Dataset Information

De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis.

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.

SUBMITTER: Zhou XJ

PROVIDER: S-EPMC4490475 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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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 Xiao-Jun XJ Wang Yue-Yue YY Xu Ya-Nan YN Yan Rong-Shan RS Zhao Peng P Liu Wen-Zhe WZ

International journal of molecular sciences 20150605 6

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 a ...[more]

PMID: 26057749

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Project description:Background and aimsTapiscia sinensis (Tapisciaceae) is a functional androdioecious species with both male and hermaphroditic individuals, and fruit ripening overlaps with flowering in the hermaphroditic individuals. Pollen vitality was lower in the hermaphrodites than in the males. Anther development requires nutrients, and carbohydrates are the basic nutrients; abnormal carbohydrate metabolism will result in pollen abortion. The aim of this research was to gain insight into the relationship between carbohydrate metabolism and the weakening of the male function of hermaphroditic flowers in T. sinensis.MethodsObservation of morphology and microscopic and sub-microscopic structures was carried out. Sugar measurements and quantitative real-time PCR analysis were performed for the genes related to sugar metabolism and transport in the development of anthers in both males and hermaphrodites. The expression pattern of Cell wall invertase 2 (CWI2) and Sucrose transporter 2 (ST2) was explored by in situ hybridization.Key resultsAt the vacuolate microspore (VM) stage, polysaccharides accumulated in the connective tissue of the hermaphroditic anthers, and the levels of total soluble sugar, sucrose and starch in the hermaphroditic anthers were significantly lower than in the male anthers. Most of the hermaphroditic pollen grains were empty, with degradation of the cytoplasm, absence of an intine layer and defective exines. There was a significant differential expression between male and hermaphroditic flowers of several key genes that are involved in sugar metabolism, transport and intine development. CWI2 and ST2 were expressed in the tapetum and microspores. The expression of CWI2 was significantly lower in hermaphrodites than in the males.ConclusionsFruit ripening overlaps with flowering, leading to a severe reproductive burden on the hermaphroditic individuals. The hermaphroditic flowers regulating carbohydrate metabolism and transport to affect resources are biased towards the female function to ensure reproduction, causing a deficiency in resources for the development of pollen; thus, the pollen viability is lower. This makes it easier for males to invade the hermaphroditic population and form a functional androdioecious breeding system.

Project description:Background and aimsThe phylogeography of plant species in sub-tropical China remains largely unclear. This study used Tapiscia sinensis, an endemic and endangered tree species widely but disjunctly distributed in sub-tropical China, as a model to reveal the patterns of genetic diversity and phylogeographical history of Tertiary relict plant species in this region. The implications of the results are discussed in relation to its conservation management.MethodsSamples were taken from 24 populations covering the natural geographical distribution of T. sinensis. Genetic structure was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). Phylogenetic relationships among haplotypes were constructed with maximum parsimony and haplotype network methods. Historical population expansion events were tested with pairwise mismatch distribution analysis and neutrality tests. Species potential range was deduced by ecological niche modelling (ENM).Key resultsA low level of genetic diversity was detected at the population level. A high level of genetic differentiation and a significant phylogeographical structure were revealed. The mean divergence time of the haplotypes was approx. 1·33 million years ago. Recent range expansion in this species is suggested by a star-like haplotype network and by the results from the mismatch distribution analysis and neutrality tests.ConclusionsClimatic oscillations during the Pleistocene have had pronounced effects on the extant distribution of Tapiscia relative to the Last Glacial Maximum (LGM). Spatial patterns of molecular variation and ENM suggest that T. sinensis may have retreated in south-western and central China and colonized eastern China prior to the LGM. Multiple montane refugia for T. sinense existing during the LGM are inferred in central and western China. The populations adjacent to or within these refugia of T. sinense should be given high priority in the development of conservation policies and management strategies for this endangered species.

Dataset Information

De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis.

Publications

De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis.

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