tailieunhanh - báo cáo khoa học: " Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing"

Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành y học dành cho các bạn tham khảo đề tài: Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing | Kalavacharla et al. BMC Plant Biology 2011 11 135 http 1471 -2229 11 135 BMC Plant Biology RESEARCH ARTICLE Open Access Identification and analysis of common bean Phaseolus vulgaris L. transcriptomes by massively parallel pyrosequencing Venu Kalavacharla1 4 Zhanji Liu1 Blake C Meyers2 Jyothi Thimmapuram3 and Kalpalatha Melmaiee1 Abstract Background Common bean Phaseolus vulgaris is the most important food legume in the world. Although this crop is very important to both the developed and developing world as a means of dietary protein supply resources available in common bean are limited. Global transcriptome analysis is important to better understand gene expression genetic variation and gene structure annotation in addition to other important features. However the number and description of common bean sequences are very limited which greatly inhibits genome and transcriptome research. Here we used 454 pyrosequencing to obtain a substantial transcriptome dataset for common bean. Results We obtained 1 692 972 reads with an average read length of 207 nucleotides nt . These reads were assembled into 59 295 unigenes including 39 572 contigs and 19 723 singletons in addition to 35 328 singletons less than 100 bp. Comparing the unigenes to common bean ESTs deposited in GenBank we found that or 31 664 of these unigenes had no matches to this dataset and can be considered as new common bean transcripts. Functional annotation of the unigenes carried out by Gene Ontology assignments from hits to Arabidopsis and soybean indicated coverage of a broad range of GO categories. The common bean unigenes were also compared to the bean bacterial artificial chromosome BAC end sequences and a total of 21 of the unigenes 12 724 including 9 199 contigs and 3 256 singletons match to the 8 823 BAC-end sequences. In addition a large number of simple sequence repeats SSRs and transcription factors were also identified in this study. Conclusions This work provides