Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)

Merly Escalona; Jake VanCampen; Nicholas W Maurer; Marina Haukness; Mariam Okhovat; Robert S Harris; Allison Watwood; Gabrielle A Hartley; Rachel J O'Neill; Paul Medvedev; Kateryna D Makova; Christopher Vollmers; Lucia Carbone; Richard E Green

doi:10.1093/jhered/esac043

Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)

J Hered. 2023 Mar 16;114(1):35-43. doi: 10.1093/jhered/esac043.

Authors

Merly Escalona¹, Jake VanCampen², Nicholas W Maurer¹, Marina Haukness^{1

3}, Mariam Okhovat², Robert S Harris⁴, Allison Watwood⁴, Gabrielle A Hartley^{5

6}, Rachel J O'Neill^{5

6}, Paul Medvedev^{7

8

9

10}, Kateryna D Makova^{4

7

8}, Christopher Vollmers¹, Lucia Carbone^{2

11

12

13}, Richard E Green¹

Affiliations

¹ Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
² Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239, USA.
³ University of California Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA.
⁴ Department of Biology, Pennsylvania State University, University Park, PA, USA.
⁵ Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06296, USA.
⁶ Institute for Systems Genomics, University of Connecticut, Storrs, CT 06296, USA.
⁷ Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA.
⁸ Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA.
⁹ Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA.
¹⁰ Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
¹¹ Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239, USA.
¹² Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
¹³ Department of Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA.

Abstract

The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.

Keywords: Hi-C; genome assembly; gibbon; long reads; proximity ligation.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Animals
Endangered Species
Forests
Genome*
Hylobates* / genetics
Indonesia

Abstract

Publication types

MeSH terms

Grants and funding