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2. A genomic basis of vocal rhythm in birds

Author

Sebastianelli, Matteo, Lukhele, Sifiso M., Secomandi, Simona, de Souza, Stacey G., Haase, Bettina, Moysi, Michaella, Nikiforou, Christos, Hutfluss, Alexander, Mountcastle, Jacquelyn, Balacco, Jennifer, Pelan, Sarah, Chow, William, Fedrigo, Olivier, Downs, Colleen T., Monadjem, Ara, Dingemanse, Niels J., Jarvis, Erich D., Brelsford, Alan, vonHoldt, Bridgett M., and Kirschel, Alexander N. G.

Published
2024
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3. Chromosome level genome assembly of the Etruscan shrew Suncus etruscus

Author

Bukhman, Yury V., Meyer, Susanne, Chu, Li-Fang, Abueg, Linelle, Antosiewicz-Bourget, Jessica, Balacco, Jennifer, Brecht, Michael, Dinatale, Erica, Fedrigo, Olivier, Formenti, Giulio, Fungtammasan, Arkarachai, Giri, Swagarika Jaharlal, Hiller, Michael, Howe, Kerstin, Kihara, Daisuke, Mamott, Daniel, Mountcastle, Jacquelyn, Pelan, Sarah, Rabbani, Keon, Sims, Ying, Tracey, Alan, Wood, Jonathan M. D., Jarvis, Erich D., Thomson, James A., Chaisson, Mark J. P., and Stewart, Ron

Published
2024
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5. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Author

Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D., Rabbani, Keon, Antunes, Agostinho, Balacco, Jennifer R., Chaisson, Mark J. P., Cheng, Haoyu, Collins, Joanna, Couture, Melanie, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, Horan, Kathleen, Jain, Nivesh, Johnson, Cassidy, Kim, Heebal, Lee, Chul, Marques-Bonet, Tomas, O’Toole, Brian, Rhie, Arang, Secomandi, Simona, Sozzoni, Marcella, Tilley, Tatiana, Uliano-Silva, Marcela, van den Beek, Marius, Williams, Robert W., Waterhouse, Robert M., Phillippy, Adam M., Jarvis, Erich D., Schatz, Michael C., Nekrutenko, Anton, and Formenti, Giulio

Published
2024
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6. A draft human pangenome reference

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A, Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Antonacci-Fulton, Lucinda L, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Schultz, Baergen I, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Françoise, and Tricomi, Francesca Floriana

Subjects
Biological Sciences, Genetics, 2.1 Biological and endogenous factors, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Humans, Diploidy, Genome, Human, Haplotypes, Sequence Analysis, DNA, Genomics, Reference Standards, Cohort Studies, Alleles, Genetic Variation, General Science & Technology
Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

7. Gaps and complex structurally variant loci in phased genome assemblies

Author

Porubsky, David, Vollger, Mitchell R, Harvey, William T, Rozanski, Allison N, Ebert, Peter, Hickey, Glenn, Hasenfeld, Patrick, Sanders, Ashley D, Stober, Catherine, Consortium, Human Pangenome Reference, Korbel, Jan O, Paten, Benedict, Marschall, Tobias, Eichler, Evan E, Abel, Haley J, Antonacci-Fulton, Lucinda L, Asri, Mobin, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Bourque, Guillaume, Buonaiuto, Silvia, Carroll, Andrew, Chaisson, Mark JP, Chang, Pi-Chuan, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Cody, Sarah, Colonna, Vincenza, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Doerr, Daniel, Ebler, Jana, Eizenga, Jordan M, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Feng, Xiaowen, Fischer, Christian, Flicek, Paul, Formenti, Giulio, Frankish, Adam, Fulton, Robert S, Gao, Yan, Garg, Shilpa, Garrison, Erik, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Groza, Cristian, Guarracino, Andrea, Haggerty, Leanne, Hall, Ira M, Haukness, Marina, Haussler, David, Heumos, Simon, Hoekzema, Kendra, Hourlier, Thibaut, Howe, Kerstin, Jain, Miten, Jarvis, Erich D, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Li, Heng, Liao, Wen-Wei, Lu, Shuangjia, Lu, Tsung-Yu, Lucas, Julian K, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, Markello, Charles, Martin, Fergal J, McCartney, Ann, McDaniel, Jennifer, Miga, Karen H, Mitchell, Matthew W, Monlong, Jean, Mountcastle, Jacquelyn, Munson, Katherine M, Mwaniki, Moses Njagi, Nattestad, Maria, Novak, Adam M, and Nurk, Sergey

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Humans, DNA, Satellite, Polymorphism, Genetic, Haplotypes, Segmental Duplications, Genomic, Sequence Analysis, DNA, Human Pangenome Reference Consortium, Medical and Health Sciences, Bioinformatics
Abstract

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.

Published
2023

9. Semi-automated assembly of high-quality diploid human reference genomes

Author

Jarvis, Erich D, Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R, Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A, Carnevali, Paolo, Chaisson, Mark JP, Chin, Chen-Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S, Fulton, Lucinda L, Garg, Shilpa, Gerton, Jennifer L, Ghurye, Jay, Granat, Anastasiya, Green, Richard E, Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B, Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O, Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W, McDaniel, Jennifer, Nie, Fan, Olsen, Hugh E, Olson, Nathan D, Pesout, Trevor, Potapova, Tamara, Puiu, Daniela, Regier, Allison, Ruan, Jue, Salzberg, Steven L, Sanders, Ashley D, Schatz, Michael C, Schmitt, Anthony, Schneider, Valerie A, Selvaraj, Siddarth, Shafin, Kishwar, Shumate, Alaina, Stitziel, Nathan O, Stober, Catherine, Torrance, James, Wagner, Justin, Wang, Jianxin, Wenger, Aaron, Xiao, Chuanle, Zimin, Aleksey V, Zhang, Guojie, Wang, Ting, Li, Heng, Garrison, Erik, Haussler, David, Hall, Ira, Zook, Justin M, Eichler, Evan E, Phillippy, Adam M, Paten, Benedict, Howe, Kerstin, and Miga, Karen H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Humans, Chromosome Mapping, Diploidy, Genome, Human, Haplotypes, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Reference Standards, Genomics, Chromosomes, Human, Genetic Variation, Human Pangenome Reference Consortium, General Science & Technology
Abstract

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Published
2022

10. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.

Author

Toh, Huishi, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Jarvis, Erich, Thomson, James, Stewart, Ron, Chaisson, Mark, Bukhman, Yury, and Clegg, Dennis

Subjects
Arvicanthis niloticus, Diabetes, Diurnal, Genome, Germline mutation rate, Heterozygosity, Long-read genome assembly, Orthology, Positive selection, Retrogenes, Segmental duplications, Humans, Animals, Haplotypes, Diabetes Mellitus, Type 2, Murinae, Genome, Genomics
Abstract

BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. RESULTS: We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. CONCLUSIONS: Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.

Published
2022

11. Robust haplotype-resolved assembly of diploid individuals without parental data

Author

Cheng, Haoyu, Jarvis, Erich D., Fedrigo, Olivier, Koepfli, Klaus-Peter, Urban, Lara, Gemmell, Neil J., and Li, Heng

Subjects
Quantitative Biology - Genomics
Abstract

Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of comparable quality to the best pedigree-based assemblies.

Published
2021

13. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Author

Rice, Edward S., Alberdi, Antton, Alfieri, James, Athrey, Giridhar, Balacco, Jennifer R., Bardou, Philippe, Blackmon, Heath, Charles, Mathieu, Cheng, Hans H., Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A. F., Gilbert, M. Thomas P., Hearn, Cari J., Jarvis, Erich D., Klopp, Christophe, Marcos, Sofia, Mason, Andrew S., Velez-Irizarry, Deborah, Xu, Luohao, and Warren, Wesley C.

Published
2023
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14. Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks

Author

Sendell-Price, Ashley T., Tulenko, Frank J., Pettersson, Mats, Kang, Du, Montandon, Margo, Winkler, Sylke, Kulb, Kathleen, Naylor, Gavin P., Phillippy, Adam, Fedrigo, Olivier, Mountcastle, Jacquelyn, Balacco, Jennifer R., Dutra, Amalia, Dale, Rebecca E., Haase, Bettina, Jarvis, Erich D., Myers, Gene, Burgess, Shawn M., Currie, Peter D., Andersson, Leif, and Schartl, Manfred

Published
2023
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15. The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes

Author

Bond, Donna M., Ortega-Recalde, Oscar, Laird, Melanie K., Hayakawa, Takashi, Richardson, Kyle S., Reese, Finlay.C. B., Kyle, Bruce, McIsaac-Williams, Brooke E., Robertson, Bruce C., van Heezik, Yolanda, Adams, Amy L., Chang, Wei-Shan, Haase, Bettina, Mountcastle, Jacquelyn, Driller, Maximilian, Collins, Joanna, Howe, Kerstin, Go, Yasuhiro, Thibaud-Nissen, Francoise, Lister, Nicholas C., Waters, Paul D., Fedrigo, Olivier, Jarvis, Erich D., Gemmell, Neil J., Alexander, Alana, and Hore, Timothy A.

Published
2023
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16. The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Published
2023
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17. Population genomics of the critically endangered kākāpō

Author

Dussex, Nicolas, van der Valk, Tom, Morales, Hernán E, Wheat, Christopher W, Díez-del-Molino, David, von Seth, Johanna, Foster, Yasmin, Kutschera, Verena E, Guschanski, Katerina, Rhie, Arang, Phillippy, Adam M, Korlach, Jonas, Howe, Kerstin, Chow, William, Pelan, Sarah, Damas, Joanna D Mendes, Lewin, Harris A, Hastie, Alex R, Formenti, Giulio, Fedrigo, Olivier, Guhlin, Joseph, Harrop, Thomas WR, Le Lec, Marissa F, Dearden, Peter K, Haggerty, Leanne, Martin, Fergal J, Kodali, Vamsi, Thibaud-Nissen, Françoise, Iorns, David, Knapp, Michael, Gemmell, Neil J, Robertson, Fiona, Moorhouse, Ron, Digby, Andrew, Eason, Daryl, Vercoe, Deidre, Howard, Jason, Jarvis, Erich D, Robertson, Bruce C, and Dalén, Love

Subjects
Human Genome, Genetics, Life on Land, bottleneck, conservation, inbreeding, kākāpō, mutational load, purging
Abstract

The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.

Published
2021

18. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A, Archer, Frederick I, Avila, Catherine D, Balacco, Jennifer R, Bukhman, Yury V, Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A, Fungtammasan, Arkarachai, Gulland, Frances MD, Haase, Bettina, Heide‐Jorgensen, Mads Peter, Houck, Marlys L, Howe, Kerstin, Misuraca, Ann C, Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas‐Bracho, Lorenzo, Rowles, Teri K, Ryder, Oliver A, Smith, Cynthia R, Stevenson, Sacha, Taylor, Barbara L, Teilmann, Jonas, Torrance, James, Wells, Randall S, Westgate, Andrew J, and Jarvis, Erich D

Subjects
Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Life on Land, Animals, Chromosomes, Endangered Species, Female, Genetics, Population, Genome, Phocoena, Conservation genomics, genome diversity, historical demography, Phocoena sinus, porpoise, Vertebrate Genomes Project, Biological Sciences, Evolutionary Biology
Abstract

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Published
2021

19. Platypus and echidna genomes reveal mammalian biology and evolution

Author

Zhou, Yang, Shearwin-Whyatt, Linda, Li, Jing, Song, Zhenzhen, Hayakawa, Takashi, Stevens, David, Fenelon, Jane C, Peel, Emma, Cheng, Yuanyuan, Pajpach, Filip, Bradley, Natasha, Suzuki, Hikoyu, Nikaido, Masato, Damas, Joana, Daish, Tasman, Perry, Tahlia, Zhu, Zexian, Geng, Yuncong, Rhie, Arang, Sims, Ying, Wood, Jonathan, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Li, Qiye, Yang, Huanming, Wang, Jian, Johnston, Stephen D, Phillippy, Adam M, Howe, Kerstin, Jarvis, Erich D, Ryder, Oliver A, Kaessmann, Henrik, Donnelly, Peter, Korlach, Jonas, Lewin, Harris A, Graves, Jennifer, Belov, Katherine, Renfree, Marilyn B, Grutzner, Frank, Zhou, Qi, and Zhang, Guojie

Subjects
Genetics, Human Genome, Biotechnology, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Biological Evolution, Female, Genome, Male, Mammals, Phylogeny, Platypus, Sex Chromosomes, Tachyglossidae, Base Pairing, Base Sequence, Cattle, Chromosome Mapping, Chromosomes, Mammalian, DNA, Evolution, Molecular, Molecular Sequence Data, Mutation, Recombination, Genetic, X Chromosome, Y Chromosome, General Science & Technology
Abstract

Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.

Published
2021

20. Towards complete and error-free genome assemblies of all vertebrate species

Author

Rhie, Arang, McCarthy, Shane A, Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L, Cantin, Lindsey J, Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grutzner, Frank, Warren, Wesley C, Balakrishnan, Christopher N, Burt, Dave, George, Julia M, Biegler, Matthew T, Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F, Franchini, Paolo, Detrich, H William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin JP, Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T, Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B, Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E, Putnam, Nicholas H, Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E, Guan, Dengfeng, London, Sarah E, Clayton, David F, Mello, Claudio V, Friedrich, Samantha R, Lovell, Peter V, Osipova, Ekaterina, Al-Ajli, Farooq O, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S, Makova, Kateryna D, Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P, Kwak, Woori, and Clawson, Hiram

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Animals, Birds, Gene Library, Genome, Genome Size, Genome, Mitochondrial, Genomics, Haplotypes, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Sequence Alignment, Sequence Analysis, DNA, Sex Chromosomes, Vertebrates, General Science & Technology
Abstract

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Published
2021

21. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A, Archer, Frederick I, Avila, Catherine D, Balacco, Jennifer R, Bukhman, Yury V, Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A, Fungtammasan, Arkarachai, Gulland, Frances MD, Haase, Bettina, Heide-Jorgensen, Mads Peter, Houck, Marlys L, Howe, Kerstin, Misuraca, Ann C, Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas-Bracho, Lorenzo, Rowles, Teri K, Ryder, Oliver A, Smith, Cynthia R, Stevenson, Sacha, Taylor, Barbara L, Teilmann, Jonas, Torrance, James, Wells, Randall S, Westgate, Andrew, and Jarvis, Erich D

Subjects
Human Genome, Genetics, Generic health relevance, Life on Land
Abstract

AbstractThe vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Published
2020

22. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D., Puiu, Daniela, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sirén, Jouni, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M.D., Zimin, Aleksey V., Popejoy, Alice B., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Jarvis, Erich D., Miga, Karen H., Wang, Ting, Garrison, Erik, Marschall, Tobias, Hall, Ira, Li, Heng, Paten, Benedict, Greer, Stephanie U., Pavlichin, Dmitri S., Zhou, Bo, Urban, Alexander E., and Weissman, Tsachy

Published
2023
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23. How genomics can help biodiversity conservation

Author

Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim do Rosario, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe C., Chueca, Luis J., Čiampor, Fedor, Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Agius, Dolores R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Theissinger, Kathrin, Fernandes, Carlos, Formenti, Giulio, Bista, Iliana, Berg, Paul R., Bleidorn, Christoph, Bombarely, Aureliano, Crottini, Angelica, Gallo, Guido R., Godoy, José A., Jentoft, Sissel, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Secomandi, Simona, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Jarvis, Erich D., Bálint, Miklós, Ciofi, Claudio, Waterhouse, Robert M., Mazzoni, Camila J., and Höglund, Jacob

Published
2023
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24. Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer

Author

Webster, Andrew L. H., Sanders, Mathijs A., Patel, Krupa, Dietrich, Ralf, Noonan, Raymond J., Lach, Francis P., White, Ryan R., Goldfarb, Audrey, Hadi, Kevin, Edwards, Matthew M., Donovan, Frank X., Hoogenboezem, Remco M., Jung, Moonjung, Sridhar, Sunandini, Wiley, Tom F., Fedrigo, Olivier, Tian, Huasong, Rosiene, Joel, Heineman, Thomas, Kennedy, Jennifer A., Bean, Lorenzo, Rosti, Rasim O., Tryon, Rebecca, Gonzalez, Ashlyn-Maree, Rosenberg, Allana, Luo, Ji-Dung, Carroll, Thomas S., Shroff, Sanjana, Beaumont, Michael, Velleuer, Eunike, Rastatter, Jeff C., Wells, Susanne I., Surrallés, Jordi, Bagby, Grover, MacMillan, Margaret L., Wagner, John E., Cancio, Maria, Boulad, Farid, Scognamiglio, Theresa, Vaughan, Roger, Beaumont, Kristin G., Koren, Amnon, Imielinski, Marcin, Chandrasekharappa, Settara C., Auerbach, Arleen D., Singh, Bhuvanesh, Kutler, David I., Campbell, Peter J., and Smogorzewska, Agata

Published
2022
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25. An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

Author

Timoshevskaya, Nataliya, Eşkut, Kaan İ., Timoshevskiy, Vladimir A., Robb, Sofia M.C., Holt, Carson, Hess, Jon E., Parker, Hugo J., Baker, Cindy F., Miller, Allison K., Saraceno, Cody, Yandell, Mark, Krumlauf, Robb, Narum, Shawn R., Lampman, Ralph T., Gemmell, Neil J., Mountcastle, Jacquelyn, Haase, Bettina, Balacco, Jennifer R., Formenti, Giulio, Pelan, Sarah, Sims, Ying, Howe, Kerstin, Fedrigo, Olivier, Jarvis, Erich D., and Smith, Jeramiah J.

Published
2023
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26. The Earth BioGenome Project 2020 : Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Forment, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hacke, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnsona, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mac, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., and Zhang, Guojie

Published
2022

27. A chromosome-level reference genome and pangenome for barn swallow population genomics

Author

Secomandi, Simona, Gallo, Guido R., Sozzoni, Marcella, Iannucci, Alessio, Galati, Elena, Abueg, Linelle, Balacco, Jennifer, Caprioli, Manuela, Chow, William, Ciofi, Claudio, Collins, Joanna, Fedrigo, Olivier, Ferretti, Luca, Fungtammasan, Arkarachai, Haase, Bettina, Howe, Kerstin, Kwak, Woori, Lombardo, Gianluca, Masterson, Patrick, Messina, Graziella, Møller, Anders P., Mountcastle, Jacquelyn, Mousseau, Timothy A., Ferrer Obiol, Joan, Olivieri, Anna, Rhie, Arang, Rubolini, Diego, Saclier, Marielle, Stanyon, Roscoe, Stucki, David, Thibaud-Nissen, Françoise, Torrance, James, Torroni, Antonio, Weber, Kristina, Ambrosini, Roberto, Bonisoli-Alquati, Andrea, Jarvis, Erich D., Gianfranceschi, Luca, and Formenti, Giulio

Published
2023
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29. A draft genome sequence of the elusive giant squid, Architeuthis dux

Author

da Fonseca, Rute R, Couto, Alvarina, Machado, Andre M, Brejova, Brona, Albertin, Carolin B, Silva, Filipe, Gardner, Paul, Baril, Tobias, Hayward, Alex, Campos, Alexandre, Ribeiro, Ângela M, Barrio-Hernandez, Inigo, Hoving, Henk-Jan, Tafur-Jimenez, Ricardo, Chu, Chong, Frazão, Barbara, Petersen, Bent, Peñaloza, Fernando, Musacchia, Francesco, Alexander, Graham C, Osório, Hugo, Winkelmann, Inger, Simakov, Oleg, Rasmussen, Simon, Rahman, M Ziaur, Pisani, Davide, Vinther, Jakob, Jarvis, Erich, Zhang, Guojie, Strugnell, Jan M, Castro, L Filipe C, Fedrigo, Olivier, Patricio, Mateus, Li, Qiye, Rocha, Sara, Antunes, Agostinho, Wu, Yufeng, Ma, Bin, Sanges, Remo, Vinar, Tomas, Blagoev, Blagoy, Sicheritz-Ponten, Thomas, Nielsen, Rasmus, and Gilbert, M Thomas P

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Life Below Water, Animals, Biological Evolution, Chromatography, Liquid, Computational Biology, DNA Transposable Elements, Decapodiformes, Gene Expression Profiling, Genome, Genomics, Molecular Sequence Annotation, Multigene Family, RNA, Untranslated, Tandem Mass Spectrometry, Transcriptome, Whole Genome Sequencing, cephalopod, invertebrate, genome assembly
Abstract

BackgroundThe giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.FindingsWe present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.ConclusionsThis annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

Published
2020

30. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

Author

Hardwick, Simon A., Hu, Wen, Joglekar, Anoushka, Fan, Li, Collier, Paul G., Foord, Careen, Balacco, Jennifer, Lanjewar, Samantha, Sampson, Maureen McGuirk, Koopmans, Frank, Prjibelski, Andrey D., Mikheenko, Alla, Belchikov, Natan, Jarroux, Julien, Lucas, Anne Bergstrom, Palkovits, Miklós, Luo, Wenjie, Milner, Teresa A., Ndhlovu, Lishomwa C., Smit, August B., Trojanowski, John Q., Lee, Virginia M. Y., Fedrigo, Olivier, Sloan, Steven A., Tombácz, Dóra, Ross, M. Elizabeth, Jarvis, Erich, Boldogkői, Zsolt, Gan, Li, and Tilgner, Hagen U.

Published
2022
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31. Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia.

Author

Al-Ajli, Farooq Omar, Formenti, Giulio, Fedrigo, Olivier, Tracey, Alan, Sims, Ying, Howe, Kerstin, Al-Karkhi, Ikdam M., Althani, Asmaa Ali, Jarvis, Erich D., Rahman, Sadequr, and Ayub, Qasim

Subjects
WHOLE genome sequencing, LIFE sciences, GENETIC variation, CHROMOSOMES, CONSERVATION genetics
Abstract

The taxonomic classification of a falcon population found in the Mongolian Altai region in Asia has been heavily debated for two centuries and previous studies have been inconclusive, hindering a more informed conservation approach. Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 49 falcons from different species and populations, including "Altai" falcons, we analyzed their population structure, admixture patterns, and demographic history. We find that the Altai falcons are genomic mosaics of saker and gyrfalcon ancestries, and carry distinct W and mitochondrial haplotypes that cluster with the lanner falcon. The Altai maternally-inherited haplotypes diverged 422,000 years before present (290,000–550,000 YBP) from the ancestor of sakers and gyrfalcons, both of which, in turn, split 109,000 YBP (70,000–150,000 YBP). The Altai W chromosome has 31 coding variants in 29 genes that may possibly influence important structural, behavioral, and reproductive traits. These findings provide insights into the question of Altai falcons as a candidate distinct species. [ABSTRACT FROM AUTHOR]

Published
2025
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32. Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population.

Author

Lesturgie, Pierre, Denton, John S. S., Yang, Lei, Corrigan, Shannon, Kneebone, Jeff, Laso-Jadart, Romuald, Lynghammar, Arve, Fedrigo, Olivier, Mona, Stefano, and Naylor, Gavin J. P.

Subjects
GENETIC variation, LIFE sciences, WHOLE genome sequencing, ASSORTATIVE mating, GENETIC polymorphisms
Abstract

The Thorny Skate (Amblyraja radiata) is a vulnerable species displaying a discrete size-polymorphism in the northwest Atlantic Ocean (NWA). We conducted whole genome sequencing of samples collected across its range. Genetic diversity was similar at all sampled sites, but we discovered a ~ 31 megabase bi-allelic supergene associated with the size polymorphism, with the larger size allele having introgressed in the last ~160,000 years B.P. While both Gulf of Maine (GoM) and Canadian (CAN) populations exhibit the size polymorphism, we detected a significant deficit of heterozygotes at the supergene and longer stretches of homozygosity in GoM population. This suggests inbreeding driven by assortative mating for size in GoM but not in CAN. Coalescent-based demographic modelling reveals strong migration between regions maintaining genetic variability in the recombining genome, preventing speciation between morphs. This study highlights short-term context-dependent evolutionary consequences of a size-determining supergene providing new insights for the management of vulnerable species. The thorny skate is a vulnerable species in the northwest Atlantic ocean with a discreet size polymorphism. Here, the authors have sequenced 49 thorny skate individuals, finding a supergene locus that is associated with skate size. [ABSTRACT FROM AUTHOR]

Published
2025
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33. A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy.

Author

Velotta, Jonathan P, Iqbal, Azwad R, Glenn, Emma S, Franckowiak, Ryan P, Formenti, Giulio, Mountcastle, Jacquelyn, Balacco, Jennifer, Tracey, Alan, Sims, Ying, Howe, Kerstin, Fedrigo, Olivier, Jarvis, Erich D, and Therkildsen, Nina O

Subjects
LIFE history theory, NATURAL selection, MARINE biology, WHOLE genome sequencing, COMPARATIVE genomics
Abstract

Transitions across ecological boundaries, such as those separating freshwater from the sea, are major drivers of phenotypic innovation and biodiversity. Despite their importance to evolutionary history, we know little about the mechanisms by which such transitions are accomplished. To help shed light on these mechanisms, we generated the first high-quality, near-complete assembly and annotation of the genome of the American shad (Alosa sapidissim a), an ancestrally diadromous (migratory between salinities) fish in the order Clupeiformes of major cultural and historical significance. Among the Clupeiformes, there is a large amount of variation in salinity habitat and many independent instances of salinity boundary crossing, making this taxon well-suited for studies of mechanisms underlying ecological transitions. Our initial analysis of the American shad genome reveals several unique insights for future study including: (i) that genomic repeat content is among the highest of any fish studied to date; (ii) that genome-wide heterozygosity is low and may be associated with range-wide population collapses since the 19th century; and (iii) that natural selection has acted on the branch leading to the diadromous genus Alosa. Our analysis suggests that functional targets of natural selection may include diet, particularly lipid metabolism, as well as cytoskeletal remodeling and sensing of salinity changes. Natural selection on these functions is expected in the transition from a marine to diadromous life history, particularly in the tolerance of nutrient- and ion-devoid freshwater. We anticipate that our assembly of the American shad genome will be used to test future hypotheses on adaptation to novel environments, the origins of diadromy, and adaptive variation in life history strategies, among others. [ABSTRACT FROM AUTHOR]

Published
2025
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34. Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.

Author

Ishigohoka, Jun, Bascón-Cardozo, Karen, Bours, Andrea, Fuß, Janina, Rhie, Arang, Mountcastle, Jacquelyn, Haase, Bettina, Chow, William, Collins, Joanna, Howe, Kerstin, Uliano-Silva, Marcela, Fedrigo, Olivier, Jarvis, Erich D, Pérez-Tris, Javier, Illera, Juan Carlos, and Liedvogel, Miriam

Subjects
GENETIC variation, HAPLOTYPES, GENOMICS, GENOMES, DATA mapping
Abstract

Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome. [ABSTRACT FROM AUTHOR]

Published
2024
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35. The era of reference genomes in conservation genomics

Author

Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Höglund, Jacob, Palsbøll, Per J., Ruiz-López, María J., Zhang, Guojie, and Jarvis, Erich D.

Published
2022
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36. Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19

Author

Sahajpal, Nikhil Shri, Jill Lai, Chi-Yu, Hastie, Alex, Mondal, Ashis K., Dehkordi, Siavash Raeisi, van der Made, Caspar I., Fedrigo, Olivier, Al-Ajli, Farooq, Jalnapurkar, Sawan, Byrska-Bishop, Marta, Kanagal-Shamanna, Rashmi, Levy, Brynn, Schieck, Maximilian, Illig, Thomas, Bacanu, Silviu-Alin, Chou, Janet S., Randolph, Adrienne G., Rojiani, Amyn M., Zody, Michael C., Brownstein, Catherine A., Beggs, Alan H., Bafna, Vineet, Jarvis, Erich D., Hoischen, Alexander, Chaubey, Alka, and Kolhe, Ravindra

Published
2022
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39. Evolutionary and biomedical insights from a marmoset diploid genome assembly

Author

Yang, Chentao, Zhou, Yang, Marcus, Stephanie, Formenti, Giulio, Bergeron, Lucie A., Song, Zhenzhen, Bi, Xupeng, Bergman, Juraj, Rousselle, Marjolaine Marie C., Zhou, Chengran, Zhou, Long, Deng, Yuan, Fang, Miaoquan, Xie, Duo, Zhu, Yuanzhen, Tan, Shangjin, Mountcastle, Jacquelyn, Haase, Bettina, Balacco, Jennifer, Wood, Jonathan, Chow, William, Rhie, Arang, Pippel, Martin, Fabiszak, Margaret M., Koren, Sergey, Fedrigo, Olivier, Freiwald, Winrich A., Howe, Kerstin, Yang, Huanming, Phillippy, Adam M., Schierup, Mikkel Heide, Jarvis, Erich D., and Zhang, Guojie

Published
2021
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41. A region of suppressed recombination misleads neoavian phylogenomics

Author

Mirarab, Siavash, primary, Rivas-González, Iker, additional, Feng, Shaohong, additional, Stiller, Josefin, additional, Fang, Qi, additional, Mai, Uyen, additional, Hickey, Glenn, additional, Chen, Guangji, additional, Brajuka, Nadolina, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Wolf, Jochen B. W., additional, Howe, Kerstin, additional, Antunes, Agostinho, additional, Schierup, Mikkel H., additional, Paten, Benedict, additional, Jarvis, Erich D., additional, Zhang, Guojie, additional, and Braun, Edward L., additional

Published
2024
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42. A region of suppressed recombination misleads neoavian phylogenomics

Author

Mirarab, Siavash, Rivas-González, Iker, Feng, Shaohong, Stiller, Josefin, Fang, Qi, Mai, Uyen, Hickey, Glenn, Chen, Guangji, Brajuka, Nadolina, Fedrigo, Olivier, Formenti, Giulio, Wolf, Jochen B. W., Howe, Kerstin, Antunes, Agostinho, Schierup, Mikkel H., Paten, Benedict, Jarvis, Erich D., Zhang, Guojie, Braun, Edward L., Mirarab, Siavash, Rivas-González, Iker, Feng, Shaohong, Stiller, Josefin, Fang, Qi, Mai, Uyen, Hickey, Glenn, Chen, Guangji, Brajuka, Nadolina, Fedrigo, Olivier, Formenti, Giulio, Wolf, Jochen B. W., Howe, Kerstin, Antunes, Agostinho, Schierup, Mikkel H., Paten, Benedict, Jarvis, Erich D., Zhang, Guojie, and Braun, Edward L.

Abstract

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.

Published
2024

43. Six reference-quality genomes reveal evolution of bat adaptations

Author

Jebb, David, Huang, Zixia, Pippel, Martin, Hughes, Graham M., Lavrichenko, Ksenia, Devanna, Paolo, Winkler, Sylke, Jermiin, Lars S., Skirmuntt, Emilia C., Katzourakis, Aris, Burkitt-Gray, Lucy, Ray, David A., Sullivan, Kevin A. M., Roscito, Juliana G., Kirilenko, Bogdan M., Dávalos, Liliana M., Corthals, Angelique P., Power, Megan L., Jones, Gareth, Ransome, Roger D., Dechmann, Dina K. N., Locatelli, Andrea G., Puechmaille, Sébastien J., Fedrigo, Olivier, Jarvis, Erich D., Hiller, Michael, Vernes, Sonja C., Myers, Eugene W., and Teeling, Emma C.

Published
2020
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44. A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

Author

Joglekar, Anoushka, Prjibelski, Andrey, Mahfouz, Ahmed, Collier, Paul, Lin, Susan, Schlusche, Anna Katharina, Marrocco, Jordan, Williams, Stephen R., Haase, Bettina, Hayes, Ashley, Chew, Jennifer G., Weisenfeld, Neil I., Wong, Man Ying, Stein, Alexander N., Hardwick, Simon A., Hunt, Toby, Wang, Qi, Dieterich, Christoph, Bent, Zachary, Fedrigo, Olivier, Sloan, Steven A., Risso, Davide, Jarvis, Erich D., Flicek, Paul, Luo, Wenjie, Pitt, Geoffrey S., Frankish, Adam, Smit, August B., Ross, M. Elizabeth, and Tilgner, Hagen U.

Published
2021
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45. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Author

Kronenberg, Zev N., Rhie, Arang, Koren, Sergey, Concepcion, Gregory T., Peluso, Paul, Munson, Katherine M., Porubsky, David, Kuhn, Kristen, Mueller, Kathryn A., Low, Wai Yee, Hiendleder, Stefan, Fedrigo, Olivier, Liachko, Ivan, Hall, Richard J., Phillippy, Adam M., Eichler, Evan E., Williams, John L., Smith, Timothy P. L., Jarvis, Erich D., Sullivan, Shawn T., and Kingan, Sarah B.

Published
2021
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46. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

Author

Bukhman, Yury V, primary, Morin, Phillip A, additional, Meyer, Susanne, additional, Chu, Li-Fang, additional, Jacobsen, Jeff K, additional, Antosiewicz-Bourget, Jessica, additional, Mamott, Daniel, additional, Gonzales, Maylie, additional, Argus, Cara, additional, Bolin, Jennifer, additional, Berres, Mark E, additional, Fedrigo, Olivier, additional, Steill, John, additional, Swanson, Scott A, additional, Jiang, Peng, additional, Rhie, Arang, additional, Formenti, Giulio, additional, Phillippy, Adam M, additional, Harris, Robert S, additional, Wood, Jonathan M D, additional, Howe, Kerstin, additional, Kirilenko, Bogdan M, additional, Munegowda, Chetan, additional, Hiller, Michael, additional, Jain, Aashish, additional, Kihara, Daisuke, additional, Johnston, J Spencer, additional, Ionkov, Alexander, additional, Raja, Kalpana, additional, Toh, Huishi, additional, Lang, Aimee, additional, Wolf, Magnus, additional, Jarvis, Erich D, additional, Thomson, James A, additional, Chaisson, Mark J P, additional, and Stewart, Ron, additional

Published
2024
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47. A chromosome-level genome assembly for the dugong (Dugong dugon)

Author

Baker, Dorothy Nevé, primary, Abueg, Linelle, additional, Escalona, Merly, additional, Farquharson, Katherine A, additional, Lanyon, Janet M, additional, Le Duc, Diana, additional, Schöneberg, Torsten, additional, Absolon, Dominic, additional, Sims, Ying, additional, Fedrigo, Olivier, additional, Jarvis, Erich D, additional, Belov, Katherine, additional, Hogg, Carolyn J, additional, and Shapiro, Beth, additional

Published
2024
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48. A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments

Author

Cadena, Daniel, primary, Pabon, Laura, additional, DoNascimiento, Carlos, additional, Abueg, Linelle, additional, Tiley, Tatiana, additional, O-Toole, Brian, additional, Absolon, Dominic, additional, Sims, Ying, additional, Formenti, Giulio, additional, Fedrigo, Olivier, additional, Jarvis, Erich, additional, and Torres, Mauricio, additional

Published
2023
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49. Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761

Author

Skorupski, Jakub, primary, Brandes, Florian, additional, Seebass, Christian, additional, Festl, Wolfgang, additional, Śmietana, Przemysław, additional, Balacco, Jennifer, additional, Jain, Nivesh, additional, Tilley, Tatiana, additional, Abueg, Linelle, additional, Wood, Jonathan, additional, Sims, Ying, additional, Formenti, Giulio, additional, Fedrigo, Olivier, additional, and Jarvis, Erich D., additional

Published
2023
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