Micro RNAs（mi RNAs） are small, single stranded, non-coding RNA molecules, about 19–25 nucleotides in length, which regulate the development and functions of reproductive system of mammal.To discover novel mi RNAs a...Micro RNAs（mi RNAs） are small, single stranded, non-coding RNA molecules, about 19–25 nucleotides in length, which regulate the development and functions of reproductive system of mammal.To discover novel mi RNAs and identify the differential expression of them in ovine ovary and testis tissues, the study constructed two libraries by using next-generation sequencing technologies（Solexa high-throughput sequencing technique）.As a result, 9 321 775 and 9 511 538 clean reads were obtained from the ovary and testis separately, which included 130 562（90 genes of ovary） and 56 272（85 genes of testis） of known mi RNAs and 486 potential novel mi RNAs reads.In this study, a total of 65 conserved mi RNAs were significantly differentially expressed（P〈0.01） between the two samples.Among them, 28 mi RNAs were up-regulated and 3 mi RNAs were down-regulated on ovary compared with testis.In addition, the known mi RNAs with the highest expression level（5 mi RNAs） and 30 novel mi RNAs with the functions related to reproduction were validated using the real-time quantitative RT-PCR.Moreover, the gene ontology（GO） annotation and Kyoto encyclopedia of genes and genomes（KEGG） pathway analysis showed that differentially expressed mi RNAs were involved in ovary and testis physiology, including signal transduction, gonad development, sex differentiation, gematogenesis, fertilization and embryo development.The results will be helpful to facilitate studies on the regulation of mi RNAs during ruminant reproduction.展开更多
With high-throughput Solexa sequencing technology,we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated,which were assem...With high-throughput Solexa sequencing technology,we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated,which were assembled into 31538 unigenes. Blast analysis showed that 56.7%unigenes were novel,which represented the specific genes of Porphyra and/or rhodophytes. Several hundreds of unigenes related to stress tolerance were discovered,including genes related to desiccation-(211) and high light-tolerance(31) ,flavonoid biosynthesis(10) ,reactive oxygen scavenging(48) and other stress-tolerance processes(208) ,which indicated there existed complex and diversity modes of stress tolerance in this species.A complete set of essential genes involved in the C3-(57) and C4-(44) carbon fixation pathway(except pyruvate phosphate dikinase) were discovered,which not only proved that they were actively transcribed but also clearly outlined the panoptic view of carbon fixation in Porphyra.Moreover,by statistically analyzing the types,proportions and frequencies of the interspersed repeats(TEs) and simple sequence repeats(SSRs) ,we discovered that the top three types of TEs were all retrotransposons and the trinucleotide was the absolute predominant type among SSRs,promoting our understanding of structural characteristics of the transcriptome.This study substantially improved the global view of the Porphyra genome and provided a valuable resource for future research.展开更多
基金supported by the Department of Agriculture and Animal Husbandry of Gansu,China(2011zx08008-003)the Ministry of Agriculture of China(2009ZX08008008-002)the Scientific Research Basic Business Expenses of Colleges and Universities,China(2011zx08008-003)
文摘Micro RNAs（mi RNAs） are small, single stranded, non-coding RNA molecules, about 19–25 nucleotides in length, which regulate the development and functions of reproductive system of mammal.To discover novel mi RNAs and identify the differential expression of them in ovine ovary and testis tissues, the study constructed two libraries by using next-generation sequencing technologies（Solexa high-throughput sequencing technique）.As a result, 9 321 775 and 9 511 538 clean reads were obtained from the ovary and testis separately, which included 130 562（90 genes of ovary） and 56 272（85 genes of testis） of known mi RNAs and 486 potential novel mi RNAs reads.In this study, a total of 65 conserved mi RNAs were significantly differentially expressed（P〈0.01） between the two samples.Among them, 28 mi RNAs were up-regulated and 3 mi RNAs were down-regulated on ovary compared with testis.In addition, the known mi RNAs with the highest expression level（5 mi RNAs） and 30 novel mi RNAs with the functions related to reproduction were validated using the real-time quantitative RT-PCR.Moreover, the gene ontology（GO） annotation and Kyoto encyclopedia of genes and genomes（KEGG） pathway analysis showed that differentially expressed mi RNAs were involved in ovary and testis physiology, including signal transduction, gonad development, sex differentiation, gematogenesis, fertilization and embryo development.The results will be helpful to facilitate studies on the regulation of mi RNAs during ruminant reproduction.
基金supported by the National Natural Science Foundation of China(30972247,30700621)Special Fund for Agro-scientific Research in the Public Interest(200903030)+2 种基金National High Technology Research and Development Program of China(2006AA10A402,2006AA10A413)Program for New Century Excellent Talents in University(NCET-06-0596)Promotive Research Fund for Young and Middle-aged Scientisits of Shandong Province(2008BS06002)
文摘With high-throughput Solexa sequencing technology,we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated,which were assembled into 31538 unigenes. Blast analysis showed that 56.7%unigenes were novel,which represented the specific genes of Porphyra and/or rhodophytes. Several hundreds of unigenes related to stress tolerance were discovered,including genes related to desiccation-(211) and high light-tolerance(31) ,flavonoid biosynthesis(10) ,reactive oxygen scavenging(48) and other stress-tolerance processes(208) ,which indicated there existed complex and diversity modes of stress tolerance in this species.A complete set of essential genes involved in the C3-(57) and C4-(44) carbon fixation pathway(except pyruvate phosphate dikinase) were discovered,which not only proved that they were actively transcribed but also clearly outlined the panoptic view of carbon fixation in Porphyra.Moreover,by statistically analyzing the types,proportions and frequencies of the interspersed repeats(TEs) and simple sequence repeats(SSRs) ,we discovered that the top three types of TEs were all retrotransposons and the trinucleotide was the absolute predominant type among SSRs,promoting our understanding of structural characteristics of the transcriptome.This study substantially improved the global view of the Porphyra genome and provided a valuable resource for future research.
