BMC Genomics paper abstract 20120912

From Horsegenome.net

(Difference between revisions)
Jump to: navigation, search
 
Line 1: Line 1:
<p><span style="font-size: x-large; ">Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq</span></p>
<p><span style="font-size: x-large; ">Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq</span></p>
<div class="singleins" style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-size: 11.199999809265137px; font-family: Verdana, Arial, Helvetica, sans-serif; vertical-align: baseline; line-height: 12.800000190734863px; ">
<div class="singleins" style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-size: 11.199999809265137px; font-family: Verdana, Arial, Helvetica, sans-serif; vertical-align: baseline; line-height: 12.800000190734863px; ">
-
<p class="authors" style="padding: 0px; margin: 0.2em 0px 0px; border: 0px; outline: 0px; font-style: inherit; font-size: 1em; font-family: inherit; vertical-align: baseline; overflow: visible; line-height: 1.3em; "><strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Kyung-Do Park</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Jongsun Park</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Junsu Ko</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Byung Chul Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Heui-Soo Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Kung Ahn</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Kyoung-Tag Do</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Hansol Choi</strong>,<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Hak-Min Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Sanghoon Song</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Sunghoon Lee</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Sungwoong Jho</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Hong-Sik Kong</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Young Mok Yang</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Byung-Hak Jhun</strong>,<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Chulhong Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Tae-Hyung Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Seungwoo Hwang</strong>, <b>[[</b><strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Jong Bhak]]</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Hak-Kyo Lee</strong>&nbsp;and&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Byung-Wook Cho</strong></p>
+
<p class="authors" style="padding: 0px; margin: 0.2em 0px 0px; border: 0px; outline: 0px; font-style: inherit; font-size: 1em; font-family: inherit; vertical-align: baseline; overflow: visible; line-height: 1.3em; "><strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Kyung-Do Park</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Jongsun Park</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Junsu Ko</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Byung Chul Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Heui-Soo Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Kung Ahn</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Kyoung-Tag Do</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Hansol Choi</strong>,<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Hak-Min Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Sanghoon Song</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Sunghoon Lee</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Sungwoong Jho</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Hong-Sik Kong</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Young Mok Yang</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Byung-Hak Jhun</strong>,<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Chulhong Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Tae-Hyung Kim</strong>,&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Seungwoo Hwang</strong>, [[Jong Bhak]],&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Hak-Kyo Lee</strong>&nbsp;and&nbsp;<strong style="padding: 0px; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-family: inherit; vertical-align: baseline; ">Byung-Wook Cho</strong></p>
<p class="authors" style="padding: 0px; margin: 0.2em 0px 0px; border: 0px; outline: 0px; font-style: inherit; font-size: 1em; font-family: inherit; vertical-align: baseline; overflow: visible; line-height: 1.3em; ">&nbsp;</p>
<p class="authors" style="padding: 0px; margin: 0.2em 0px 0px; border: 0px; outline: 0px; font-style: inherit; font-size: 1em; font-family: inherit; vertical-align: baseline; overflow: visible; line-height: 1.3em; ">&nbsp;</p>
<p class="authors" style="padding: 0px; margin: 0.2em 0px 0px; border: 0px; outline: 0px; font-style: inherit; font-size: 1em; font-family: inherit; vertical-align: baseline; overflow: visible; line-height: 1.3em; "><span style="font-size: large; ">Background</span></p>
<p class="authors" style="padding: 0px; margin: 0.2em 0px 0px; border: 0px; outline: 0px; font-style: inherit; font-size: 1em; font-family: inherit; vertical-align: baseline; overflow: visible; line-height: 1.3em; "><span style="font-size: large; ">Background</span></p>

Latest revision as of 05:35, 14 September 2012

Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq

Kyung-Do ParkJongsun ParkJunsu KoByung Chul KimHeui-Soo KimKung AhnKyoung-Tag DoHansol Choi,Hak-Min KimSanghoon SongSunghoon LeeSungwoong JhoHong-Sik KongYoung Mok YangByung-Hak Jhun,Chulhong KimTae-Hyung KimSeungwoo Hwang, Jong BhakHak-Kyo Lee and Byung-Wook Cho

 

Background

Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes.

Results

We present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) of the unigene clusters did not match any current equine gene model. We also identified 189,973 single nucleotide variations (SNVs) from the sequences aligned against the horse reference genome. Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases. Using differential expression analysis, we further identified a number of exercise-regulated genes: 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle. Six of 28 previously-known exercise-related genes were over-expressed in the muscle after exercise. Among the differentially expressed genes, there were 91 transcription factor-encoding genes, which included 56 functionally unknown transcription factor candidates that are probably associated with an early regulatory exercise mechanism. In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.

Conclusion

The first sequencing-based horse transcriptome data, extensive analyses results, deferentially expressed genes before and after exercise, and candidate genes that are related to the exercise are provided in this study.

provisional_PDF._The_fully_formatted_PDF_and_HTML_versions_are_in_production.">The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.

 

 

Personal tools