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

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.

First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

“…The resulting 31,417 protein-coding genes of A. f. fusciceps are comparable with what other mammal genome assemblies have reported like the case of the lowland anoa ( Bubalus depressicornis ) with 32,393 predicted protein-coding genes ( Porrelli et al . 2022 ).…”

Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

“…The resulting 31,417 protein-coding genes of A. f. fusciceps are comparable to what other mammal genome assemblies have reported like the case of the lowland anoa (Bubalus depressicornis) with 32,393 predicted protein-coding genes (Porrelli et al, 2022). Nonetheless, gene count is slightly higher than expected when compared to the 22,027 protein-coding genes predicted for Callithrix jacchus (GCA_011100555.1) (Warren et al, 2009) and the 20,350 protein-coding genes for Sapajus apella (GCF_009761245.1) (Culibrk et al, 2019); both closely related primate species of A. f. fusciceps.…”