De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)

doi:10.1371/journal.pone.0082674

	De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)
	Zhang, Jian ; Franks, Robert G.; Liu, Xiang ; Kang, Ming ; Keebler, Jonathan E. M.; Schaff, Jennifer E.; Huang, Hong-Wen ; Xiang, Qiu-Yun (Jenny)
	2013
发表期刊	PLOS ONE
ISSN	1932-6203
卷号	8 期号:12
摘要	Background: Transcriptome sequencing analysis is a powerful tool in molecular genetics and evolutionary biology. Here we report the results of de novo 454 sequencing, characterization, and comparison of inflorescence transcriptomes of two closely related dogwood species, Cornus canadensis and C. florida (Cornaceae). Our goals were to build a preliminary source of genome sequence data, and to identify genes potentially expressed differentially between the inflorescence transcriptomes for these important horticultural species. Results: The sequencing of cDNAs from inflorescence buds of C. canadensis (cc) and C. florida (cf), and normalized cDNAs from leaves of C. canadensis resulted in 251799 (ccBud), 96245 (ccLeaf) and 114648 (cfBud) raw reads, respectively. The de novo assembly of the high quality (HQ) reads resulted in 36088, 17802 and 21210 unigenes for ccBud, ccLeaf and cfBud. A reference transcriptome for C. canadensis was built by assembling HQ reads of ccBud and ccLeaf, containing 40884 unigenes. Reference mapping and comparative analyses found 10926 sequences were putatively specific to ccBud, and 6979 putatively specific to cfBud. Putative differentially expressed genes between ccBud and cfBud that are related to flower development and/or stress response were identified among 7718 shared sequences by ccBud and cfBud. Bidirectional BLAST found 87 (41.83% of 208) of Arabidopsis genes related to inflorescence development had putative orthologs in the dogwood transcriptomes. Comparisons of the shared sequences by ccBud and cfBud yielded 65931 high quality SNPs between two species. The twenty unigenes with the most SNPs are listed as potential genetic markers for evolutionary studies. Conclusions: The data provide an important, although preliminary, information platform for functional genomics and evolutionary developmental biology in Cornus. The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and/or disease resistance in dogwoods for future analyses. Results of the study also provide markers useful for dogwood phylogenomic studies.
学科领域	Multidisciplinary Sciences
DOI	10.1371/journal.pone.0082674
收录类别	SCI
语种	英语
WOS关键词	PHYLOGENETIC-RELATIONSHIPS ; FLORAL TRANSCRIPTOME ; ARABIDOPSIS-THALIANA ; FLOWER DEVELOPMENT ; GENE-EXPRESSION ; S. L. ; EVOLUTION ; LEAFY ; ELONGATION ; DOGWOOD
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000329117900013
出版者	PUBLIC LIBRARY SCIENCE
文献子类	Article
出版地	SAN FRANCISCO
资助机构	National Nature Science Foundation of the United States ; CAS/SAFEA International Partnership Program for Creative Research Teams from China ; National Nature Science Foundation of China(National Natural Science Foundation of China (NSFC))
作者邮箱	Kang, Ming/M-2368-2019 ; Xiang, Jenny/ADU-6318-2022
作品OA属性	Green Accepted, Green Published, Green Submitted, gold
引用统计	被引频次：11[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/27845
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 2.Zhang, Jian; Franks, Robert G.; Liu, Xiang; Xiang, Qiu-Yun (Jenny)] N Carolina State Univ, Dept Plant & Microbial Biol, Raleigh, NC 27695 USA 3.Chinese Acad Sci, CAS Key Lab Plant Resource Conservat & Sustainabl, South China Bot Garden, Guangzhou, Guangdong, Peoples R China 4.Keebler, Jonathan E. M.; Schaff, Jennifer E.] N Carolina State Univ, Bioinformat Analyst & Consultant Genom Sci Lab, Raleigh, NC 27695 USA
推荐引用方式 GB/T 7714	Zhang, Jian,Franks, Robert G.,Liu, Xiang,et al. De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)[J]. PLOS ONE,2013,8(12).
APA	Zhang, Jian.,Franks, Robert G..,Liu, Xiang.,Kang, Ming.,Keebler, Jonathan E. M..,...&Xiang, Qiu-Yun .(2013).De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae).PLOS ONE,8(12).
MLA	Zhang, Jian,et al."De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)".PLOS ONE 8.12(2013).

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