De novo transcriptome assembly and development of SSR markers of oaks Quercus austrocochinchinensis and Q. kerrii (Fagaceae)

An, Malaviya; Deng, Min; Zheng, Sisi

doi:10.1007/s11295-016-1060-5

Cited by 26 publications

(21 citation statements)

References 46 publications

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“…Among these 38,611 unigenes, one SSR site was found per 6.73 kb (55,977 SSRs within 83.18 Mb) and the frequency of SSRs was 41.14%. The SSR tandem repeat lengths differed from 10 to 228 bp, and a 15 bp length occurred most frequently (12,896,26.95%). The most identified SSRs (excluding mono-nucleotides) were di-nucleotide repeats (17,193,40.40%), followed by tri-nucleotide (11,260,27.11%) and tetra-nucleotide (7273, 17.64%) repeats, and the other SSR types accounted for 13.86% in total.…”

Section: Frequency and Distribution Of Ssrsmentioning

confidence: 99%

“…Recently, NGS has been widely applied in many non-model plants [26]. In the evaluation of genetic diversity, cultivar DNA fingerprinting, genome organization, and marker-assisted breeding, and in genome-wide association studies [36,37], SSR markers have been widely used.…”

Section: Characterization Of the S Japonicus Transcriptomementioning

confidence: 99%

“…The average unigene length was shorter than that of Quercus kerrii Hu. (719 bp) [26], Pinus bungeana Zucc. ex Endl.…”

Section: Characterization Of the S Japonicus Transcriptomementioning

confidence: 99%

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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: Frequency and Distribution Of Ssrsmentioning

confidence: 99%

Section: Characterization Of the S Japonicus Transcriptomementioning

confidence: 99%

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

Zhang

Jiang

et al. 2018

Forests

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“…Without considering mononucleotide repeats, the SSR distribution frequency was 5.79%, which is higher than corn (1.5%), barley (3.4%), rice (4.7%) [28], cucumber (4.03%) [29], Taxus chinensis (2.24%) [30], and Korean pine (4. 24%) [31]; similar to peanut (6.63%) [32], pepper (7.83%) [33], and dal (7.6%) [34]; and lower than Rosa roxburghii (20.37%) [35], oak (27.61%) [36], and precocious trifoliate orange (26.88%) [37]. These differences may re ect actual variations in SSR abundance across species if we ignore the in uence of the amount and source of EST data [35].…”

Section: Discussionmentioning

confidence: 99%

EST-SSR markers identification based on RNA-sequencing and application in Schisandra chinensis

Shi¹,

Wang²,

Dongxiao³

et al. 2020

Preprint

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Background: Schisandra chinensis, a climbing woody vine, is the best-known and representative genus of the Schisandraceae family which is an important plant in Chinese herbal medicine; however, the application of molecular breeding is restricted by the few genetic markers for this species. Results: In this study, we performed transcriptome sequencing of S. chinensis using the Illumina HiSeq platform to establish a library of expressed sequence tag-simple sequence repeat (EST-SSR) markers. A total of 59,786 unigenes were obtained and 6254 putative SSR sites were detected with a frequency of 10.46%. The predominant type of repeat motif was dinucleotide (35.71%), followed by trinucleotide (13.22%), hexanucleotide (0.50%), tetranucleotide (0.06%), and pentanucleotide (0.22%). We randomly selected 50 EST-SSR primer pairs and used 14 of these for genetic diversity analysis in 42 S. chinensis genotypes. All 42 accessions were successfully identified and formed four major clusters, indicating that the SSR markers can be used for genetic diversity analysis and genetic linkage map construction. In addition, using the polymorphic bands associated with 10 markers as DNA fingerprints, we generated a manual cultivar identification diagram that can distinguish between the 42 accessions, with different individuals identifiable based on polymorphic band patterns. Conclusion: S. chinensis transcriptome data is an effective resource for developing SSR markers. These results can provide a basis for the identification of S. chinensis accessions and construction of genetic linkage maps as part of future selective breeding and conservation efforts for this valuable plant.

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“…(1219 bp, 793 bp) [36], Millettia pinnata Forst. (699 bp, 534 bp) [37], Quercus kerrii Craib (1166 bp, 720 bp), and Quercus austrocochinchinensis Hickel & A.Camus (1335 bp, 782 bp) [38].…”

Section: Transcriptome Sequencing De Novo Assembly and Annotation Fmentioning

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 assembly and development of SSR markers of oaks Quercus austrocochinchinensis and Q. kerrii (Fagaceae)

Cited by 26 publications

References 46 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

EST-SSR markers identification based on RNA-sequencing and application in Schisandra chinensis

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

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