Limits...
Differential gene expression in ovaries of Qira black sheep and Hetian sheep using RNA-Seq technique.

Chen HY, Shen H, Jia B, Zhang YS, Wang XH, Zeng XC - PLoS ONE (2015)

Bottom Line: After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively.A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep.This study provides a basic data for future research of the sheep reproduction.

View Article: PubMed Central - PubMed

Affiliation: School of Pharmacy, Shihezi University, Shihezi, Xinjiang, China.

ABSTRACT
The Qira black sheep and the Hetian sheep are two local breeds in the Northwest of China, which are characterized by high-fecundity and low-fecundity breed respectively. The elucidation of mRNA expression profiles in the ovaries among different sheep breeds representing fecundity extremes will helpful for identification and utilization of major prolificacy genes in sheep. In the present study, we performed RNA-seq technology to compare the difference in ovarian mRNA expression profiles between Qira black sheep and Hetian sheep. From the Qira black sheep and the Hetian sheep libraries, we obtained a total of 11,747,582 and 11,879,968 sequencing reads, respectively. After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively. A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep. Eight differentially expressed genes were randomly selected for validation by real-time RT-PCR. This study provides a basic data for future research of the sheep reproduction.

No MeSH data available.


Distribution of genes′ coverage in the two ovine libraries.Gene coverage is the percentage of a gene covered by reads. This value is equal to the ratio of total base count in a gene covered by uniquely mapped reads to the total base count for that gene.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4366253&req=5

pone.0120170.g002: Distribution of genes′ coverage in the two ovine libraries.Gene coverage is the percentage of a gene covered by reads. This value is equal to the ratio of total base count in a gene covered by uniquely mapped reads to the total base count for that gene.

Mentions: The RPKM method was used to evaluate the gene expression levels. As a result, 16,763 and 16,814 reference genes were identified from Qira black sheep and Hetian sheep libraries, respectively, which shared 16,425 genes in common (S1 Table). As shown in Table 2, approximately 88% and a little more than 1.7% of the reference genes were expressed at less than 100 RPKM and more than 500 RPKM respectively. As shown in Fig. 2, 20% of the reference genes had 80–90% coverage, and 31% and 35% of the annotated genes had 90–100% coverage in Qira black sheep and Hetian sheep libraries respectively, suggesting that the read distributions are similar between the two libraries.


Differential gene expression in ovaries of Qira black sheep and Hetian sheep using RNA-Seq technique.

Chen HY, Shen H, Jia B, Zhang YS, Wang XH, Zeng XC - PLoS ONE (2015)

Distribution of genes′ coverage in the two ovine libraries.Gene coverage is the percentage of a gene covered by reads. This value is equal to the ratio of total base count in a gene covered by uniquely mapped reads to the total base count for that gene.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4366253&req=5

pone.0120170.g002: Distribution of genes′ coverage in the two ovine libraries.Gene coverage is the percentage of a gene covered by reads. This value is equal to the ratio of total base count in a gene covered by uniquely mapped reads to the total base count for that gene.
Mentions: The RPKM method was used to evaluate the gene expression levels. As a result, 16,763 and 16,814 reference genes were identified from Qira black sheep and Hetian sheep libraries, respectively, which shared 16,425 genes in common (S1 Table). As shown in Table 2, approximately 88% and a little more than 1.7% of the reference genes were expressed at less than 100 RPKM and more than 500 RPKM respectively. As shown in Fig. 2, 20% of the reference genes had 80–90% coverage, and 31% and 35% of the annotated genes had 90–100% coverage in Qira black sheep and Hetian sheep libraries respectively, suggesting that the read distributions are similar between the two libraries.

Bottom Line: After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively.A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep.This study provides a basic data for future research of the sheep reproduction.

View Article: PubMed Central - PubMed

Affiliation: School of Pharmacy, Shihezi University, Shihezi, Xinjiang, China.

ABSTRACT
The Qira black sheep and the Hetian sheep are two local breeds in the Northwest of China, which are characterized by high-fecundity and low-fecundity breed respectively. The elucidation of mRNA expression profiles in the ovaries among different sheep breeds representing fecundity extremes will helpful for identification and utilization of major prolificacy genes in sheep. In the present study, we performed RNA-seq technology to compare the difference in ovarian mRNA expression profiles between Qira black sheep and Hetian sheep. From the Qira black sheep and the Hetian sheep libraries, we obtained a total of 11,747,582 and 11,879,968 sequencing reads, respectively. After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively. A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep. Eight differentially expressed genes were randomly selected for validation by real-time RT-PCR. This study provides a basic data for future research of the sheep reproduction.

No MeSH data available.