Comparative transcriptomics identifies patterns of selection in roses
Li, Shubin1,5; Zhong, Micai2,3; Dong, Xue2; Jiang, Xiaodong2,3; Xu, Yuxing3; Sun, Yibo2,3; Cheng, Fang2; Li, De-zhu4; Tang, Kaixue5; Wang, Siqing1; Dai, Silan1; Hu, Jin-Yong2
2018-12-22
发表期刊BMC PLANT BIOLOGY
ISSN1471-2229
卷号18页码:12
摘要BackgroundRoses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge.ResultsHere, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis Old Blush' (OB) and R. wichuriana Basye's Thornless' (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000bp. Two roses shared about 10,073 transcripts (N50=2282bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes.ConclusionsWe expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding.
关键词Rosa sp Selection pattern Comparative transcriptomics Rosaceae-common Rosa-specific
资助信息National Natural Science Foundation of China; CAS Pioneer Hundred Talents Program; Yunnan Applied Basic Research Projects; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia (CAS); Yunnan Recruitment Program of Experts in Science
收录类别SCI
语种英语
资助项目National Natural Science Foundation of China[31660583] ; National Natural Science Foundation of China[31570311] ; National Natural Science Foundation of China[31501034] ; CAS Pioneer Hundred Talents Program[292015312D11035] ; Yunnan Applied Basic Research Projects[2016FB040] ; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia (CAS) ; Yunnan Recruitment Program of Experts in Science
引用统计
文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/63405
专题中国科学院东亚植物多样性与生物地理学重点实验室
通讯作者Wang, Siqing; Dai, Silan; Hu, Jin-Yong
作者单位1.Beijing Forestry Univ, Beijing Key Lab Ornamental Plants Germplasm Innov, Natl Engn Res Ctr Floriculture,Key Lab Genet & Br, Beijing Lab Urban & Rural Ecol Environm,Minist Ed, 35 East Qinghua Rd, Beijing 100083, Peoples R China
2.Chinese Acad Sci, Kunming Inst Bot, Grp Plant Mol Genet & Adaptat, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China
5.Yunnan Agr Acad Sci, Flower Res Inst, Kunming 650231, Yunnan, Peoples R China
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GB/T 7714
Li, Shubin,Zhong, Micai,Dong, Xue,et al. Comparative transcriptomics identifies patterns of selection in roses[J]. BMC PLANT BIOLOGY,2018,18:12.
APA Li, Shubin.,Zhong, Micai.,Dong, Xue.,Jiang, Xiaodong.,Xu, Yuxing.,...&Hu, Jin-Yong.(2018).Comparative transcriptomics identifies patterns of selection in roses.BMC PLANT BIOLOGY,18,12.
MLA Li, Shubin,et al."Comparative transcriptomics identifies patterns of selection in roses".BMC PLANT BIOLOGY 18(2018):12.
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