Characterization of transcriptome and development of novel EST-SSR makers based on next-generation sequencing technology in Neolitsea sericea (Lauraceae) endemic to East Asian land-bridge islands

Chen, Lu-Yao; Cao, Yanan; Ni, Yuan; Nakamura, Kaoru; Wang, Guo‐Ming; Qiu, Ying‐Xiong

doi:10.1007/s11032-015-0379-1

Cited by 46 publications

(65 citation statements)

References 68 publications

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“…The average of one SSR site was found per 6.73 kb, which is similar to that observed for E. sibiricus (1/6.59 kb) [8], lower than Neolitsea sericea Koidz. (1/3.8 kb) and R. latoucheae [13,42], and higher than Paeonia suffruticosa Andr. (1/9.24 kb) [55].…”

Section: Ssr Markers In the Transcriptome Of S Japonicusmentioning

confidence: 82%

De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

Zhang

Jiang

et al. 2018

Forests

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Styrax japonicus sieb. et Zucc. is widely distributed in China with ornamental and medicinal values. However, the transcriptome of S. japonicus has not yet been reported. In this study, we carried out the first transcriptome analysis of S. japonicus and developed a set of expressed sequence tag-simple sequence repeats (EST-SSRs). We obtained 338,570,222 clean reads in total, of which the mean GC content was 41.58%. In total, 136,071 unigenes were obtained having an average length of 611 bp and 71,226 unigenes were favorably annotated in the database. In total, we identified 55,977 potential EST-SSRs from 38,611 unigenes, of which there was 1 SSR per 6.73 kb. The di-nucleotide repeats (40.40%) were the most identified SSRs. One set of 60 primer pairs was randomly selected, and the amplified products in S. japonicus were validated; 28 primer pairs successfully produced clear amplicons. A total of 21 (35%) polymorphic genic SSR markers were identified between two populations. In total, 15 alleles were detected and the average number was 6. The average of observed heterozygosity and expected heterozygosity was 0.614 and 0.552, respectively. The polymorphism information content (PIC) value fluctuated between 0.074 and 0.855, with a mean value of 0.504, which was also the middle level. This study provides useful information for diversity studies and resource assessments of S. japonicus.

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Section: Ssr Markers In the Transcriptome Of S Japonicusmentioning

confidence: 82%

De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

Zhang

Jiang

et al. 2018

Forests

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“…Additionally, high stability among technical replicates makes RNA-Seq data more useful [23]. RNA-seq presently has been applied for EST-SSR development in many plant species, such as Rosa roxburghii [24], Neolitsea sericea [25], Salix [26], Elymus sibiricus [27], Xanthoceras sorbifolia [28], etc. In this study, a total of 11,289 putative SSRs were identified.…”

Section: Methods For Development Of Ssr Markers In Plantmentioning

confidence: 99%

Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification

Liu

et al. 2020

BMC Plant Biol

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Background: Angelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhile, the diversity of cultivars of A. dahurica has decreased as a result of long-term artificial cultivation. However, there are no population genetics studies of natural A. dahurica reported yet, especially for using microsatellite markers (SSRs) to investigate population genetics of the species.Results: Sixteen polymorphic EST-SSR loci were isolated from A. dahurica with transcriptome sequencing technology (RNA-Seq). The number of alleles varied from 2 to 15 per polymorphic locus over populations with the observed and expected heterozygosities ranging from 0.000 to 1.000 and from 0.000 to 0.829, respectively. Significant deviations from Hardy-Weinberg equilibrium were observed at 8 loci. Tests of linkage disequilibrium showed 11 informative locus pairs were significant across all populations. Cross-species amplification showed that 14 out of 16 SSR loci have the transferability in cultivar-A. dahurica cv. 'Hangbaizhi' and A. decursiva. Conclusions:The 16 newly developed loci microsatellite primers with RNA-Seq will be useful for further investigating population genetics of A. dahurica, cultivars and other members of this genus.

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“…The transcriptome sequencing was conducted at Beijing Novogene Biological Information Technology Co., Ltd., Beijing, China (http://www.novogene.com/). The generated 100 bp paired-end reads were filtered by strict principles [24,25], and the assembly of these high-quality reads were carried out by Trinity [26,27] with min_kmer_cov set to 2 and other parameters set to default. The longest transcripts of each gene were pooled as "unigenes", and unigene annotations were performed and analyzed by searching and comparing the public databases [25].…”

Section: Plant Materials and Preparationmentioning

confidence: 99%

“…The generated 100 bp paired-end reads were filtered by strict principles [24,25], and the assembly of these high-quality reads were carried out by Trinity [26,27] with min_kmer_cov set to 2 and other parameters set to default. The longest transcripts of each gene were pooled as "unigenes", and unigene annotations were performed and analyzed by searching and comparing the public databases [25]. Additionally, the transcript sequence data used here were submitted to the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/).…”

Section: Plant Materials and Preparationmentioning

confidence: 99%

De Novo Transcriptome Analysis of Dalbergia odorifera 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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Characterization of transcriptome and development of novel EST-SSR makers based on next-generation sequencing technology in Neolitsea sericea (Lauraceae) endemic to East Asian land-bridge islands

Cited by 46 publications

References 68 publications

De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification

De Novo Transcriptome Analysis of Dalbergia odorifera and Transferability of SSR Markers Developed from the Transcriptome

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