A Multi-Tissue Gene Expression Atlas of Water Buffalo (Bubalus bubalis) Reveals Transcriptome Conservation between Buffalo and Cattle

Si, Jingfang; Dai, Dongmei; Li, Kun; Fang, Lingzhao; Yi, Zhang

doi:10.3390/genes14040890

Cited by 3 publications

(3 citation statements)

References 41 publications

(61 reference statements)

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“…Interestingly, the non-coding second exon was also not expressed in any of the bison tissues, although it is not affected by the deletion. We then aligned 73 transcriptomic data from 19 tissues from 4 water buffaloes (Si et al, 2023) against the Bos taurus taurus reference sequence. Water buffalo is substantially more diverged from cattle than wisent and bison, but the expression profile of both THRSP exons was similar to cattle with the highest transcript abundance in adipose tissue (9,776 TPM), mammary gland (1,570 TPM), skin (440 TPM), liver (298 TPM), and skeletal muscle (37 TPM) ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Publicly available RNA sequencing data from bison (BioProject: PRJNA257088, (Dobson et al, 2021)) and water buffalo (BioProject: PRJNA951806, (Si et al, 2023)) were aligned to the ARS-UCD1.2 assembly and Refseq version 106 annotation with STAR v2.7.9a (Dobin et al, 2013). Integrative Genomics Viewer v2.14.0 (Robinson et al, 2011) was used to visualize the alignments.…”

Section: Methodsmentioning

confidence: 99%

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Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene

Bortoluzzi,

Mapel,

Neuenschwander

et al. 2024

Preprint

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The wisent (Bison bonasus) is Europe's largest land mammal. A restoration program established from 12 captive individuals rescued the wisent from extinction in the early 20th century. We produced a PacBio HiFi-read based assembly (GenBank accession: GCA_963879515.1) containing 99.7% of the near-universal mammalian single copy genes with a contig N50 value of 91 Mb which improves contiguity a thousand-fold over the existing draft wisent assembly. Excessive runs of homozygosity in the genome of the wisent compromised the separation of the HiFi reads into parental-specific read sets, which resulted in inferior haplotype assemblies. A bovine super-pangenome built with assemblies from wisent, bison, gaur, yak, taurine and indicine cattle identified a 1,580 bp deletion removing the entire protein-coding sequence of THRSP encoding thyroid hormone-responsive protein from the wisent and bison genomes. Analysis of 725 whole genome sequenced samples across the Bovinae subfamily showed that the deletion is fixed in Bison but absent in Bos and Bubalus. Transcriptomic data revealed that the THRSP transcript is highly abundant in adipose, fat, liver, muscle, and mammary gland tissue of Bos and Bubalus, but absent in Bison indicating that the deletion inactivates THRSP which might contribute to low milk and meat fat content observed in Bison. Our findings demonstrate that super-pangenomes can reveal potentially trait-associated variation across phylogenies, but also emphasize that haplotype assemblies from species that went through population bottlenecks warrant scrutiny, as they may have accumulated long runs of homozygosity that complicate phasing.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene

Bortoluzzi,

Mapel,

Neuenschwander

et al. 2024

Preprint

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“…Using a combination of genomics and transcriptomics was first proposed by the Functional Annotation of Animal Genomes (FFANG) Consortium to identify the genes that code for proteins that are involved in critical production traits in farm animals 5 . Transcriptomic atlases were generated for common domestic animals such as pigs, cattle, sheep, and chickens [6][7][8][9][10] as well as other species of herbivores such as donkey 11 , water buffalo 12 , and goat 13 . While these published transcriptomic atlases of herbivores are valuable, they are published in independent databases, with no standard protocols for sample collection, RNA sequencing, or data processing.…”

Section: Background and Summarymentioning

confidence: 99%

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore

Wang,

Huang,

Zhen

et al. 2024

Sci Data

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Domesticated herbivores are an important agricultural resource that play a critical role in global food security, particularly as they can adapt to varied environments, including marginal lands. An understanding of the molecular basis of their biology would contribute to better management and sustainable production. Thus, we conducted transcriptome sequencing of 100 to 105 tissues from two females of each of seven species of herbivore (cattle, sheep, goats, sika deer, horses, donkeys, and rabbits) including two breeds of sheep. The quality of raw and trimmed reads was assessed in terms of base quality, GC content, duplication sequence rate, overrepresented k-mers, and quality score distribution with FastQC. The high-quality filtered RNA-seq raw reads were deposited in a public database which provides approximately 54 billion high-quality paired-end sequencing reads in total, with an average mapping rate of ~93.92%. Transcriptome databases represent valuable resources that can be used to study patterns of gene expression, and pathways that are related to key biological processes, including important economic traits in herbivores.

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Can the male germline offer insight into mammalian brain size expansion?

Bush,

Goriely

2024

Andrology

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Recent advances in single‐cell transcriptomic data have greatly expanded our understanding of both spermatogenesis and the molecular mechanisms of male infertility. However, this growing wealth of data could also shed light on a seemingly unrelated biological problem: the genetic basis of mammalian brain size expansion throughout evolution. It is now increasingly recognized that the testis and brain share many cellular and molecular similarities including pivotal roles for the RAS/MAPK and PI3K/AKT/mTOR pathways, mutations in which are known to have a pronounced impact on cell proliferation. Most notably, in the stem cell lineages of both organs, new mutations have been shown to increase cellular output over time. These include ‘selfish’ mutations in spermatogonial stem cells, which disproportionately increase the proportion of mutant sperm, and—to draw a parallel—human‐specific mutations in neural stem cells which, by increasing the number of neurons, have been implicated in neocortical expansion. Here we speculate that the origin for many ‘expansion’‐associated mutations is the male germline and that as such, a deeper understanding of the mechanisms controlling testicular turnover may yield fresh insight into the biology and evolution of the brain.

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A Multi-Tissue Gene Expression Atlas of Water Buffalo (Bubalus bubalis) Reveals Transcriptome Conservation between Buffalo and Cattle

Cited by 3 publications

References 41 publications

Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene

Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore

Can the male germline offer insight into mammalian brain size expansion?

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