Draft genome of the gayal, Bos frontalis

Abstract

Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal.

The complete mitochondrial genome of Indian gaur, Bos gaurus and its phylogenetic implications

“…Genetic divergence was also much lower (0.031) between www.nature.com/scientificreports/ gaur and mithun than between mithun and the other two cattle species ( ≥ 0.052). Moreover, studies based on descriptive characteristics, protein polymorphism, karyotype, and microsatellite marker have showed significant differences between domestic mithun and cattle 11,[51][52][53][54][55] . Therefore, based on the results of present and previous studies, we strongly suggest that, wild gaur is the maternal ancestor of domestic mithun.…”

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun

“…The domestic form of gaur is considered as a distinct species, Bos frontalis, and commonly known as mithun (India) and gayal (China). It is believed to have evolved from wild gaur more than 8000 years ago (Simoons, 1984;Dorji et al, 2010;Qu et al, 2012;Wang et al, 2017). However, there are different views for the origin of domestic mithun, and the recent studies have strongly supported the widely accepted view that presumes gaur as the ancestral species of domestic mithun (Mukherjee et al, 2018;Prabhu et al, 2019).…”

Predicting human health from biofluid-based metabolomics using machine learning

“…Select feature sets are then used by algorithms like partial least squares discriminant analysis (PLS-DA) for both additional dimensionality reduction and health-state classification. Machine learning (ML) classifiers including random forests (RFs) 27 – 29 , support vector machines (SVMs) 30 as well as neural networks 31 and multiple forms of logistic regression 32 , 33 have also been employed. Several ML classifiers have recently been compared on 10 curated data sets in a meta-analysis that found minimal, if any, improvement in classification when using SVMs, RFs or neural networks relative to PLS models 34 .…”

“…Several ML classifiers have recently been compared on 10 curated data sets in a meta-analysis that found minimal, if any, improvement in classification when using SVMs, RFs or neural networks relative to PLS models 34 . Other analyses are strictly based on univariate or multivariate receiver operating characteristic-area under the curve (ROC-AUC) 29 , 35 .…”