng, Coyne, Clarice J., Bansal, Kailash C., Nguyen, Henry T., Ronen, Gil, Aiden, Erez Lieberman, Veneklaas, Erik, Siddique, Kadambot H. M., Liu, Xin, Edwards, David, and Varshney, Rajeev K.

Published
2024
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2. Emx2 underlies the development and evolution of marsupial gliding membranes

Author

Moreno, Jorge A., Dudchenko, Olga, Feigin, Charles Y., Mereby, Sarah A., Chen, Zhuoxin, Ramos, Raul, Almet, Axel A., Sen, Harsha, Brack, Benjamin J., Johnson, Matthew R., Li, Sha, Wang, Wei, Gaska, Jenna M., Ploss, Alexander, Weisz, David, Omer, Arina D., Yao, Weijie, Colaric, Zane, Kaur, Parwinder, Leger, Judy St., Nie, Qing, Mena, Alexandria, Flanagan, Joseph P., Keller, Greta, Sanger, Thomas, Ostrow, Bruce, Plikus, Maksim V., Kvon, Evgeny Z., Aiden, Erez Lieberman, and Mallarino, Ricardo

Published
2024
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4. Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism

Author

Pujadas Liwag, Emily M., Wei, Xiaolong, Acosta, Nicolas, Carter, Lucas M., Yang, Jiekun, Almassalha, Luay M., Jain, Surbhi, Daneshkhah, Ali, Rao, Suhas S. P., Seker-Polat, Fidan, MacQuarrie, Kyle L., Ibarra, Joe, Agrawal, Vasundhara, Aiden, Erez Lieberman, Kanemaki, Masato T., Backman, Vadim, and Adli, Mazhar

Published
2024
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5. Cooperation among an anonymous group protected Bitcoin during failures of decentralization

Author

Blackburn, Alyssa, Huber, Christoph, Eliaz, Yossi, Shamim, Muhammad S., Weisz, David, Seshadri, Goutham, Kim, Kevin, Hang, Shengqi, and Aiden, Erez Lieberman

Subjects
Computer Science - Computer Science and Game Theory, Computer Science - Computers and Society, Physics - Physics and Society
Abstract

Bitcoin is a digital currency designed to rely on a decentralized, trustless network of anonymous agents. Using a pseudonymous-address-linking procedure that achieves >99% sensitivity and >99% specificity, we reveal that between launch (January 3rd, 2009), and when the price reached $1 (February 9th, 2011), most bitcoin was mined by only sixty-four agents. This was due to the rapid emergence of Pareto distributions in bitcoin income, producing such extensive resource centralization that almost all contemporary bitcoin addresses can be connected to these top agents by a chain of six transactions. Centralization created a social dilemma. Attackers could routinely exploit bitcoin via a "51% attack", making it possible for them to repeatedly spend the same bitcoins. Yet doing so would harm the community. Strikingly, we find that potential attackers always chose to cooperate instead. We model this dilemma using an N-player Centipede game in which anonymous players can choose to exploit, and thereby undermine, an appreciating good. Combining theory and economic experiments, we show that, even when individual payoffs are unchanged, cooperation is more frequent when the game is played by an anonymous group. Although bitcoin was designed to rely on a decentralized, trustless network of anonymous agents, its early success rested instead on cooperation among a small group of altruistic founders., Comment: 12 pages main text 6 main text figures 76 total pages 23 supplemental figures

Published
2022

6. Author Correction: Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea

Author

Khan, Aamir W., Garg, Vanika, Sun, Shuai, Gupta, Saurabh, Dudchenko, Olga, Roorkiwal, Manish, Chitikineni, Annapurna, Bayer, Philipp E., Shi, Chengcheng, Upadhyaya, Hari D., Bohra, Abhishek, Bharadwaj, Chellapilla, Mir, Reyazul Rouf, Baruch, Kobi, Yang, Bicheng, Coyne, Clarice J., Bansal, Kailash C., Nguyen, Henry T., Ronen, Gil, Aiden, Erez Lieberman, Veneklaas, Erik, Siddique, Kadambot H. M., Liu, Xin, Edwards, David, and Varshney, Rajeev K.

Published
2024
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7. Response to Bakker et al.

Author

Robinson, Jacqueline A, Bowie, Rauri CK, Dudchenko, Olga, Aiden, Erez Lieberman, Hendrickson, Sher L, Steiner, Cynthia C, Ryder, Oliver A, Mindell, David P, and Wall, Jeffrey D

Subjects
Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Robinson and colleagues respond to the points raised about their paper by Bakker et al.

Published
2022

11. Convergent and complementary selection shaped gains and losses of eusociality in sweat bees

Author

Jones, Beryl M., Rubin, Benjamin E. R., Dudchenko, Olga, Kingwell, Callum J., Traniello, Ian M., Wang, Z. Yan, Kapheim, Karen M., Wyman, Eli S., Adastra, Per A., Liu, Weijie, Parsons, Lance R., Jackson, S. RaElle, Goodwin, Katharine, Davidson, Shawn M., McBride, Matthew J., Webb, Andrew E., Omufwoko, Kennedy S., Van Dorp, Nikki, Otárola, Mauricio Fernández, Pham, Melanie, Omer, Arina D., Weisz, David, Schraiber, Joshua, Villanea, Fernando, Wcislo, William T., Paxton, Robert J., Hunt, Brendan G., Aiden, Erez Lieberman, and Kocher, Sarah D.

Published
2023
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12. Genome-wide diversity in the California condor tracks its prehistoric abundance and decline

Author

Robinson, Jacqueline A, Bowie, Rauri CK, Dudchenko, Olga, Aiden, Erez Lieberman, Hendrickson, Sher L, Steiner, Cynthia C, Ryder, Oliver A, Mindell, David P, and Wall, Jeffrey D

Subjects
Human Genome, Genetics, Life on Land, Animals, Ecosystem, Endangered Species, Falconiformes, Female, Genome, Genomics, Population Density, conservation, demographic history, extinction, genomics, inbreeding, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.1 During the latter half of the twentieth century, North America's largest soaring bird,2 the California condor (Gymnogyps californianus; Critically Endangered3), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor's recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented,4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable3) and the turkey vulture (Cathartes aura; Least Concern3). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.

Published
2021

14. Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity

Author

Houck, Marlys L., Koepfli, Klaus-Peter, Hains, Taylor, Khan, Ruqayya, Charter, Suellen J., Fronczek, Julie A., Misuraca, Ann C., Kliver, Sergei, Perelman, Polina L., Beklemisheva, Violetta, Graphodatsky, Alexander, Luo, Shu-Jin, O’Brien, Stephen J., Lim, Norman T.-L., Chin, Jason S. C., Guerra, Vanessa, Tamazian, Gaik, Omer, Arina, Weisz, David, Kaemmerer, Kenneth, Sturgeon, Ginger, Gaspard, Joseph, Hahn, Alicia, McDonough, Mark, Garcia-Treviño, Isabel, Gentry, Jordan, Coke, Rob L., Janecka, Jan E., Harrigan, Ryan J., Tinsman, Jen, Smith, Thomas B., Aiden, Erez Lieberman, and Dudchenko, Olga

Published
2023
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16. Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

Author

Garg, Vanika, Dudchenko, Olga, Wang, Jinpeng, Khan, Aamir W., Gupta, Saurabh, Kaur, Parwinder, Han, Kai, Saxena, Rachit K., Kale, Sandip M., Pham, Melanie, Yu, Jigao, Chitikineni, Annapurna, Zhang, Zhikang, Fan, Guangyi, Lui, Christopher, Valluri, Vinodkumar, Meng, Fanbo, Bhandari, Aditi, Liu, Xiaochuan, Yang, Tao, Chen, Hua, Valliyodan, Babu, Roorkiwal, Manish, Shi, Chengcheng, Yang, Hong Bin, Durand, Neva C., Pandey, Manish K., Li, Guowei, Barmukh, Rutwik, Wang, Xingjun, Chen, Xiaoping, Lam, Hon-Ming, Jiang, Huifang, Zong, Xuxiao, Liang, Xuanqiang, Liu, Xin, Liao, Boshou, Guo, Baozhu, Jackson, Scott, Nguyen, Henry T., Zhuang, Weijian, Shubo, Wan, Wang, Xiyin, Aiden, Erez Lieberman, Bennetzen, Jeffrey L., and Varshney, Rajeev K.

Published
2022
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17. Improved reference genome of Aedes aegypti informs arbovirus vector control.

Author

Matthews, Benjamin J, Dudchenko, Olga, Kingan, Sarah B, Koren, Sergey, Antoshechkin, Igor, Crawford, Jacob E, Glassford, William J, Herre, Margaret, Redmond, Seth N, Rose, Noah H, Weedall, Gareth D, Wu, Yang, Batra, Sanjit S, Brito-Sierra, Carlos A, Buckingham, Steven D, Campbell, Corey L, Chan, Saki, Cox, Eric, Evans, Benjamin R, Fansiri, Thanyalak, Filipović, Igor, Fontaine, Albin, Gloria-Soria, Andrea, Hall, Richard, Joardar, Vinita S, Jones, Andrew K, Kay, Raissa GG, Kodali, Vamsi K, Lee, Joyce, Lycett, Gareth J, Mitchell, Sara N, Muehling, Jill, Murphy, Michael R, Omer, Arina D, Partridge, Frederick A, Peluso, Paul, Aiden, Aviva Presser, Ramasamy, Vidya, Rašić, Gordana, Roy, Sourav, Saavedra-Rodriguez, Karla, Sharan, Shruti, Sharma, Atashi, Smith, Melissa Laird, Turner, Joe, Weakley, Allison M, Zhao, Zhilei, Akbari, Omar S, Black, William C, Cao, Han, Darby, Alistair C, Hill, Catherine A, Johnston, J Spencer, Murphy, Terence D, Raikhel, Alexander S, Sattelle, David B, Sharakhov, Igor V, White, Bradley J, Zhao, Li, Aiden, Erez Lieberman, Mann, Richard S, Lambrechts, Louis, Powell, Jeffrey R, Sharakhova, Maria V, Tu, Zhijian, Robertson, Hugh M, McBride, Carolyn S, Hastie, Alex R, Korlach, Jonas, Neafsey, Daniel E, Phillippy, Adam M, and Vosshall, Leslie B

Subjects
Animals, Aedes, Arboviruses, Dengue Virus, Arbovirus Infections, Pyrethrins, Glutathione Transferase, Genetics, Population, Genomics, Insect Control, Insecticide Resistance, Multigene Family, Reference Standards, Female, Male, Genome, Insect, Genetic Variation, DNA Copy Number Variations, Sex Determination Processes, Molecular Sequence Annotation, Mosquito Vectors, Genetics, Population, Genome, Insect, General Science & Technology
Abstract

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.

Published
2018

18. Using Deep Learning and Google Street View to Estimate the Demographic Makeup of the US

Author

Gebru, Timnit, Krause, Jonathan, Wang, Yilun, Chen, Duyun, Deng, Jia, Aiden, Erez Lieberman, and Fei-Fei, Li

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

The United States spends more than $1B each year on initiatives such as the American Community Survey (ACS), a labor-intensive door-to-door study that measures statistics relating to race, gender, education, occupation, unemployment, and other demographic factors. Although a comprehensive source of data, the lag between demographic changes and their appearance in the ACS can exceed half a decade. As digital imagery becomes ubiquitous and machine vision techniques improve, automated data analysis may provide a cheaper and faster alternative. Here, we present a method that determines socioeconomic trends from 50 million images of street scenes, gathered in 200 American cities by Google Street View cars. Using deep learning-based computer vision techniques, we determined the make, model, and year of all motor vehicles encountered in particular neighborhoods. Data from this census of motor vehicles, which enumerated 22M automobiles in total (8% of all automobiles in the US), was used to accurately estimate income, race, education, and voting patterns, with single-precinct resolution. (The average US precinct contains approximately 1000 people.) The resulting associations are surprisingly simple and powerful. For instance, if the number of sedans encountered during a 15-minute drive through a city is higher than the number of pickup trucks, the city is likely to vote for a Democrat during the next Presidential election (88% chance); otherwise, it is likely to vote Republican (82%). Our results suggest that automated systems for monitoring demographic trends may effectively complement labor-intensive approaches, with the potential to detect trends with fine spatial resolution, in close to real time., Comment: 41 pages including supplementary material. Under review at PNAS

Published
2017
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19. Genetic determinants of co-accessible chromatin regions in activated T cells across humans

Author

Gate, Rachel E, Cheng, Christine S, Aiden, Aviva P, Siba, Atsede, Tabaka, Marcin, Lituiev, Dmytro, Machol, Ido, Gordon, M Grace, Subramaniam, Meena, Shamim, Muhammad, Hougen, Kendrick L, Wortman, Ivo, Huang, Su-Chen, Durand, Neva C, Feng, Ting, De Jager, Philip L, Chang, Howard Y, Aiden, Erez Lieberman, Benoist, Christophe, Beer, Michael A, Ye, Chun J, and Regev, Aviv

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Stem Cell Research, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Adult, Autoimmune Diseases, CD4-Positive T-Lymphocytes, Chromatin, Female, Gene Expression Regulation, Genotype, Humans, Male, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression.

Published
2018

20. An encyclopedia of enhancer-gene regulatory interactions in the human genome

Author

Gschwind, Andreas R., primary, Mualim, Kristy S., additional, Karbalayghareh, Alireza, additional, Sheth, Maya U., additional, Dey, Kushal K., additional, Jagoda, Evelyn, additional, Nurtdinov, Ramil N., additional, Xi, Wang, additional, Tan, Anthony S., additional, Jones, Hank, additional, Ma, X. Rosa, additional, Yao, David, additional, Nasser, Joseph, additional, Avsec, Žiga, additional, James, Benjamin T., additional, Shamim, Muhammad S., additional, Durand, Neva C., additional, Rao, Suhas S. P., additional, Mahajan, Ragini, additional, Doughty, Benjamin R., additional, Andreeva, Kalina, additional, Ulirsch, Jacob C., additional, Fan, Kaili, additional, Perez, Elizabeth M., additional, Nguyen, Tri C., additional, Kelley, David R., additional, Finucane, Hilary K., additional, Moore, Jill E., additional, Weng, Zhiping, additional, Kellis, Manolis, additional, Bassik, Michael C., additional, Price, Alkes L., additional, Beer, Michael A., additional, Guigó, Roderic, additional, Stamatoyannopoulos, John A., additional, Aiden, Erez Lieberman, additional, Greenleaf, William J., additional, Leslie, Christina S., additional, Steinmetz, Lars M., additional, Kundaje, Anshul, additional, and Engreitz, Jesse M., additional

Published
2023
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22. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

Author

Edwards, Richard J., Field, Matt A., Ferguson, James M., Dudchenko, Olga, Keilwagen, Jens, Rosen, Benjamin D., Johnson, Gary S., Rice, Edward S., Hillier, La Deanna, Hammond, Jillian M., Towarnicki, Samuel G., Omer, Arina, Khan, Ruqayya, Skvortsova, Ksenia, Bogdanovic, Ozren, Zammit, Robert A., Aiden, Erez Lieberman, Warren, Wesley C., and Ballard, J. William O.

Published
2021
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23. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

Author

Fulco, Charles P., Nasser, Joseph, Jones, Thouis R., Munson, Glen, Bergman, Drew T., Subramanian, Vidya, Grossman, Sharon R., Anyoha, Rockwell, Doughty, Benjamin R., Patwardhan, Tejal A., Nguyen, Tung H., Kane, Michael, Perez, Elizabeth M., Durand, Neva C., Lareau, Caleb A., Stamenova, Elena K., Aiden, Erez Lieberman, Lander, Eric S., and Engreitz, Jesse M.

Published
2019
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24. Chromosome-Level Genome Assembly and Annotation of a Periodical Cicada Species: Magicicada septendecula.

Author

Bush, Jonas, Webster, Cynthia, Wegrzyn, Jill, Simon, Chris, Wilcox, Edward, Khan, Ruqayya, Weisz, David, Dudchenko, Olga, Aiden, Erez Lieberman, and Frandsen, Paul

Subjects
CICADAS, LIFE cycles (Biology), GENOMICS, HOMOPTERA, GENOMES, REPTILES
Abstract

We present a high-quality assembly and annotation of the periodical cicada species, Magicicada septendecula (Hemiptera: Auchenorrhyncha: Cicadidae). Periodical cicadas have a significant ecological impact, serving as a food source for many mammals, reptiles, and birds. Magicicada are well known for their massive emergences of 1 to 3 species that appear in different locations in the eastern United States nearly every year. These year classes ("broods") emerge dependably every 13 or 17 yr in a given location. Recently, it has become clear that 4-yr early or late emergences of a sizeable portion of a population are an important part of the history of brood formation; however, the biological mechanisms by which they track the passage of time remain a mystery. Using PacBio HiFi reads in conjunction with Hi-C proximity ligation data, we have assembled and annotated the first whole genome for a periodical cicada, an important resource for future phylogenetic and comparative genomic analysis. This also represents the first quality genome assembly and annotation for the Hemipteran superfamily Cicadoidea. With a scaffold N50 of 518.9 Mb and a complete BUSCO score of 96.7%, we are confident that this assembly will serve as a vital resource toward uncovering the genomic basis of periodical cicadas' long, synchronized life cycles and will provide a robust framework for further investigations into these insects. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Genomic signatures of barley breeding for environmental adaptation to the new continents

Author

Hu, Haifei, primary, Wang, Penghao, additional, Angessa, Tefera Tolera, additional, Zhang, Xiao‐Qi, additional, Chalmers, Kenneth J., additional, Zhou, Gaofeng, additional, Hill, Camilla Beate, additional, Jia, Yong, additional, Simpson, Craig, additional, Fuller, John, additional, Saxena, Alka, additional, Al Shamaileh, Hadi, additional, Iqbal, Munir, additional, Chapman, Brett, additional, Kaur, Parwinder, additional, Dudchenko, Olga, additional, Aiden, Erez Lieberman, additional, Keeble‐Gagnere, Gabriel, additional, Westcott, Sharon, additional, Leah, David, additional, Tibbits, Josquin F., additional, Waugh, Robbie, additional, Langridge, Peter, additional, Varshney, Rajeev, additional, He, Tianhua, additional, and Li, Chengdao, additional

Published
2023
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31. Depletion of lamins B1 and B2 alters chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism

Author

Pujadas, Emily M., primary, Wei, Xiaolong, additional, Acosta, Nicolas, additional, Carter, Lucas, additional, Yang, Jiekun, additional, Almassalha, Luay, additional, Daneshkhah, Ali, additional, Rao, Suhas S.P., additional, Agrawal, Vasundhara, additional, Seker-Polat, Fidan, additional, Aiden, Erez Lieberman, additional, Kanemaki, Masato T., additional, Backman, Vadim, additional, and Adli, Mazhar, additional

Published
2023
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32. Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

Author

Harris, Hannah L., primary, Gu, Huiya, additional, Olshansky, Moshe, additional, Wang, Ailun, additional, Farabella, Irene, additional, Eliaz, Yossi, additional, Kalluchi, Achyuth, additional, Krishna, Akshay, additional, Jacobs, Mozes, additional, Cauer, Gesine, additional, Pham, Melanie, additional, Rao, Suhas S. P., additional, Dudchenko, Olga, additional, Omer, Arina, additional, Mohajeri, Kiana, additional, Kim, Sungjae, additional, Nichols, Michael H., additional, Davis, Eric S., additional, Gkountaroulis, Dimos, additional, Udupa, Devika, additional, Aiden, Aviva Presser, additional, Corces, Victor G., additional, Phanstiel, Douglas H., additional, Noble, William Stafford, additional, Nir, Guy, additional, Di Pierro, Michele, additional, Seo, Jeong-Sun, additional, Talkowski, Michael E., additional, Aiden, Erez Lieberman, additional, and Rowley, M. Jordan, additional

Published
2023
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34. Emx2underlies the development and evolution of marsupial gliding membranes

Author

Moreno, Jorge A., Dudchenko, Olga, Feigin, Charles Y., Mereby, Sarah A., Chen, Zhuoxin, Ramos, Raul, Almet, Axel A., Sen, Harsha, Brack, Benjamin J., Johnson, Matthew R., Li, Sha, Wang, Wei, Gaska, Jenna M., Ploss, Alexander, Weisz, David, Omer, Arina D., Yao, Weijie, Colaric, Zane, Kaur, Parwinder, Leger, Judy St., Nie, Qing, Mena, Alexandria, Flanagan, Joseph P., Keller, Greta, Sanger, Thomas, Ostrow, Bruce, Plikus, Maksim V., Kvon, Evgeny Z., Aiden, Erez Lieberman, and Mallarino, Ricardo

Abstract

Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium—an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.

Published
2024
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35. Cicersuper-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea

Author

Khan, Aamir W., Garg, Vanika, Sun, Shuai, Gupta, Saurabh, Dudchenko, Olga, Roorkiwal, Manish, Chitikineni, Annapurna, Bayer, Philipp E., Shi, Chengcheng, Upadhyaya, Hari D., Bohra, Abhishek, Bharadwaj, Chellapilla, Mir, Reyazul Rouf, Baruch, Kobi, Yang, Bicheng, Coyne, Clarice J., Bansal, Kailash C., Nguyen, Henry T., Ronen, Gil, Aiden, Erez Lieberman, Veneklaas, Erik, Siddique, Kadambot H. M., Liu, Xin, Edwards, David, and Varshney, Rajeev K.

Abstract

Chickpea (Cicer arietinumL.)—an important legume crop cultivated in arid and semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicersuper-pangenome based on the de novo genome assemblies of eight annual Cicerwild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicerspecies into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.

Published
2024
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36. A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing.

Author

Adastra, Per A., Durand, Neva C., Mitra, Namita, Pulido, Saul Godinez, Mahajan, Ragini, Blackburn, Alyssa, Colaric, Zane L., Theisen, Joshua W. M., Weisz, David, Dudchenko, Olga, Gnirke, Andreas, Rao, Suhas S. P., Kaur, Parwinder, Aiden, Erez Lieberman, and Aiden, Aviva Presser

Subjects
NUCLEOTIDE sequencing, COVID-19, SARS-CoV-2, COVID-19 testing, DNA sequencing, DRUG target
Abstract

Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control's 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach. [ABSTRACT FROM AUTHOR]

Published
2023
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37. A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly

Author

Tolman, Ethan R, primary, Beatty, Christopher D, additional, Bush, Jonas, additional, Kohli, Manpreet, additional, Moreno, Carlos M, additional, Ware, Jessica L, additional, Weber, K Scott, additional, Khan, Ruqayya, additional, Maheshwari, Chirag, additional, Weisz, David, additional, Dudchenko, Olga, additional, Aiden, Erez Lieberman, additional, and Frandsen, Paul B, additional

Published
2023
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38. The Australasian dingo archetype:De novochromosome-length genome assembly, DNA methylome, and cranial morphology

Author

Ballard, J. William O., primary, Field, Matt A., additional, Edwards, Richard J., additional, Wilson, Laura A.B., additional, Koungoulos, Loukas G., additional, Rosen, Benjamin D., additional, Chernoff, Barry, additional, Dudchenko, Olga, additional, Omer, Arina, additional, Keilwagen, Jens, additional, Skvortsova, Ksenia, additional, Bogdanovic, Ozren, additional, Chan, Eva, additional, Zammit, Robert, additional, Hayes, Vanessa, additional, and Aiden, Erez Lieberman, additional

Published
2023
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39. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Author

Ballard, J William O, primary, Field, Matt A, additional, Edwards, Richard J, additional, Wilson, Laura A B, additional, Koungoulos, Loukas G, additional, Rosen, Benjamin D, additional, Chernoff, Barry, additional, Dudchenko, Olga, additional, Omer, Arina, additional, Keilwagen, Jens, additional, Skvortsova, Ksenia, additional, Bogdanovic, Ozren, additional, Chan, Eva, additional, Zammit, Robert, additional, Hayes, Vanessa, additional, and Aiden, Erez Lieberman, additional

Published
2023
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42. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes).

Author

Kliver, Sergei, Houck, Marlys L, Perelman, Polina L, Totikov, Azamat, Tomarovsky, Andrey, Dudchenko, Olga, Omer, Arina D, Colaric, Zane, Weisz, David, Aiden, Erez Lieberman, Chan, Saki, Hastie, Alex, Komissarov, Aleksey, Ryder, Oliver A, Graphodatsky, Alexander, Johnson, Warren E, Maldonado, Jesús E, Pukazhenthi, Budhan S, Marinari, Paul E, and Wildt, David E

Subjects
KARYOTYPES, FERRET, GENOMES, ENDANGERED species, CHROMOSOMES, DISEASE susceptibility
Abstract

The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species. [ABSTRACT FROM AUTHOR]

Published
2023
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44. A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)

Author

Brůna, Tomáš, primary, Aryal, Rishi, additional, Dudchenko, Olga, additional, Sargent, Daniel James, additional, Mead, Daniel, additional, Buti, Matteo, additional, Cavallini, Andrea, additional, Hytönen, Timo, additional, Andrés, Javier, additional, Pham, Melanie, additional, Weisz, David, additional, Mascagni, Flavia, additional, Usai, Gabriele, additional, Natali, Lucia, additional, Bassil, Nahla, additional, Fernandez, Gina E, additional, Lomsadze, Alexandre, additional, Armour, Mitchell, additional, Olukolu, Bode, additional, Poorten, Thomas, additional, Britton, Caitlin, additional, Davik, Jahn, additional, Ashrafi, Hamid, additional, Aiden, Erez Lieberman, additional, Borodovsky, Mark, additional, and Worthington, Margaret, additional

Published
2022
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45. Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models

Author

Mohajeri, Kiana, primary, Yadav, Rachita, additional, D'haene, Eva, additional, Boone, Philip M., additional, Erdin, Serkan, additional, Gao, Dadi, additional, Moyses-Oliveira, Mariana, additional, Bhavsar, Riya, additional, Currall, Benjamin B., additional, O'Keefe, Kathryn, additional, Burt, Nicholas D., additional, Lowther, Chelsea, additional, Lucente, Diane, additional, Salani, Monica, additional, Larson, Mathew, additional, Redin, Claire, additional, Dudchenko, Olga, additional, Aiden, Erez Lieberman, additional, Menten, Björn, additional, Tai, Derek J.C., additional, Gusella, James F., additional, Vergult, Sarah, additional, and Talkowski, Michael E., additional

Published
2022
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46. A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly

Author

Tolman, Ethan R., primary, Beatty, Christopher D., additional, Bush, Jonas, additional, Kohli, Manpreet, additional, Moreno, Carlos M., additional, Ware, Jessica L., additional, Weber, K. Scott, additional, Khan, Ruqayya, additional, Maheshwari, Chirag, additional, Weisz, David, additional, Dudchenko, Olga, additional, Aiden, Erez Lieberman, additional, and Frandsen, Paul B., additional

Published
2022
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47. A pan‐genome and chromosome‐length reference genome of narrow‐leafed lupin ( Lupinus angustifolius ) reveals genomic diversity and insights into key industry and biological traits

Author

Garg, Gagan, primary, Kamphuis, Lars G., additional, Bayer, Philipp E., additional, Kaur, Parwinder, additional, Dudchenko, Olga, additional, Taylor, Candy M., additional, Frick, Karen M., additional, Foley, Rhonda C., additional, Gao, Ling‐Ling, additional, Aiden, Erez Lieberman, additional, Edwards, David, additional, and Singh, Karam B., additional

Published
2022
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48. A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

Author

Wilder, Aryn P, primary, Dudchenko, Olga, additional, Curry, Caitlin, additional, Korody, Marisa, additional, Turbek, Sheela P, additional, Daly, Mark, additional, Misuraca, Ann, additional, Wang, Gaojianyong, additional, Khan, Ruqayya, additional, Weisz, David, additional, Fronczek, Julie, additional, Aiden, Erez Lieberman, additional, Houck, Marlys L, additional, Shier, Debra M, additional, Ryder, Oliver A, additional, and Steiner, Cynthia C, additional

Published
2022
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50. Essential role of Cp190 in physical and regulatory boundary formation

Author

Kaushal, Anjali, primary, Dorier, Julien, additional, Wang, Bihan, additional, Mohana, Giriram, additional, Taschner, Michael, additional, Cousin, Pascal, additional, Waridel, Patrice, additional, Iseli, Christian, additional, Semenova, Anastasiia, additional, Restrepo, Simon, additional, Guex, Nicolas, additional, Aiden, Erez Lieberman, additional, and Gambetta, Maria Cristina, additional

Published
2022
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