A high-quality bonobo genome refines the analysis of hominid evolution.
Animals
Eukaryotic Initiation Factor-4A
/ genetics
Evolution, Molecular
Female
Genes
Genome
/ genetics
Genomics
Gorilla gorilla
/ genetics
Molecular Sequence Annotation
/ standards
Pan paniscus
/ genetics
Pan troglodytes
/ genetics
Phylogeny
Pongo
/ genetics
Segmental Duplications, Genomic
Sequence Analysis, DNA
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
06 2021
06 2021
Historique:
received:
21
08
2020
accepted:
07
04
2021
pubmed:
7
5
2021
medline:
27
7
2021
entrez:
6
5
2021
Statut:
ppublish
Résumé
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation
Identifiants
pubmed: 33953399
doi: 10.1038/s41586-021-03519-x
pii: 10.1038/s41586-021-03519-x
pmc: PMC8172381
mid: NIHMS1695658
doi:
Substances chimiques
Eukaryotic Initiation Factor-4A
EC 2.7.7.-
Types de publication
Comparative Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
77-81Subventions
Organisme : NHGRI NIH HHS
ID : K99 HG011041
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG010961
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL137183
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG010972
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG008345
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG002939
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM059290
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG010485
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG007990
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG002385
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000035
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG007234
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG010329
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG009081
Pays : United States
Références
Prüfer, K. et al. The bonobo genome compared with the chimpanzee and human genomes. Nature 486, 527–531 (2012).
doi: 10.1038/nature11128
Takemoto, H., Kawamoto, Y. & Furuichi, T. How did bonobos come to range south of the Congo River? Reconsideration of the divergence of Pan paniscus from other Pan populations. Evol. Anthropol. 24, 170–184 (2015).
doi: 10.1002/evan.21456
Scally, A. et al. Insights into hominid evolution from the gorilla genome sequence. Nature 483, 169–175 (2012).
doi: 10.1038/nature10842
Locke, D. P. et al. Comparative and demographic analysis of orang-utan genomes. Nature 469, 529–533 (2011).
doi: 10.1038/nature09687
The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005).
doi: 10.1038/nature04072
Luo, C., Tsementzi, D., Kyrpides, N., Read, T. & Konstantinidis, K. T. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7, e30087 (2012).
doi: 10.1371/journal.pone.0030087
Prado-Martinez, J. et al. Great ape genetic diversity and population history. Nature 499, 471–475 (2013).
doi: 10.1038/nature12228
Sudmant, P. H. et al. Global diversity, population stratification, and selection of human copy-number variation. Science 349, aab3761 (2015).
doi: 10.1126/science.aab3761
Logsdon, G. A., Vollger, M. R. & Eichler, E. E. Long-read human genome sequencing and its applications. Nat. Rev. Genet. 21, 597–614 (2020).
doi: 10.1038/s41576-020-0236-x
Ventura, M. et al. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res. 21, 1640–1649 (2011).
doi: 10.1101/gr.124461.111
Fiddes, I. T. et al. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 28, 1029–1038 (2018).
doi: 10.1101/gr.233460.117
Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637–644 (2008).
doi: 10.1093/bioinformatics/btn013
Gordon, D. et al. Long-read sequence assembly of the gorilla genome. Science 352, aae0344 (2016).
doi: 10.1126/science.aae0344
Kronenberg, Z. N. et al. High-resolution comparative analysis of great ape genomes. Science 360, eaar6343 (2018).
doi: 10.1126/science.aar6343
Pavlidis, P. & Alachiotis, N. A survey of methods and tools to detect recent and strong positive selection. J. Biol. Res. (Thessalon.) 24, 7 (2017).
doi: 10.1186/s40709-017-0064-0
de Manuel, M. et al. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354, 477–481 (2016).
doi: 10.1126/science.aag2602
Marques-Bonet, T. et al. A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457, 877–881 (2009).
doi: 10.1038/nature07744
Vollger, M. R. et al. Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads. Ann. Hum. Genet. 84, 125–140 (2020).
doi: 10.1111/ahg.12364
Vollger, M. R. et al. Long-read sequence and assembly of segmental duplications. Nat. Methods 16, 88–94 (2019).
doi: 10.1038/s41592-018-0236-3
Sudmant, P. H. et al. Evolution and diversity of copy number variation in the great ape lineage. Genome Res. 23, 1373–1382 (2013).
doi: 10.1101/gr.158543.113
The ENCODE Project Consortium et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583, 699–710 (2020).
doi: 10.1038/s41586-020-2493-4
Rice, G. I. et al. Mutations in ADAR1 cause Aicardi–Goutières syndrome associated with a type I interferon signature. Nat. Genet. 44, 1243–1248 (2012).
doi: 10.1038/ng.2414
Savva, Y. A., Rieder, L. E. & Reenan, R. A. The ADAR protein family. Genome Biol. 13, 252 (2012).
doi: 10.1186/gb-2012-13-12-252
Gallo, A., Vukic, D., Michalík, D., O’Connell, M. A. & Keegan, L. P. ADAR RNA editing in human disease; more to it than meets the I. Hum. Genet. 136, 1265–1278 (2017).
doi: 10.1007/s00439-017-1837-0
O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44 (D1), D733–D745 (2016).
doi: 10.1093/nar/gkv1189
Huang, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols 4, 44–57 (2009).
doi: 10.1038/nprot.2008.211
Chin, C. S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).
doi: 10.1038/nmeth.2474
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
doi: 10.1371/journal.pone.0112963
Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. Preprint at https://arxiv.org/abs/1207.3907 (2012).
Ghareghani, M. et al. Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. Bioinformatics 34, i115–i123 (2018).
doi: 10.1093/bioinformatics/bty290
Porubsky, D. et al. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nat. Biotechnol. 39, 302–308 (2021).
doi: 10.1038/s41587-020-0719-5
Falconer, E. et al. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat. Methods 9, 1107–1112 (2012).
doi: 10.1038/nmeth.2206
Sanders, A. D. et al. Characterizing polymorphic inversions in human genomes by single-cell sequencing. Genome Res. 26, 1575–1587 (2016).
doi: 10.1101/gr.201160.115
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2021).
doi: 10.1186/s13059-020-02134-9
Huddleston, J. et al. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res. 24, 688–696 (2014).
doi: 10.1101/gr.168450.113
Marchetto, M. C. et al. Species-specific maturation profiles of human, chimpanzee and bonobo neural cells. eLife 8, e37527 (2019).
doi: 10.7554/eLife.37527
Bailey, J. A., Yavor, A. M., Massa, H. F., Trask, B. J. & Eichler, E. E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 11, 1005–1017 (2001).
doi: 10.1101/gr.GR-1871R
Sedlazeck, F. J. et al. Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods 15, 461–468 (2018).
doi: 10.1038/s41592-018-0001-7
Chen, S. et al. Paragraph: a graph-based structural variant genotyper for short-read sequence data. Genome Biol. 20, 291 (2019).
doi: 10.1186/s13059-019-1909-7