Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina)

Porrelli, Stefano, Gerbault-Seureau, Michèle, Rozzi, Roberto, Chikhi, Rayan, Curaudeau, Manon, Ropiquet, Anne ORCID logoORCID: https://orcid.org/0000-0003-3755-5467 and Hassanin, Alexandre (2022) Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina). G3 Genes|Genomes|Genetics , jkac234. ISSN 2160-1836 [Article] (Published online first) (doi:10.1093/g3journal/jkac234)

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Abstract

Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf buffalo, the lowland anoa (Bubalus depressicornis), produced a draft genome assembly, and made comparison to published buffalo genomes. The lowland anoa genome assembly was 2.56 Gbp long and contained 103,135 contigs, the longest contig being 337.39 kbp long. N50 and L50 values were 38.73 kbp and 19.83 kbp, respectively, mean coverage was 44x and GC content was 41.74%. Two strategies were adopted to evaluate genome completeness: (i) determination of genomic features with de novo and homology-based predictions using annotations of chromosome-level genome assembly of the river buffalo, and (ii) employment of benchmarking against universal single-copy orthologs (BUSCO). Homology-based predictions identified 94.51% complete and 3.65% partial genomic features. De novo gene predictions identified 32,393 genes, representing 97.14% of the reference's annotated genes, whilst BUSCO search against the mammalian orthologues database identified 71.1% complete, 11.7% fragmented and 17.2% missing orthologues, indicating a good level of completeness for downstream analyses. Repeat analyses indicated that the lowland anoa genome contains 42.12% of repetitive regions. The genome assembly of the lowland anoa is expected to contribute to comparative genome analyses among bovid species. [Abstract copyright: © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.]

Item Type: Article
Keywords (uncontrolled): de novo assembly, Bubalus depressicornis, lowland anoa, Bovidae, genome assembly
Research Areas: A. > School of Science and Technology > Natural Sciences
Item ID: 36387
Notes on copyright: © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
Depositing User: Jisc Publications Router
Date Deposited: 30 Sep 2022 08:36
Last Modified: 03 Oct 2022 09:38
URI: https://eprints.mdx.ac.uk/id/eprint/36387

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