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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.


The unigenes showed homology with sequences in the Nr, Swiss-Prot, COG (Clusters of Orthologous Groups of proteins) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases.
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ijms-16-12855-f002: The unigenes showed homology with sequences in the Nr, Swiss-Prot, COG (Clusters of Orthologous Groups of proteins) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases.

Mentions: We searched the 52,169 unigenes against the protein databases. 36,662 unigenes (70.27%) were annotated, 15,507 unigenes cannot be aligned to any database remained without annotation. In the annotated unigenes, 36,608 (70.17%), 27,353 (52.43%), 14,415 (27.63%) and 10,002 (19.17%) unigenes showed homology with sequences in the Nr (Non redundant), Swiss-Prot, COG (Clusters of Orthologous Groups of proteins), and KEGG databases, respectively (Figure 2). In the annotated unigenes in the Nr database, most samples (13,776 unigenes) matched the “theobroma cacao” proteins, followed by “vitis vinifera” (8474 unigenes), “fragaria vesca subsp. Vesca” (2058 unigenes), “cucumis sativus” (1887 unigenes) and “oryza sativa Japonica Group” (1317 unigenes). In the 15,507 un-annotated unigenes, 835 unigenes were established nucleotide sequence direction (5′-3′) and amino sequence of the predicted coding region by using ESTScan [21].


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 unigenes showed homology with sequences in the Nr, Swiss-Prot, COG (Clusters of Orthologous Groups of proteins) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-12855-f002: The unigenes showed homology with sequences in the Nr, Swiss-Prot, COG (Clusters of Orthologous Groups of proteins) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases.
Mentions: We searched the 52,169 unigenes against the protein databases. 36,662 unigenes (70.27%) were annotated, 15,507 unigenes cannot be aligned to any database remained without annotation. In the annotated unigenes, 36,608 (70.17%), 27,353 (52.43%), 14,415 (27.63%) and 10,002 (19.17%) unigenes showed homology with sequences in the Nr (Non redundant), Swiss-Prot, COG (Clusters of Orthologous Groups of proteins), and KEGG databases, respectively (Figure 2). In the annotated unigenes in the Nr database, most samples (13,776 unigenes) matched the “theobroma cacao” proteins, followed by “vitis vinifera” (8474 unigenes), “fragaria vesca subsp. Vesca” (2058 unigenes), “cucumis sativus” (1887 unigenes) and “oryza sativa Japonica Group” (1317 unigenes). In the 15,507 un-annotated unigenes, 835 unigenes were established nucleotide sequence direction (5′-3′) and amino sequence of the predicted coding region by using ESTScan [21].

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.