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)
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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 |
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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: | ![]() |
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