Zhang, Jian , Kang, Ming , Liu, Xiang , Franks, Robert , Xiang, Qiuyun (Jenny) .
Comparative 454 sequencing of leaf and inflorescence transcriptomes in Cornus canadensisand C. florida - data for identifying candidate genes and developing genetic markers.
Comparative transcriptome sequencing is a useful tool to search for candidate genes contributing to phenotypic differences and to develop genetic markers for evolutionary studies. Using 454 GS-FLX Titanium system, we performed the de novo transcriptome sequencing for two species of Cornus,C. canadensis (cc) and C. florida (cf), which display different inflorescence architectures, to aid identification of candidate genes controlling inflorescence architecture divergence and to develop markers for genetic analysis. As an initial step, we ran half a Titanium plate for one cDNA library from leaves of C. canadensis and two cDNA libraries from inflorescence buds of these two species. A total of 96245 (ccLeaf), 251799 (ccBud) and 114648 (cfBud) raw reads were obtained from the sequencing. Further trimming of the raw reads resulted in 85703, 251679 and114605 high quality (HQ) reads for the three transcriptomes, respectively. DeNovo assembly of the data using the CLC Bio Genomics Workbench resulted in 19110 contigs and 22011 singletons, in total 41121 unique sequences for C. canadensis transcriptome combining the ccLeaf and ccBud. Comparison of the ccTranscriptome with the ccLeaf, ccBudand cfBud HQ reads using the CLC Bio Genomics Workbench Reference Alignment found 14576, 34406 and 8686 unique sequences of ccTranscriptome aligned with ccLeaf,ccBud and cfBud reads, respectively. Among these unique sequences, 11566(ccLeaf), 23065 (ccBud) and 8345 (cfBud) were annotated based on blast search against the NCBI non-redundant (NR) protein database and the remainders are unknown proteins. The unaligned cfBud HQ reads were assembled into 14324 unique sequences and 7109 sequences have blast hits. After preliminary comparison analysis between ccBud and cfBud transcriptomes, 12205 sequences were found to be specific to ccBud, 4594 sequences were found to be specific to cfBud. There are 10860 common sequences between ccBud and cfBud including 7776 aligned ones and 3084 unaligned ones. Comparisons of the aligned common sequences between the ccBud and cfBud transcriptomes yielded 64496 SNPs. The data provide an initial important information platform for functional genomics and evolutionary developmental genetics in Cornus, in addition to developing markers for genetic mapping and phylogenetic and population geneticstudies.
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1 - North Carolina State University, Plant Biology, Gardner Hall 2115, Campus Box 7612, Raleigh, NC, 27695, USA
2 - South China Botanical Garden, Plant Conservation Genetics And Evolutionary Genetics, Xingke Road 723, Tianhe District, Guangzhou, Guangdong Province, 510650, P.R. China
3 - North Carolina State University, Plant Biology, Raleigh, NC, 27695, USA
4 - North Carolina State University, Genetics, Raleigh, NC, 27695, USA
5 - North Carolina State University, Plant Biology, Gardner Hall 2115, Raleigh, NC, 27695, USA
Presentation Type: Oral Paper:Papers for Sections
Location: Lindell C/Chase Park Plaza
Date: Wednesday, July 13th, 2011
Time: 10:30 AM