教師資料查詢 | 類別: 期刊論文 | 教師: 林莊傑CHUANG-CHIEH LIN (瀏覽個人網頁)

標題:Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants
學年103
學期2
出版(發表)日期2015/02/05
作品名稱Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants
作品名稱(其他語言)
著者Trees-Juen Chuang; Min-Yu Yang; Chuang-Chieh Lin; Ping-Hung Hsieh; Li-Yuan Hung
單位
出版者
著錄名稱、卷期、頁數BMC Plant Biology 15, 39
摘要Background: Crop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. However, current genome annotations of crop plants still suffer false-positive predictions; a more comprehensive registry of alternative splicing (AS) events is also in demand. Comparative genomics of crop plants is largely unexplored.

Results: We performed a large-scale comparative analysis (ExonFinder) of the expressed sequence tag (EST) library from nine grass plants against three crop genomes (rice, maize, and sorghum) and identified 2,879
previously-unannotated exons (i.e., novel exons) in the three crops. We validated 81% of the tested exons by
RT-PCR-sequencing, supporting the effectiveness of our in silico strategy. Evolutionary analysis reveals that the
novel exons, comparing with their flanking annotated ones, are generally under weaker selection pressure at
the protein level, but under stronger pressure at the RNA level, suggesting that most of the novel exons also
represent novel alternatively spliced variants (ASVs). However, we also observed the consistency of evolutionary rates between certain novel exons and their flanking exons, which provided further evidence of their co-occurrence in the transcripts, suggesting that previously-annotated isoforms might be subject to erroneous predictions. Our validation showed that 54% of the tested genes expressed the newly-identified isoforms that contained the novel exons, rather than the previously-annotated isoforms that excluded them. The consistent results were steadily observed across cultivated (Oryza sativa and O. glaberrima) and wild (O. rufipogon and O. nivara) rice species, asserting the necessity of our curation of the crop genome annotations. Our comparative analyses also inferred the common ancestral
transcriptome of grass plants and gain- and loss-of-ASV events.

Conclusions: We have reannotated the rice, maize, and sorghum genomes, and showed that evolutionary
rates might serve as an indicator for determining whether the identified exons were alternatively spliced. This study
not only presents an effective in silico strategy for the improvement of plant annotations, but also provides further insights into the role of AS events in the evolution and domestication of crop plants. ExonFinder and the novel exons/ASVs identified are publicly accessible at http://exonfinder.sourceforge.net/.
關鍵字Crop plants;Alternative splicing;Plant transcriptome evolution;Evolutionary rate;Comparative genomics;Bioinformatics
語言英文(美國)
ISSN1471-2229
期刊性質國外
收錄於SCI;
產學合作
通訊作者Trees-Juen Chuang
審稿制度
國別美國
公開徵稿
出版型式,電子版
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