De novo sequencing and characterization of seed transcriptome of the tree legume Millettia pinnata for gene discovery and SSR marker development

Huang, Jiaoying; Guo, Xiaohuan; Hao, Xuehong; Zhang, Wan–Ke; Chen, Shouyi; Huang, Rongfeng; Gresshoff, Peter M.; Zheng, Youliang

doi:10.1007/s11032-016-0503-x

Cited by 19 publications

(30 citation statements)

References 67 publications

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“…Further, Pavithra et al 20 , reported the FA profiles of seeds at different developmental stages of Pongamia. Very recently, parallel to the current study, Huang et al 21 , reported the seed transcriptome of Pongamia which provided valuable information about lipid biosynthetic genes and SSR markers. But the whole transcriptome information, together with gene expression patterns of lipid biosynthetic enzymes during seed development and flowering pathway genes, are far from being characterised in Pongamia.…”

supporting

confidence: 59%

Unravelling molecular mechanisms from floral initiation to lipid biosynthesis in a promising biofuel tree species, Pongamia pinnata using transcriptome analysis

Sreeharsha

Mudalkar

Singha

et al. 2016

Sci Rep

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Pongamia pinnata (L.) (Fabaceae) is a promising biofuel tree species which is underexploited in the areas of both fundamental and applied research, due to the lack of information either on transcriptome or genomic data. To investigate the possible metabolic pathways, we performed whole transcriptome analysis of Pongamia through Illumina NextSeq platform and generated 2.8 GB of paired end sequence reads. The de novo assembly of raw reads generated 40,000 contigs and 35,000 transcripts, representing leaf, flower and seed unigenes. Spatial and temporal expression profiles of photoperiod and floral homeotic genes in Pongamia, identified GIGANTEA (GI) - CONSTANS (CO) - FLOWERING LOCUS T (FT) as active signal cascade for floral initiation. Four prominent stages of seed development were selected in a high yielding Pongamia accession (TOIL 1) to follow the temporal expression patterns of key fatty acid biosynthetic genes involved in lipid biosynthesis and accumulation. Our results provide insights into an array of molecular events from flowering to seed maturity in Pongamia which will provide substantial basis for modulation of fatty acid composition and enhancing oil yields which should serve as a potential feedstock for biofuel production.

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supporting

confidence: 59%

Unravelling molecular mechanisms from floral initiation to lipid biosynthesis in a promising biofuel tree species, Pongamia pinnata using transcriptome analysis

Sreeharsha

Mudalkar

Singha

et al. 2016

Sci Rep

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“…This may be because they all belong to the family Fabaceae and share a high level of genomes sequence similarity. Similar observations have been reported on other transcriptome studies [41,42]. It is thought that KEGG provides a basic platform for systematic analysis of gene function in terms of gene product networks [43].…”

Section: Transcriptome Sequencing De Novo Assembly and Annotation Fsupporting

confidence: 83%

“…Therefore, the development of a known polymorphic SSR marker database for D. odorifera is of great use for diversity studies and breeding programs, as well as being transferable to closely Dalbergia species. In the present study, we identified 35,774 putative SSRs from the transcriptome dataset, which is of great differences in numbers, dominant repeats, and motif types reported from other legume species using Illumina sequencing [41,42,44]. This may be attributable to inconsistencies in genome structure or composition, dataset size, search method, or criteria.…”

Section: Ssr Prediction Validation and Applicationmentioning

confidence: 94%

De Novo Transcriptome Analysis of Dalbergia odorifera T. Chen (Fabaceae) and Transferability of SSR Markers Developed from the Transcriptome

Liu

Hong

Yang

et al. 2019

Forests

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Dalbergia odorifera T. Chen (Fabaceae), indigenous to Hainan Island, is a precious rosewood (Hainan hualimu) in China. However, only limited genomic information is available which has resulted in a lack of molecular markers, limiting the development and utilization of the germplasm resources. In this study, we aim to enrich genomic information of D. odorifera, and develop a series of transferable simple sequence repeat (SSR) markers for Dalbergia species. Therefore, we performed transcriptome sequencing for D. odorifera by pooling leaf tissues from three trees. A dataset of 138,516,418 reads was identified and assembled into 115,292 unigenes. Moreover, 35,774 simple sequence repeats (SSRs) were identified as potential SSR markers. A set of 19 SSR markers was successfully transferred across species of Dalbergia odorifera T. Chen, Dalbergia tonkinensis Prain, and Dalbergia cochinchinensis Pierre ex Laness. In total, 112 alleles (3-13 alleles/locus) were presented among 60 Dalbergia trees, and polymorphic information content ranged from 0.38 to 0.75. The mean observed and mean expected heterozygosity was 0.34 and 0.40 in D. odorifera, 0.27 and 0.32 in D. tonkinensis, and 0.29 and 0.33 in D. cochinchinensis, respectively. The cluster analysis classified these 60 trees into three major groups according to the three Dalbergia species based on the genetic similarity coefficients, indicating these newly developed transferable markers can be used to explore the relationships among Dalbergia species and assist genetic research. All these unigenes and SSR markers will be useful for breeding programs in the future.

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“…In this study, we have identified 35,774 putative SSR loci from the leaf transcriptome dataset, substantially more than those reported for other legume species such as 5956 in Prosopis alba Griseb. [36], 5710 in Millettia pinnata (L.) Panigrahi [18], and 7493 in Mucuna pruriens (L.) DC. [37].…”

Section: Development Of Ssr Marker For D Odoriferamentioning

confidence: 99%

“…The use of microsatellite markers to analyze the genetic diversity of D. odorifera can provide an invaluable means for conservation and protection of this endangered species. Moreover, the developments of SSR markers have been innovated by next-generation sequencing based on transcriptomes (RNA-seq), especially for species without a reference genome [17][18][19]. This approach has been applied for SSR identification, development, and association studies in many tree species [20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

Liu

Hong

et al. 2019

Forests

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Dalbergia odorifera T. Chen (Fabaceae) is a semi-deciduous tree species indigenous to Hainan Island in China. Due to its precious heartwood “Hualimu (Chinese)” and Chinese medicinal components “Jiangxiang”, D. odorifera is seriously threatened of long-term overexploitation and has been listed on the IUCN (International Union for Conservation of Nature’s) red list since 1998. Therefore, the elucidation of its genetic diversity is imperative for conservation and breeding purposes. In this study, we evaluated the genetic diversity of 42 wild D. odorifera trees from seven populations covering its whole native distribution. In total, 19 SSR (simple sequence repeat) markers harbored 54 alleles across the 42 samples, and the medium genetic diversity level was inferred by Nei’s gene diversity (0.36), observed (0.28) and expected heterozygosity (0.37). Among the seven wild populations, the expected heterozygosity (He) varied from 0.31 (HNQS) to 0.40 (HNCJ). The analysis of molecular variance (AMOVA) showed that only 3% genetic variation existed among populations. Moderate population differentiations among the investigated populations were indicated by pairwise Fst (0.042–0.115). Structure analysis suggested two clusters for the 42 samples. Moreover, the seven populations were clearly distinguished into two clusters from both the principal coordinate analysis (PCoA) and neighbor-joining (NJ) analysis. Populations from Haikou city (HNHK), Baisha autonomous county (HNBS), Ledong autonomous county (HNLD), and Dongfang city (HNDF) comprised cluster I, while cluster II comprised the populations from Wenchang city and Sansha city (HNQS), Changjiang autonomous county (HNCJ), and Wuzhisan city (HNWZS). The findings of this study provide a preliminary genetic basis for the conservation, management, and restoration of this endemic species.

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De novo sequencing and characterization of seed transcriptome of the tree legume Millettia pinnata for gene discovery and SSR marker development

Cited by 19 publications

References 67 publications

Unravelling molecular mechanisms from floral initiation to lipid biosynthesis in a promising biofuel tree species, Pongamia pinnata using transcriptome analysis

Unravelling molecular mechanisms from floral initiation to lipid biosynthesis in a promising biofuel tree species, Pongamia pinnata using transcriptome analysis

De Novo Transcriptome Analysis of Dalbergia odorifera T. Chen (Fabaceae) and Transferability of SSR Markers Developed from the Transcriptome

Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

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