基于RNA-Seq技术的京海黄鸡卵巢组织转录本预测及新基因挖掘

doi:10.16431/j.cnki.1671-7236.2017.02.028

Abstract

Abstract:

The whole genome sequencing and related genetic map have been declared completed in chicken and many species. Because of the limitations of annotation methods, there are many missing novel genes and annotation errors of existed genes. RNA-Seq is a method for transcriptome studies based on second generation sequencing. In this study,we had sequenced cDNA library that were transcribed from all RNAs in ovaries of eight 300 days old Jinghai Yellow chickens(unanimous weight and the same rearing conditions, but there were difference on the number eggs and evenly divided into two groups: High laying performance and low laying performance) by using high-throughput sequencing technologies. 4 431 new transcripts were found by analysing transcriptome data, and many potential novel genes were found and annotated by comparing all new transcripts with GO, NR, Swiss-Prot and KEGG databases. Our work provided basic data for the further improvement of chicken genome and mining functional genes.

Key words: RNA-Seq; Jinghai Yellow chichen; new transcript; new gene; function annotation

CLC Number:

DONG Xin-long, ZHANG Xiang-qian, HAN Kun-peng, LING Jiao-jiao, ZHANG Gen-xi, WANG Jin-yu, WANG Yong-juan. Prediction of Novel Transcripts and Discovery of Novel Genes on RNA-Seq Analysis of Jinghai Yellow Chicken Ovary[J]. , 2017, 44(2): 497-504.

References

[1] Costa V,Angelini C,De Feis I,et al.Uncovering the complexity of transcriptomes with RNA-Seq[J]. Bio Med Research International,2010,1:853916.
[2] Wang Z,Gerstein M,Snyder M,et al.RNA-Seq:A revolutionary tool for transcriptomics[J]. Nature Review Genetics,2009,10(1):57-63.
[3] Daines B,Wang H,Wang L,et al.The Drosophila melanogaster transcriptome by paired-end RNA sequencing[J]. Genome Research,2011,21(2):315-324.
[4] 姚娜,张文广,张兵,等.利用RNA-Seq技术筛选不同海拔地区山羊转录组SNP[A].生态环境与畜牧业可持续发展学术研讨会暨中国畜牧兽医学会2012年学术年会和全国畜牧兽医青年科技工作者学术研讨会论文集[C].2012.
[5] Zhan S,Merlin C,Boore J,et al.The monarch butterfly genome yields insights into long-distance migration[J].Cell,2011,147(5):1171-1185.
[6] You M,Yue Z,He W,et al.A heterozygous moth genome provides insights into herbivory and detoxification[J].Nature Genetics,2013,45(2):220-225.
[7] Tariq M A,Kim H J,Jejelowo O,et al.Whole-transcriptome RNAseq analysis from minute amount of total RNA[J].Nucleic Acids Research,2011,39(18):e120.
[8] Richard H,Schulz M H,Sultan M,et al.Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments[J].Nucleic Acids Research,2010,38(10):e112.
[9] Chen C,Ai H,Ren J,et al.A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing[J].BMC Genomics,2011,12(1):448.
[10] Jäger M,Ott C E,Grunhagen J,et al.Composite transcriptome assembly of RNA-Seq data in a sheep model for delayed bone healing[J].BMC Genomics,2011,12(2):1-12.
[11] Koonin E V,Fedorova N D,Jackson J D,et al.A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes[J].Genome Biology,2003,5(2):60.
[12] Deng Y Y,Li J Q,Wu S F,et al.Integrated NR database in protein annotation system and its localization[J].Computer Engineering,2006,32(5):71-74.
[13] Apweiler R,Bairoch A,Wu C H,et al.UniProt: The universal protein knowledgebase[J].Nucleic Acids Research,2004,32(Databaseissue):115-119.
[14] Ashburner M,Ball C A,Blake J A,et al.Gene ontology:Tool for the unification of biology [J].Nature Genetics,2000,25(1):25-29.
[15] Kanehisa M,Goto S,Kawashima S,et al.The KEGG resource for deciphering the genome[J]. Nucleic Acids Research,2004,32(22):D277-D280.
[16] 秦彩艳,霍金龙,王配,等.猪新基因KCNJ12编码区电子克隆、RT-PCR验证和组织表达分析[J].华北农学报,2014,29(1):41-49.
[17] 张永云,赵跃,王锐,等.猪新基因PFN3电子克隆、RT-PCR验证和组织表达分析[J].云南农业大学学报(自然科学),2014,29(2):179-186.
[18] 刘永刚.猪新基因SDHB, SNRPA, CRYBB1的分离、序列分析及组织表达谱研究[A].中国畜牧兽医学会、中国畜牧业协会.第四届中国畜牧科技论坛论文集[C].中国畜牧兽医学会、中国畜牧业协会,2009.
[19] 祁云霞,刘永斌,荣威恒.转录组研究新技术:RNA-Seq及其应用[J].遗传,2011,33(11):1191-1202.
[20] Zhang G J,Guo G W,Hu X D,et al.Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome[J]. Genome Research,2010,20(5):646-654.
[21] Wenger Y,Galliot B.RNAseq versus genome-predicted transcriptomes: A large population of novel transcripts identified in an Illumina-454 Hydra transcriptome[J].BMC Genomics,2013, 14(1):1-17.
[22] Liu W,Zhao Y,Cu I P,et al.Thousands of novel transcripts identified in mouse cerebrum, testis, and ES cells based on ribominus RNA sequencing[J].Frontiers in Genetics,2011,2:93.
[23] Sun Q Y,Schatten H.Regulation of dynamic events by microfilaments during oocyte maturation and fertilization[J].Reproduction,2006,131(2):193-205.
[24] Brunet S,Maro B.Cytoskeleton and cell cycle control during meiotic maturation of the mouse oocyte: Integrating time and space[J].Reproduction,2005,130(6):801-811.
[25] Seger R,Krebs E G.The mapk signaling cascade[J]. Faseb Journal Official Publication of the Federation of American Societies for Experimental Biology,1995,9(9):726-735.
[26] Harrouk W,Clarke H J.Mitogen-activated protein (MAP) kinase during the acquisition of meiotic competence by growing oocytes of the mouse[J]. Molecular Reproduction & Development,1995,41(1):29-36.

Prediction of Novel Transcripts and Discovery of Novel Genes on RNA-Seq Analysis of Jinghai Yellow Chicken Ovary

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