Complete sequencing of ape genomes
Abstract
Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies 1–3 . Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.
Article Details
Authors (123)
DongAhn Yoo
Arang Rhie
Prajna Hebbar
Francesca Antonacci
Glennis A. Logsdon
Steven J. Solar
Dmitry Antipov
Brandon D. Pickett
Yana Safonova
Francesco Montinaro
Yanting Luo
Joanna Malukiewicz
Jessica M. Storer
Jiadong Lin
Abigail N. Sequeira
Riley J. Mangan
Glenn Hickey
Graciela Monfort Anez
Parithi Balachandran
Anton Bankevich
Christine R. Beck
Arjun Biddanda
Matthew Borchers
Gerard G. Bouffard
Emry Brannan
Shelise Y. Brooks
Lucia Carbone
Laura Carrel
Agnes P. Chan
Juyun Crawford
Mark Diekhans
Eric Engelbrecht
Cedric Feschotte
Giulio Formenti
Gage H. Garcia
Luciana de Gennaro
David Gilbert
Richard E. Green
Andrea Guarracino
Ishaan Gupta
Diana Haddad
Junmin Han
Robert S. Harris
Gabrielle A. Hartley
William T. Harvey
Michael Hiller
Kendra Hoekzema
Marlys L. Houck
Hyeonsoo Jeong
Kaivan Kamali
Manolis Kellis
Bryce Kille
Chul Lee
Youngho Lee
William Lees
Alexandra P. Lewis
Qiuhui Li
Mark Loftus
Yong Hwee Eddie Loh
Hailey Loucks
Jian Ma
Yafei Mao
Juan F. I. Martinez
Patrick Masterson
Rajiv C. McCoy
Barbara McGrath
Sean McKinney
Britta S. Meyer
Karen H. Miga
Saswat K. Mohanty
Katherine M. Munson
Karol Pal
Matt Pennell
Pavel A. Pevzner
David Porubsky
Tamara Potapova
Francisca R. Ringeling
Joana L. Rocha
Oliver A. Ryder
Samuel Sacco
Swati Saha
Takayo Sasaki
Michael C. Schatz
Nicholas J. Schork
Cole Shanks
Linnéa Smeds
Dongmin R. Son
Cynthia Steiner
Alexander P. Sweeten
Michael G. Tassia
Françoise Thibaud-Nissen
Edmundo Torres-González
Mihir Trivedi
Wenjie Wei
Julie Wertz
Muyu Yang
Panpan Zhang
Shilong Zhang
Yang Zhang
Zhenmiao Zhang
Sarah A. Zhao
Yixin Zhu
Erich D. Jarvis
Jennifer L. Gerton
Iker Rivas-González
Benedict Paten
Zachary A. Szpiech
Christian D. Huber
Tobias L. Lenz
Miriam K. Konkel
Soojin V. Yi
Stefan Canzar
Corey T. Watson
Peter H. Sudmant
Erin Molloy
Erik Garrison
Craig B. Lowe
Mario Ventura
Rachel J. O’Neill
Sergey Koren
Kateryna D. Makova
Adam M. Phillippy
Evan E. Eichler