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.
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.
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通过双端 RNA 测序，对具有生长和脂肪沉积极端表型的全同胞对的三种组织中的猪转录组进行全局观察
DOI：
10.1186/1471-2164-12-448
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发表时间：
2011-09-10
期刊：
影响因子：
4.4
通讯作者：
Huang L
中科院分区：
文献类型：
--
作者：
Chen C;Ai H;Ren J;Li W;Li P;Qiao R;Ouyang J;Yang M;Ma J;Huang L
猪转录组的阐明对于解释基因组的功能元件和理解复杂性状（如脂肪沉积、代谢和生长）的遗传结构至关重要。在这里，我们使用大规模并行高通量RNA测序，以产生一个高分辨率的地图，猪的mRNA和miRNA转录组在肝脏，背最长肌和腹部脂肪从两个全同胞F2杂交猪分离的表型生长，血液生理和生化参数，和脂肪沉积。我们获得了8，508，418 - 10，219，332个独特定位的读段，覆盖了目前注释的转录本的78.0%，并鉴定了48，045 - 122，931个新的转录片段，这些片段在六个测试样品中构成了17，085 - 29，499个新的转录活性区域。我们发现，约18.8%的注释基因显示出选择性剪接模式，并且选择性3'剪接是猪中最常见的选择性剪接事件类型。跨组织比较显示，许多转录事件是组织差异性的，并与其相应组织中的重要生物学功能相关。我们还检测到总共164个潜在的新miRNAs，其中大部分是组织特异性鉴定的。全基因组关联分析和差异基因表达的综合分析揭示了复杂性状的候选基因，如IGF 2、CYP 1A 1、CKM和CES 1分别与心脏重量、血红蛋白、猪肉pH值和血清胆固醇有关。这项研究为猪转录组的复杂性提供了一个全面的视角，并为猪的选择性剪接、基因边界和miRNA提供了广泛的新知识。全基因组关联分析和基因差异表达的综合分析有助于寻找猪复杂性状的重要候选基因。
Elucidation of the pig transcriptome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits such as fat deposition, metabolism and growth. Here we used massive parallel high-throughput RNA sequencing to generate a high-resolution map of the porcine mRNA and miRNA transcriptome in liver, longissimus dorsi and abdominal fat from two full-sib F2 hybrid pigs with segregated phenotypes on growth, blood physiological and biochemical parameters, and fat deposition. We obtained 8,508,418-10,219,332 uniquely mapped reads that covered 78.0% of the current annotated transcripts and identified 48,045-122,931 novel transcript fragments, which constituted 17,085-29,499 novel transcriptional active regions in six tested samples. We found that about 18.8% of the annotated genes showed alternative splicing patterns, and alternative 3' splicing is the most common type of alternative splicing events in pigs. Cross-tissue comparison revealed that many transcriptional events are tissue-differential and related to important biological functions in their corresponding tissues. We also detected a total of 164 potential novel miRNAs, most of which were tissue-specifically identified. Integrated analysis of genome-wide association study and differential gene expression revealed interesting candidate genes for complex traits, such as IGF2, CYP1A1, CKM and CES1 for heart weight, hemoglobin, pork pH value and serum cholesterol, respectively. This study provides a global view of the complexity of the pig transcriptome, and gives an extensive new knowledge about alternative splicing, gene boundaries and miRNAs in pigs. Integrated analysis of genome wide association study and differential gene expression allows us to find important candidate genes for porcine complex traits.
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影响因子：
2.4
作者：
Johansson, A;Pielberg, G;Edfors-Lilja, I
通讯作者：
Edfors-Lilja, I
影响因子：
3.7
作者：
Creighton CJ;Benham AL;Zhu H;Khan MF;Reid JG;Nagaraja AK;Fountain MD;Dziadek O;Han D;Ma L;Kim J;Hawkins SM;Anderson ML;Matzuk MM;Gunaratne PH
通讯作者：
Gunaratne PH
影响因子：
64.8
作者：
Baek, Daehyun;Villen, Judit;Shin, Chanseok;Camargo, Fernando D.;Gygi, Steven P.;Bartel, David P.
通讯作者：
Bartel, David P.
影响因子：
2.7
作者：
Hettmann, T;Barton, K;Leiden, TM
通讯作者：
Leiden, TM
影响因子：
30.8
作者：
Barrett, Jeffrey C.;Clayton, David G.;Concannon, Patrick;Akolkar, Beena;Cooper, Jason D.;Erlich, Henry A.;Julier, Cecile;Morahan, Grant;Nerup, Jorn;Nierras, Concepcion;Plagnol, Vincent;Pociot, Flemming;Schuilenburg, Helen;Smyth, Deborah J.;Stevens, Helen;Todd, John A.;Walker, Neil M.;Rich, Stephen S.
通讯作者：
Rich, Stephen S.