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1. Dense sampling of bird diversity increases power of comparative genomics

Author

25621572 - Van der Zwan, Henriëtte, 21224919 - Van der Sluis, Rencia, Feng, Shaohong, Van der Zwan, Henriëtte, Van der Sluis, Rencia, Stiller, Josefin, 25621572 - Van der Zwan, Henriëtte, 21224919 - Van der Sluis, Rencia, Feng, Shaohong, Van der Zwan, Henriëtte, Van der Sluis, Rencia, and Stiller, Josefin

Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species

Published
2020

2. Development of an <scp>SNP</scp> ‐based parentage verification panel for lovebirds

Author

M Schoonen, Carina Visser, H van der Zwan, R van der Sluis, 21224919 - Van der Sluis, Rencia, 20574495 - Schoonen, Maryke, and 25621572 - Van der Zwan, Henriëtte

Subjects
Male, 0301 basic medicine, Population, Single-nucleotide polymorphism, Breeding, Biology, Polymorphism, Single Nucleotide, Genome, Agapornis, Loss of heterozygosity, 03 medical and health sciences, Genetics, Animals, SNP, education, Selection (genetic algorithm), Parrot breeding, education.field_of_study, Pigmentation, 0402 animal and dairy science, Pedigree confirmation, 04 agricultural and veterinary sciences, General Medicine, Feathers, 040201 dairy & animal science, Pedigree, Minor allele frequency, Whole‐genome resequencing, 030104 developmental biology, Female, Animal Science and Zoology, Reference genome
Abstract

The genus Agapornis, or lovebirds, are popular pet parrots worldwide. Currently, breeders are dependent on pedigree records as a selection tool as no molecular parentage verification test is available for any of the nine species. The A. roseicollis reference genome was recently assembled. This was followed by the sequencing of the whole genomes of the parents of the reference genome individual at 30× coverage. The parents' reads were mapped against the reference genome to identify SNPs. Over 1.6 million SNPs, shared between the parents, were discovered using the Genome Analysis Toolkit pipeline. SNPs were filtered to a panel of 480 SNPs based on Genome Analysis Toolkit parameters. The panel of 480 SNPs was genotyped in a population of 960 lovebirds across seven species. A panel of 262 SNPs was compiled that included SNPs successfully amplified across all species. The 262-SNP panel was reduced based on the observed heterozygosity (HO ) and minor allele frequency (MAF) values per SNP to include the lowest number of SNPs with the highest exclusion power for parentage verification. Two smaller panels consisting of 195 SNPs with MAF and HO values >0.1 and 40 SNPs with MAF and HO values >0.3, were constructed. The panels were verified using 43 families from different species with known relationships to evaluate the exclusion power of each panel. The 195 SNP panel with an average exclusion probability of 99.9% and MAF and HO values >0.1 was proposed as the routine Agapornis parentage verification panel.

Published
2019
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3. Dense sampling of bird diversity increases power of comparative genomics

Author

Rencia van der Sluis, Nadine Thiele, Borja Milá, Araxi O. Urrutia, Josefin Stiller, Joel Cracraft, Zongji Wang, Qiye Li, Barney A. Schlinger, Guojie Zhang, Ana Tereza Ribeiro de Vasconcelos, Oliver A. Ryder, Rebecca B. Dikow, Thomas L. Parchman, Emily Cavill, John G. Blake, Libby C. Megna, Andrew G. Clark, Christopher C. Witt, Ángela M. Parody-Merino, Jason T. Weir, Wanjun Chen, Jason T. Howard, T. Brandt Ryder, Michael G. Campana, Jon Fjeldså, Robb T. Brumfield, M. Thomas P. Gilbert, Alexandre Aleixo, Gerald Borgia, Qi Fang, Phil F. Battley, Ellen D. Ketterson, Matthew I. M. Louder, Scott A. Taylor, Glaucia Del-Rio, Scott V. Edwards, Sergio Andreu-Sánchez, Fumin Lei, Irby J. Lovette, Neil J. Gemmell, Mikkel-Holger S. Sinding, Carole A. Parent, Huanming Yang, André E. R. Soares, David W. Burt, Guanliang Meng, André Corvelo, Nicolas Dussex, Jimmy A. McGuire, Kira E. Delmore, Marc P. Hoeppner, Julio Rozas, Ângela M. Ribeiro, Les Christidis, Haw Chuan Lim, Guillermo Friis, Guangji Chen, Martin Stervander, Mads F. Bertelsen, Siavash Mirarab, Biao Wang, Hanna Sigeman, Lara Puetz, Qi Zhou, Marta Riutort, Knud A. Jønsson, Christopher N. Balakrishnan, Alexander Suh, Edward L. Braun, Nicholas Costa Barroso Lima, Jeffrey M. DaCosta, Reed Bowman, Yang Liu, Kim Rutherford, Ashot Margaryan, Peter Njoroge, Beth Shapiro, Benedict Paten, Shaohong Feng, Adam M. Fudickar, Jacob González-Solís, Bent O. Petersen, Subir B. Shakya, Henrik Mouritsen, Glauco Camenisch, Maude W. Baldwin, Andrew Hart Reeve, Bruce C. Robertson, Morgan Wirthlin, Shannon J. Hackett, Chunxue Guo, Bengt Hansson, Peter G. Ryan, Miriam Liedvogel, Alain Vignal, Saul J. Cowen, Matthew J. Fuxjager, Robert C. Fleischer, Dustin J. Foote, Joel Armstrong, Joann Mudge, Nancy F. Chen, Santiago Claramunt, Joan Ferrer-Obiol, John W. Fitzpatrick, Leopold Eckhart, Mark E. Hauber, Michael Bunce, Carsten Rahbek, George Pacheco, Dieter Thomas Tietze, Gang Song, Jérôme Fuchs, John P. Dumbacher, Henriette van der Zwan, Love Dalén, Michael J. Braun, Lukas F. Keller, Yuan Deng, Jian Wang, Thomas Sicheritz-Pontén, Tamás Székely, Erich D. Jarvis, Alison Cloutier, David Haussler, Matthew D. Carling, Carina Visser, Paul B. Frandsen, Anna Tigano, Andre Franke, Suvi Ponnikas, Claudio V. Mello, Vicki L. Friesen, Timothy B. Sackton, Rute R. da Fonseca, Frederick H. Sheldon, Duo Xie, Brant C. Faircloth, Bette A. Loiselle, Gary R. Graves, Ian G. Jamieson, Mark Diekhans, Lainy B. Day, Peter A. Hosner, Murray P. Cox, Oliver Krone, Andrew E. Fidler, Peter Houde, Francisco Prosdocimi, Zoology, Chinese Academy of Sciences, Carlsberg Foundation, Velux Foundation, National Natural Science Foundation of China, Howard Hughes Medical Institute, National Institutes of Health (US), China National GeneBank, Kunming Institute of Zoology, Chinese Academy of Sciences [Beijing] (CAS), Beijing Genomics Institute [Shenzhen] (BGI), University of Copenhagen = Københavns Universitet (KU), University of California [Santa Cruz] (UCSC), University of California, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of Chinese Academy of Sciences [Beijing] (UCAS), Louisiana State University (LSU), Museum of Natural Science, IT University of Copenhagen, AIMST University, Zhejiang University, University of Vienna [Vienna], Zhejiang University School of Medicine [China], Institute of Molecular Biology of the National Academy of Sciences of Armenia (IMB NAS RA), National Academy of Sciences of the Republic of Armenia [Yerevan] (NAS RA), Novogene, Duke University Medical Center, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), United States Department of Health & Human Services, National Institutes of Health (NIH) - USA, NIH National Human Genome Research Institute (NHGRI) (U54 HG007990, T32 HG008345, R01 HG010053), NIH National Heart Lung & Blood Institute (NHLBI) (U01 HL137183), 25621572 - Van der Zwan, Henriëtte, and 21224919 - Van der Sluis, Rencia

Subjects
0106 biological sciences, GENES, PROTEINS, Tree of life, Genomics, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Genome, Article, Evolutionary genetics, génomique, Evolutionsbiologi, 03 medical and health sciences, Phylogenetics, ACCELERATED EVOLUTION, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, REVEALS, genomics, Genetics, DIVERGENCE, Genomes, Genetik, Cladistic analysis, Selection (genetic algorithm), TREE, 030304 developmental biology, Comparative genomics, 0303 health sciences, Evolutionary Biology, Multidisciplinary, Phylogenetic tree, SEQUENCES, Human evolutionary genetics, Cladística, Biodiversity, DNA, 15. Life on land, échantillonnage, Sampling Methods, Biodiversitat, DUPLICATION, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Evolutionary biology, 1181 Ecology, evolutionary biology, PACKAGE
Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Published
2020
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