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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 results of the SSR-PCR that produced clear bands. M refers to DNA markers pBR322 DNA/MspI. Numbers 1 to 24 represent twenty-four individuals of T. sinensis. The products of primer TS061 are single bands without polymorphism, while those of TS062 are clear polymorphic bands.
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ijms-16-12855-f007: The results of the SSR-PCR that produced clear bands. M refers to DNA markers pBR322 DNA/MspI. Numbers 1 to 24 represent twenty-four individuals of T. sinensis. The products of primer TS061 are single bands without polymorphism, while those of TS062 are clear polymorphic bands.

Mentions: A suit of 150 pairs of primers was synthetized and assessed in the 24 T. sinensis individuals. The result shows that, 117 pairs (78%) successfully amplified target fragments for SSR-PCR (Simple Sequence Repeat Polymerase Chain Reaction), including 68 pairs that were able to produce clear polymorphic bands (45.5%) and 49 pairs of primers that were able to produce single bands without polymorphism. The results of the SSR-PCR amplification are shown as examples in Figure 7. Of 68 polymorphic SSR markers (N = 24), the detected number of alleles per locus ranged from 2 to 6 with an average of 3.24 alleles per locus, and the observed and expected heterozygosity varied from 0.000 to 1.000 and from 0.042 to 0.782, respectively. Polymorphic information content varied 0.040 to 0.729. Details of the 68 polymorphic SSR markers from T. sinensis are shown in Table S5. In addition, the Bayesian clustering analysis of the 51 individuals was constructed based on six polymorphic SSR markers, with the characteristics shown in Table 3. The analysis indicated that we developed SSR markers can differentiate population genetic differences of different geographic locations, dividing the 51 individuals into two main groups of 29 (fromWuling Mountains) and 22 (from Qinling Mountains) (Figure 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 results of the SSR-PCR that produced clear bands. M refers to DNA markers pBR322 DNA/MspI. Numbers 1 to 24 represent twenty-four individuals of T. sinensis. The products of primer TS061 are single bands without polymorphism, while those of TS062 are clear polymorphic bands.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-12855-f007: The results of the SSR-PCR that produced clear bands. M refers to DNA markers pBR322 DNA/MspI. Numbers 1 to 24 represent twenty-four individuals of T. sinensis. The products of primer TS061 are single bands without polymorphism, while those of TS062 are clear polymorphic bands.
Mentions: A suit of 150 pairs of primers was synthetized and assessed in the 24 T. sinensis individuals. The result shows that, 117 pairs (78%) successfully amplified target fragments for SSR-PCR (Simple Sequence Repeat Polymerase Chain Reaction), including 68 pairs that were able to produce clear polymorphic bands (45.5%) and 49 pairs of primers that were able to produce single bands without polymorphism. The results of the SSR-PCR amplification are shown as examples in Figure 7. Of 68 polymorphic SSR markers (N = 24), the detected number of alleles per locus ranged from 2 to 6 with an average of 3.24 alleles per locus, and the observed and expected heterozygosity varied from 0.000 to 1.000 and from 0.042 to 0.782, respectively. Polymorphic information content varied 0.040 to 0.729. Details of the 68 polymorphic SSR markers from T. sinensis are shown in Table S5. In addition, the Bayesian clustering analysis of the 51 individuals was constructed based on six polymorphic SSR markers, with the characteristics shown in Table 3. The analysis indicated that we developed SSR markers can differentiate population genetic differences of different geographic locations, dividing the 51 individuals into two main groups of 29 (fromWuling Mountains) and 22 (from Qinling Mountains) (Figure 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.