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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.


Unigenes were assigned to Gene Ontology.
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ijms-16-12855-f003: Unigenes were assigned to Gene Ontology.

Mentions: Based on Nr annotation, 15,690 unigenes were assigned gene ontology (GO) with 83,842 functional terms. In total, 36,497 terms were assigned to the biological processes group, 30,925 terms were assigned to the cellular components group and 16,420 terms were assigned to the molecular functions group (Figure 3). Of the biological process category, metabolic process (8526, 23.36%) and cellular process (8406, 23.03%) were the most frequent terms used. Genes related to response to stimulus (3476 unigenes), anatomical structure formation (270 unigenes), and rhythmic process (105 unigenes) were also identified in this group. In the class of “response to stimulus”, unigene0008775, unigene0005239, and unigene0049385, that were respectively annotated as “Pedicel, carpel, stamen, petal differentiation and expansion stage, group 2-like protein”, “Phytochrome and flowering time regulatory protein isoform 2”, and “Protein early flowering 3”, which putatively related to response to environmental stimulus were discovered. In the class of “rhythmic process”, unigene0044321 and unigene0017817, which were respectively annotated as “circadian clock-associated FKF1” and “Protein EARLY FLOWERING 4 OS”, were found. In the class of “anatomical structure formation”, unigene0011847 was annotated as “Sex determination protein tasselseed-2-like” was found. These unigenes may involve in flower development, differentiation and flowering time determination in T. sinensis. Regarding the cellular components category, the cell and cell parts were the most prominent terms. In the molecular functions category, catalytic activity (7861 unigenes) and binding (6905 unigenes) were the most highly represented terms.


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)

Unigenes were assigned to Gene Ontology.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-12855-f003: Unigenes were assigned to Gene Ontology.
Mentions: Based on Nr annotation, 15,690 unigenes were assigned gene ontology (GO) with 83,842 functional terms. In total, 36,497 terms were assigned to the biological processes group, 30,925 terms were assigned to the cellular components group and 16,420 terms were assigned to the molecular functions group (Figure 3). Of the biological process category, metabolic process (8526, 23.36%) and cellular process (8406, 23.03%) were the most frequent terms used. Genes related to response to stimulus (3476 unigenes), anatomical structure formation (270 unigenes), and rhythmic process (105 unigenes) were also identified in this group. In the class of “response to stimulus”, unigene0008775, unigene0005239, and unigene0049385, that were respectively annotated as “Pedicel, carpel, stamen, petal differentiation and expansion stage, group 2-like protein”, “Phytochrome and flowering time regulatory protein isoform 2”, and “Protein early flowering 3”, which putatively related to response to environmental stimulus were discovered. In the class of “rhythmic process”, unigene0044321 and unigene0017817, which were respectively annotated as “circadian clock-associated FKF1” and “Protein EARLY FLOWERING 4 OS”, were found. In the class of “anatomical structure formation”, unigene0011847 was annotated as “Sex determination protein tasselseed-2-like” was found. These unigenes may involve in flower development, differentiation and flowering time determination in T. sinensis. Regarding the cellular components category, the cell and cell parts were the most prominent terms. In the molecular functions category, catalytic activity (7861 unigenes) and binding (6905 unigenes) were the most highly represented terms.

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.