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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.


Length distributions of the unigenes in the assembled transcriptome.
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ijms-16-12855-f001: Length distributions of the unigenes in the assembled transcriptome.

Mentions: In this project, we obtained 97,431,176 clean reads, with a mean length of 100 base pairs (bp). The percentage of Q20, N, and GC was 98.31%, 0.00%, and 45.59%, respectively. The clean reads were de novo assembled using Trinity into 55,711 contigs, with a mean length of 1133 bp and an N50 of 1768 bp. The total number of unigenes was 52,169, with a mean length of 1116 bp and an N50 of 1768 bp. Of all of the unigenes, the majority (30,046 unigenes) were in the range of 201 to 1000 bp, which accounted for 57.59%. 13,723 of the unigenes (26.3%) ranged from 1001 to 2000 bp in length, while 8400 of the unigenes (16.1%) had lengths of more than 2000 bp (Figure 1).


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)

Length distributions of the unigenes in the assembled transcriptome.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-12855-f001: Length distributions of the unigenes in the assembled transcriptome.
Mentions: In this project, we obtained 97,431,176 clean reads, with a mean length of 100 base pairs (bp). The percentage of Q20, N, and GC was 98.31%, 0.00%, and 45.59%, respectively. The clean reads were de novo assembled using Trinity into 55,711 contigs, with a mean length of 1133 bp and an N50 of 1768 bp. The total number of unigenes was 52,169, with a mean length of 1116 bp and an N50 of 1768 bp. Of all of the unigenes, the majority (30,046 unigenes) were in the range of 201 to 1000 bp, which accounted for 57.59%. 13,723 of the unigenes (26.3%) ranged from 1001 to 2000 bp in length, while 8400 of the unigenes (16.1%) had lengths of more than 2000 bp (Figure 1).

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.