De novo transcriptome analysis of Fraxinus velutina using Illumina platform and development of EST-SSR markers

Liu, Yan; Liu, C.-L.; Wu, Donghui; Li, L.; Shu, Jia; Sun, Chao; Xia, Ying; Zhao, Lina

doi:10.1007/s10535-016-0681-8

Cited by 16 publications

(16 citation statements)

References 34 publications

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“…Transcriptome sequences can be used to create EST-SSR markers to facilitate research into genetic diversity and marker-assisted selection. A total of 55,977 possible EST-SSRs were determined (including 14,447 mono-nucleotides) in the present study, with di-nucleotide repeats the most noted SSRs, similar to previous studies [43,51,52]. The frequency of AG/CT was the highest in the di-nucleotide repeats and the CG/CG motif was the least abundant, which might be related to the methylation of cytosine [42].…”

Section: Ssr Markers In the Transcriptome Of S Japonicussupporting

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 Japonicussupporting

confidence: 82%

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

Zhang

Jiang

et al. 2018

Forests

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“…Furthermore, EST-SSRs can be used directly to obtain gene expression data due to their close link to functional genes 14 . Previous studies have shown that a large number of potential EST-SSRs are found in transcriptome sequencing data 47,48 . In this study, a total of 23,539 SSRs (including 12,520 mononucleotide repeats) were identified from the abovementioned 16,057 SSR-containing sequences ( Table 3).…”

Section: Discussionmentioning

confidence: 99%

“…In this study, a total of 23,539 SSRs (including 12,520 mononucleotide repeats) were identified from the abovementioned 16,057 SSR-containing sequences ( Table 3). The distribution density, predominant repeat motif, and types of SSRs show www.nature.com/scientificreports/ differences among different plants 14,48 . In this study, one SSR site was found per 2.64 kb (23,539 SSR loci within 89,101,859 bp), and this SSR density is higher than the density of 1/3.88 kb found through EST-SSRs developed using 20,023 EST sequences from Populus deltoides and Populus euramericana 49 .…”

Section: Discussionmentioning

confidence: 99%

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Zang

Xie³

et al. 2020

Sci Rep

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Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.

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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%

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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De novo transcriptome analysis of Fraxinus velutina using Illumina platform and development of EST-SSR markers

Cited by 16 publications

References 34 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

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

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

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