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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 COG classifications.
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ijms-16-12855-f004: Unigenes were assigned to COG classifications.

Mentions: Furthermore, all unigenes were subjected to a search against the Clusters of Orthologous Groups of proteins (COG) database for functional prediction and classification, and 27,672 sequences were assigned to COG classifications (Figure 4). Of the 25 COG categories, the cluster for “general function prediction only” (4902, 17.71%) was the largest group, followed by “transcription” (2704, 9.77%), “replication, recombination and repair” (2451, 8.86%), “signal transduction mechanisms” (1991, 7.19%) and “posttranslational modification, protein turnover, chaperones” (1955, 7.06%). Additionally, 1605 unigenes were assigned to “carbohydrate transport and metabolism” group, which include unigene0027247 that was annotated as “Glycogen synthase”, unigene0027034 annotated as “6-phosphofructokinase”, and unigene0026072 annotated as “Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase”; 743 unigenes were assigned to “energy production and conversion”, which include unigene0032350 annotated as “Fumarase”, unigene0032531 annotated as “Glycerol-3-phosphate dehydrogenase”, unigene0038751 annotated as “Nicotinamide-adenine dinucleotid dehydrogenase, Flavin adenine dinucleotide containing subunit”, and unigene0039174 annotated as “Phosphoenolpyruvate carboxykinase (ATP)”. These key genes laid the foundation for the study of T. sinensis.


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 COG classifications.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-12855-f004: Unigenes were assigned to COG classifications.
Mentions: Furthermore, all unigenes were subjected to a search against the Clusters of Orthologous Groups of proteins (COG) database for functional prediction and classification, and 27,672 sequences were assigned to COG classifications (Figure 4). Of the 25 COG categories, the cluster for “general function prediction only” (4902, 17.71%) was the largest group, followed by “transcription” (2704, 9.77%), “replication, recombination and repair” (2451, 8.86%), “signal transduction mechanisms” (1991, 7.19%) and “posttranslational modification, protein turnover, chaperones” (1955, 7.06%). Additionally, 1605 unigenes were assigned to “carbohydrate transport and metabolism” group, which include unigene0027247 that was annotated as “Glycogen synthase”, unigene0027034 annotated as “6-phosphofructokinase”, and unigene0026072 annotated as “Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase”; 743 unigenes were assigned to “energy production and conversion”, which include unigene0032350 annotated as “Fumarase”, unigene0032531 annotated as “Glycerol-3-phosphate dehydrogenase”, unigene0038751 annotated as “Nicotinamide-adenine dinucleotid dehydrogenase, Flavin adenine dinucleotide containing subunit”, and unigene0039174 annotated as “Phosphoenolpyruvate carboxykinase (ATP)”. These key genes laid the foundation for the study of T. sinensis.

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.