Short Communication Development and characterization of novel transcriptome-derived microsatellites for genetic analysis of persimmon

Luo, Chun; Zhang, Q.L.; Luo, Zhitian

doi:10.4238/2014.april.16.10

Cited by 4 publications

(4 citation statements)

References 19 publications

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“…Moreover, 100 SSRs were selected to design the EST-SSR primers (Table 6 and Additional file 11: Table S7) from 2603 single copy orthogroups shared in nine samples, and 66% products exhibited more than one band in all nine samples. Our PCR success rate was higher than that in a previous study [40], but it was slightly lower than those reported in rubber [42]. The failure of 34 primer pairs to produce amplicons may be due to the location of the primers across the splice sites, chimeric primers, poor-quality sequences, or the high heterozygosity.…”

Section: Discussioncontrasting

confidence: 69%

“…The development of the SSRs in the genus Diospyros was mostly focused on the DK species using the traditional enriched genomic library [39]. Recently, it was reported that 42,711 SSR loci were found using Roche 454 sequencing technology, and 98 revealed polymorphisms between 15 DK genotypes [40]. However, some closely related species with DK still lack the SSR information.…”

Section: Discussionmentioning

confidence: 99%

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Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

et al. 2019

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Background Persimmon ( Diospyros kaki ) is the most economically cultivated species belonging to the genus Diospyros . However, little is known about the interspecific diversity and mechanism of domestication, partly due to the lack of genomic information that is available for closely related species of D. kaki (DK). Here, we performed transcriptome sequencing on nine samples, including DK, a variety of DK and seven closely related species, to evaluate the interspecific genetic divergence and to identify candidate genes involved in persimmon domestication. Results We obtained a total of 483,421 unigenes with N50 at 1490 bp in the nine Diospyros samples and identified 2603 orthogroups that were shared among all the samples using OrthoMCL analysis. A phylogenetic tree was established based on the tandem 2603 one-to-one single copy gene alignments, showing that DK was closely related to D. kaki var. silvestris (DKV) and that it clustered with the clade of D. deyangnsis (DD) and was farthest from the D. cathayensis (DC) species. The nonsynonymous substitutions (Ka), via synonymous substitution (Ks) ratios, was directly proportional to the genetic relationship of the different species. The higher the Ka/Ks ratios, the longer the distance was. Moreover, 31 positively selected genes (PSGs) involved in carbohydrate metabolism and phenolic metabolism were identified and isolated, and nearly all PSGs except the MATE gene had a high expression in the DK or DKV species. It was hypothesized that these genes might contribute to the domestication of the DK species. Finally, we developed the expressed sequence tag-simple sequence repeat (EST-SSR) and identified 2 unique amplicons DKSSR10 and DKSSR39: the former was absent in the DC species but was present in the other species, the latter had a long amplification product in the DJ species. Conclusion This study presents the first transcriptome resources for the closely related species of persimmon and reveals interspecific genetic divergence. It is speculated that DK is derived from the hybridization of DD and DO species. Furthermore, our analysis suggests candidate PSGs that may be crucial for the adaptation, domestication, and speciation of persimmon relatives and suggests that DKSSR10 and DKSSSR39 could potentially serve as species-specific molecular markers. Electronic supplementary material The online version of this article (10.1186/s12870-019-1839-2) contains supplementary material, which is available to authorized users.

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Section: Discussioncontrasting

confidence: 69%

Section: Discussionmentioning

confidence: 99%

Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

et al. 2019

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“…In total, 218 pairs of primers showed stable PCR amplification with products of the expected sizes; 93 pairs of primers identified polymorphisms in the 7 mango genotypes ( Table S1). The rate of polymorphism in mangoes (43.12%) was lower than the 64.7% reported in oak (Torre et al, 2014), 63.23% in persimmon (Luo et al, 2014), and 46.5% in field pea (Kaur et al, 2012), but higher than the 21.2% in Asian lotus (Zhang et al, 2014a), 27.3% in cotton (Zhang et al, 2014b), and 36% in tea (Wu et al, 2013). The sequences of the 93 pairs of primers that identified polymorphisms and the characteristics of their amplification products are given in Table S1.…”

Section: Resultsmentioning

confidence: 90%

Development of EST-SSR and TRAP markers from transcriptome sequencing data of the mango

Luo

Yao

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Mango is one of the most commercially important fruit crops in tropical and subtropical regions. To increase the efficiency of breeding strategies, two EST-derived marker systems were developed in the present study using information from the mango fruit transcriptome. Using simple sequence repeats, 218 of 230 primer pairs showed stable amplification for 7 mango genotypes with amplicons ranging from 84 to 160 bp; 93 of the primer pairs yielded polymorphic products. The proportion of polymorphic bands ranged from 16.67 to 100%, with a mean of 55.64%. In contrast, 86 primer pairs exhibited good amplification with clear bands for target region amplification polymorphism analysis, and a total of 66 primer combinations were polymorphic. These two novel sets of EST-derived markers will be of use in future studies of genetic diversity, genetic map construction, and marker-assisted selection in mango.

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“…Using Roche 454 sequencing technology, the transcriptome from RNA of the flowers of D. kaki was analyzed (Luo et al, 2014). Using Roche 454 sequencing technology, the transcriptome from RNA of the flowers of D. kaki was analyzed (Luo et al, 2014).…”

Section: Flowermentioning

confidence: 99%

High-throughput sequencing in medicinal plant transcriptome studies

Hao¹,

Gu²,

Xiao³

2015

Medicinal Plants

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Short Communication Development and characterization of novel transcriptome-derived microsatellites for genetic analysis of persimmon

Cited by 4 publications

References 19 publications

Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

Development of EST-SSR and TRAP markers from transcriptome sequencing data of the mango

High-throughput sequencing in medicinal plant transcriptome studies

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