Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

Chakraborty, Abhisek; Bisht, Manohar S.; Saxena, Rituja; Mahajan, Shruti; Pulikkan, Joby; Sharma, Vineet K.

doi:10.1007/s13258-023-01401-w

Cited by 5 publications

(7 citation statements)

References 48 publications

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“…A haplotype-resolved genome of an indicine breed has been assembled in this study. There is a significant improvement of the indicine cattle genome as compared to the presently available reference genome, as reported earlier in Canavez et al (2012 ) and recently built short-read sequencing-based genome ( Chakraborty et al, 2023 ). The use of relevant reference genomes is important and could have a large impact on studies, especially on detecting signatures of selection, as has been reported earlier ( Lloret-Villas et al, 2021 ).…”

Section: Discussionmentioning

confidence: 81%

“…For B. indicus cattle (Nellore breed), reference-based genome assembly was performed using the SOLiD sequencing platform with very short read lengths of 25 and 50 bases. The recent reference-based genome assembly was carried out using the Illumina platform with read lengths of 150 bases ( Canavez et al, 2012 ; Chakraborty et al, 2023 ), while there is a high-quality reference genome for taurine cattle breeds ( Rosen et al, 2020 ). Therefore, a quality reference genome of the indicine breed is still lacking.…”

Section: Introductionmentioning

confidence: 99%

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Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle — elucidating genetic variation

Muthusamy,

Vakayil Mani,

Kumari

et al. 2024

Front. Genet.

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Cattle contribute to the nutritional needs and economy of a place. The performance and fitness of cattle depend on the response and adaptation to local climatic conditions. Genomic and genetic studies are important for advancing cattle breeding, and availability of relevant reference genomes is essential. In the present study, the genome of a Vechur calf was sequenced on both short-read Illumina and long-read Nanopore sequencing platforms. The hybrid de novo assembly approach was deployed to obtain an average contig length of 1.97 Mbp and an N50 of 4.94 Mbp. By using a short-read genome sequence of the corresponding sire and dam, a haplotype-resolved genome was also assembled. In comparison to the taurine reference genome, we found 28,982 autosomal structural variants and 16,926,990 SNVs, with 883,544 SNVs homozygous in the trio samples. Many of these SNPs have been reported to be associated with various QTLs including growth, milk yield, and milk fat content, which are crucial determinants of cattle production. Furthermore, population genotype data analysis indicated that the present sample belongs to an Indian cattle breed forming a unique cluster of Bos indicus. Subsequent FST analysis revealed differentiation of the Vechur cattle genome at multiple loci, especially those regions related to whole body growth and cell division, especially IGF1, HMGA2, RRM2, and CD68 loci, suggesting a possible role of these genes in its small stature and better disease resistance capabilities in comparison with the local crossbreeds. This provides an opportunity to select and engineer cattle breeds optimized for local conditions.

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Section: Discussionmentioning

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle — elucidating genetic variation

Muthusamy,

Vakayil Mani,

Kumari

et al. 2024

Front. Genet.

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“…A haplotype-resolved genome of an indicine breed has been assembled in this study. There is a significant improvement of the indicine cattle genome as compared to the presently available reference genome as reported earlier in [6] and recently built short read sequencing based genome [7]. The use of relevant reference genomes is important and could have a large impact on studies, especially on detecting signatures of selection as has been reported earlier [21].…”

Section: Discussionmentioning

confidence: 96%

Hybridde novoand haplotype resolved genome assembly of Vechur cattle - elucidating genetic variation

Muthusamy,

Mani,

Kumari

et al. 2023

Preprint

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Cattle contribute to the nutritional needs and economy of a place. Performance and fitness depends on the response and adaptation to local climatic conditions. Genomic and genetic studies are important for advancing cattle breeding and availability of relevant reference genomes are essential. In the present study, the genome of a Vechur calf was sequenced on both short-read illumina and long-read nanopore platforms. Hybridde novoassembly approach was deployed to obtain an average contigs length of 1.97 Mbp and N50 of 4.94 Mbp. Using a short-read genome sequence of the corresponding sire and dam, a haplotype-resolved genome was also assembled. In comparison to the taurine reference genome, we found 28982 autosomal structural variants, 16926990 SNVs with 883544 SNVs homozygous in the trio samples suggesting high prevalence of these SNPs in the population. Many of these SNPs have been reported to be associated with various QTLs including growth, milk yield and milk fat content which are crucial determinants of cattle production. Further, population genotype data analysis indicated that the present sample belongs to an Indian cattle breed forming a unique cluster ofBos indicus. Subsequent FSTanalysis revealed differentiation of Vechur cattle genome at multiple loci, especially those regions related to whole body growth and cell division especially IGF1, HMGA2, RRM2 and CD68 loci suggesting a possible role of these genes in its small stature and better disease resistance capabilities in comparison with the local crossbreeds. This provides an opportunity to select and engineer cattle breeds optimized for local conditions.

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“…Gene families were identified from the CAFÉ analysis, and the longest gene for each gene family was extracted. The genes were mapped separately onto S. cumini genome constructed in this study and the previously available S. aromaticum ( Ouadi et al., 2022 ) and S. grande ( Low et al., 2022 ) genomes using Exonerate v2.4.0 ( https://github.com/nathanweeks/exonerate ) to construct the exon-intron structures ( Chakraborty et al., 2023 ), and for a comparative analysis across the three Syzygium species.…”

Section: Methodsmentioning

confidence: 99%

Genome sequencing of Syzygium cumini (jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

Chakraborty,

Mahajan,

Bisht

et al. 2023

Front. Plant Sci.

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Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome for the first time from the world’s largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. We also sequenced and assembled the transcriptome of S. cumini in this study. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families resulting from gene duplication events compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.

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Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

Cited by 5 publications

References 48 publications

Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle — elucidating genetic variation

Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle — elucidating genetic variation

Hybridde novoand haplotype resolved genome assembly of Vechur cattle - elucidating genetic variation

Genome sequencing of Syzygium cumini (jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

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