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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.


Frequency distribution of SSRs based on the motif types.
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ijms-16-12855-f006: Frequency distribution of SSRs based on the motif types.

Mentions: Of the 10,371 identified SSRs, the most abundant repeat motif types were di-nucleotide repeat motifs (6888, 66.42%), followed by tri-nucleotide (2486, 23.97%), tetra-nucleotide (522, 5.03%), hexa-nucleotide (296, 2.85%) and penta-nucleotide (179, 1.73%) repeat motifs. The frequencies of the SSRs with different numbers of tandem repeats are summarized in Table 2. SSRs with six tandem repeats were the most common (2797, 26.97%), followed by seven tandem repeats (1831, 17.66%), five tandem repeats (1447, 13.95%), and nine tandem repeats (1256, 12.11%). The most common type of SSR motif was AG/CT which accounted for 54.5%, followed by AT/AT and AAG/CTT (6.5%), AC/GT (5.2%), ACC/GGT (4.1%) (Figure 6). This result is consistent with previous research showing di-nucleotide repeats to be the most abundant type, followed by were tri-nucleotide repeats [17,28,29]. The most abundant di-nucleotide motifs AG/CT and tri-nucleotide motifs AAG/CTT were also coincident with earlier research [17].


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)

Frequency distribution of SSRs based on the motif types.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-12855-f006: Frequency distribution of SSRs based on the motif types.
Mentions: Of the 10,371 identified SSRs, the most abundant repeat motif types were di-nucleotide repeat motifs (6888, 66.42%), followed by tri-nucleotide (2486, 23.97%), tetra-nucleotide (522, 5.03%), hexa-nucleotide (296, 2.85%) and penta-nucleotide (179, 1.73%) repeat motifs. The frequencies of the SSRs with different numbers of tandem repeats are summarized in Table 2. SSRs with six tandem repeats were the most common (2797, 26.97%), followed by seven tandem repeats (1831, 17.66%), five tandem repeats (1447, 13.95%), and nine tandem repeats (1256, 12.11%). The most common type of SSR motif was AG/CT which accounted for 54.5%, followed by AT/AT and AAG/CTT (6.5%), AC/GT (5.2%), ACC/GGT (4.1%) (Figure 6). This result is consistent with previous research showing di-nucleotide repeats to be the most abundant type, followed by were tri-nucleotide repeats [17,28,29]. The most abundant di-nucleotide motifs AG/CT and tri-nucleotide motifs AAG/CTT were also coincident with earlier research [17].

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.