Skip to main content

An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)

Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A., Kulemzina, Anastasia I., Chemnick, Leona G., Kim, Jaebum, Ryder, Oliver A., and others. (2019) An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). GigaScience, 8 (8). Article Number 90. ISSN 2047-217X. (doi:10.1093/gigascience/giz090) (KAR id:75809)

PDF Publisher pdf
Language: English


Download (2MB) Preview
[thumbnail of Farre et al 2019, Gigascience, 8, 1-9.pdf]
Preview
This file may not be suitable for users of assistive technology.
Request an accessible format
Official URL
https://doi.org/10.1093/gigascience/giz090

Abstract

Background

Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions.

Conclusions

We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years.

Item Type: Article
DOI/Identification number: 10.1093/gigascience/giz090
Uncontrolled keywords: giraffe; Giraffa camelopardalis tippelskirchi; assembly; annotation; ruminant
Divisions: Divisions > Division of Natural Sciences > School of Biosciences
Depositing User: Marta Farre Belmonte
Date Deposited: 14 Aug 2019 15:32 UTC
Last Modified: 05 Oct 2020 14:49 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/75809 (The current URI for this page, for reference purposes)
Farré, Marta: https://orcid.org/0000-0001-9170-5767
  • Depositors only (login required):

Downloads

Downloads per month over past year