Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae

doi:10.1016/j.pld.2018.11.006

Plant Diversity ›› 2018, Vol. 40 ›› Issue (06): 253-264.DOI: 10.1016/j.pld.2018.11.006

• • 下一篇

Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae

Ruisen Lu^a, Wuqin Xu^a, Qixiang Lu^a, Pan Li^a, Jocelyn Losh^a, Faiza Hina^a, Enxiang Li^b, Yingxiong Qiu^a

a Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China;
b College of Life Sciences, Nanchang University, Nanchang, 330031, China

收稿日期:2018-10-29 修回日期:2018-11-27 出版日期:2018-12-25 发布日期:2019-01-30
通讯作者: Yingxiong Qiu
基金资助:
This research was supported by the National Natural Science Foundation of China (Grant Nos. 31370241, 31570214), the International Cooperation and Exchange of the National Natural Science Foundation of China (Grant Nos. 31511140095, 31561143015), and National Science Foundation of China (grant no. 30960027).

Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae

Ruisen Lu^a, Wuqin Xu^a, Qixiang Lu^a, Pan Li^a, Jocelyn Losh^a, Faiza Hina^a, Enxiang Li^b, Yingxiong Qiu^a

a Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China;
b College of Life Sciences, Nanchang University, Nanchang, 330031, China

Received:2018-10-29 Revised:2018-11-27 Online:2018-12-25 Published:2019-01-30
Contact: Yingxiong Qiu
Supported by:
This research was supported by the National Natural Science Foundation of China (Grant Nos. 31370241, 31570214), the International Cooperation and Exchange of the National Natural Science Foundation of China (Grant Nos. 31511140095, 31561143015), and National Science Foundation of China (grant no. 30960027).

摘要/Abstract

摘要： The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA) eEastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study, we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala (ChFlower), flowers of C. japonica (CjFlower), and leaves of C. japonica (CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes (SCNGs) and 21,460 expression sequence tags-simple sequence repeats (ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade (SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.

关键词: Croomia, Transcriptome, SCNGs, EST-SSRs, Flower symmetry, CYC/TB1

Abstract: The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA) eEastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study, we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala (ChFlower), flowers of C. japonica (CjFlower), and leaves of C. japonica (CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes (SCNGs) and 21,460 expression sequence tags-simple sequence repeats (ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade (SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.

Key words: Croomia, Transcriptome, SCNGs, EST-SSRs, Flower symmetry, CYC/TB1

Ruisen Lu, Wuqin Xu, Qixiang Lu, Pan Li, Jocelyn Losh, Faiza Hina, Enxiang Li, Yingxiong Qiu. Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae[J]. Plant Diversity, 2018, 40(06): 253-264.

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Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae

Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae

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