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De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis.

Zhou XJ, Wang YY, Xu YN, Yan RS, Zhao P, Liu WZ - Int J Mol Sci (2015)

Bottom Line: Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals.This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis.This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China. plm013@lynu.edu.cn.

ABSTRACT
Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27%) were annotated. A total of 10,002 (19.17%) unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 10,371 simple sequence repeats (SSRs) were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5%) were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.

No MeSH data available.


Related in: MedlinePlus

The male flower and hermaphrodite flower of T. sinensis, (A) and (C) are flowers from male individual; (B) and (D) are bisexual flowers from hermaphrodite individual. Anatomical images (C,D) are the difference between male and hermaphrodite flowers about pistils. Picture (C) shows degenerated pistil, picture (D) shows well-developed pistil.
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ijms-16-12855-f005: The male flower and hermaphrodite flower of T. sinensis, (A) and (C) are flowers from male individual; (B) and (D) are bisexual flowers from hermaphrodite individual. Anatomical images (C,D) are the difference between male and hermaphrodite flowers about pistils. Picture (C) shows degenerated pistil, picture (D) shows well-developed pistil.

Mentions: In the natural population of T. sinensis, male and hermaphrodite individuals coexist. The flowers of male individuals have normal stamens and degenerated pistil, and the hermaphrodite flowers have normal pistil and stamens (Figure 5). In this study we identified several unigenes that are putative homologs of Arabidopsis thaliana, Populus tomentosa, Theobroma cacao and Vitis vinifera genes that are involved in floral development. These include genes that flowering time determination, such as the MADS box genes SOC1 and Flowering Locus C, and perceive or respond to environmental signals, such as FKF1 and ELF4, and Sex determination protein tasselseed-2 (Table S2).


De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis.

Zhou XJ, Wang YY, Xu YN, Yan RS, Zhao P, Liu WZ - Int J Mol Sci (2015)

The male flower and hermaphrodite flower of T. sinensis, (A) and (C) are flowers from male individual; (B) and (D) are bisexual flowers from hermaphrodite individual. Anatomical images (C,D) are the difference between male and hermaphrodite flowers about pistils. Picture (C) shows degenerated pistil, picture (D) shows well-developed pistil.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4490475&req=5

ijms-16-12855-f005: The male flower and hermaphrodite flower of T. sinensis, (A) and (C) are flowers from male individual; (B) and (D) are bisexual flowers from hermaphrodite individual. Anatomical images (C,D) are the difference between male and hermaphrodite flowers about pistils. Picture (C) shows degenerated pistil, picture (D) shows well-developed pistil.
Mentions: In the natural population of T. sinensis, male and hermaphrodite individuals coexist. The flowers of male individuals have normal stamens and degenerated pistil, and the hermaphrodite flowers have normal pistil and stamens (Figure 5). In this study we identified several unigenes that are putative homologs of Arabidopsis thaliana, Populus tomentosa, Theobroma cacao and Vitis vinifera genes that are involved in floral development. These include genes that flowering time determination, such as the MADS box genes SOC1 and Flowering Locus C, and perceive or respond to environmental signals, such as FKF1 and ELF4, and Sex determination protein tasselseed-2 (Table S2).

Bottom Line: Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals.This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis.This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China. plm013@lynu.edu.cn.

ABSTRACT
Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27%) were annotated. A total of 10,002 (19.17%) unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 10,371 simple sequence repeats (SSRs) were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5%) were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.

No MeSH data available.


Related in: MedlinePlus