Landscape of alternative splicing in Capra_hircus

Xu, Tieshan; Feng, Xu; Gu, Lihong; Rong, Guang; Mao, Li; Qiao, Fei; Shi, Liguang; Wang, Dingfa; Xia, Wanliang; Xun, Wenjuan; Cao, Ting; Liu, Yiming; Lin, Zhemin; Zhou, Hanlin

doi:10.1038/s41598-018-33078-7

Cited by 3 publications

(2 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, RS-122-2101) was used for the construction of 18 cDNA libraries [ 24 ], and the Illumina sequencing platform (HiSeqTM 2500) was used to sequence these libraries, generating 125 bp paired-end reads [ 25 , 26 ]. Raw data underwent recognition analysis to obtain original sequencing.…”

Section: Methodsmentioning

confidence: 99%

Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)

Fan

Arbab

Zhang

et al. 2021

Animals

View full text Add to dashboard Cite

Weighted gene coexpression network analysis (WGCNA) is a novel approach that can quickly analyze the relationships between genes and traits. In this study, the milk yield, lactose, fat, and protein of Holstein dairy cows were detected in a lactation cycle. Meanwhile, a total of 18 gene expression profiles were detected using mammary glands from six lactation stages (day 7 to calving, −7 d; day 30 post-calving, 30 d; day 90 post-calving, 90 d; day 180 post-calving, 180 d; day 270 post-calving, 270 d; day 315 post-calving, 315 d). On the basis of the 18 profiles, WGCNA identified for the first time 10 significant modules that may be related to lactation stage, milk yield, and the main milk composition content. Genes in the 10 significant modules were examined with gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results revealed that the galactose metabolism pathway was a potential candidate for milk yield and milk lactose synthesis. In −7 d, ion transportation was more frequent and cell proliferation related terms became active. In late lactation, the suppressor of cytokine signaling 3 (SOCS3) might play a role in apoptosis. The sphingolipid signaling pathway was a potential candidate for milk fat synthesis. Dairy cows at 315 d were in a period of cell proliferation. Another notable phenomenon was that nonlactating dairy cows had a more regular circadian rhythm after a cycle of lactation. The results provide an important theoretical basis for the further molecular breeding of dairy cows.

show abstract

Section: Methodsmentioning

confidence: 99%

Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)

Fan

Arbab

Zhang

et al. 2021

Animals

View full text Add to dashboard Cite

show abstract

“…DYSF mutations are associated with muscular dystrophy in humans (Bashir et al, 1998) and mice (Bittner et al, 1999). DYSF has also been identified as an alternatively spliced gene in goat leg muscle, likely playing crucial roles in skeletal muscle development (Xu et al, 2018). A study has revealed several candidate genes associated with goat ear morphology (Brito et al, 2017).…”

Section: Genomic Characteristics Of the Chongming White Goat Breedmentioning

confidence: 99%

Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus)

et al. 2020

View full text Add to dashboard Cite

The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing wholegenome re-sequencing, we generated 14-20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion-deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genomewide F ST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.

show abstract

Transcriptomic Analysis and Comparison of the Gene Expression Profiles in Fast- and Slow-Growing Pearl Oysters Pinctada fucata martensii

Liu

Zhang

et al. 2022

J. Ocean Univ. China

View full text Add to dashboard Cite

Landscape of alternative splicing in Capra_hircus

Cited by 3 publications

References 69 publications

Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)

Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)

Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus)

Transcriptomic Analysis and Comparison of the Gene Expression Profiles in Fast- and Slow-Growing Pearl Oysters Pinctada fucata martensii

Contact Info

Product

Resources

About