Development and characterization of EST‐SSR markers in <i>Bombax ceiba</i> (Malvaceae)

Ju, Miao-Miao; Ma, Haiching; Xin, Peiyao; Zhou, Zhili; Tian, Bin

doi:10.3732/apps.1500001

Cited by 9 publications

(6 citation statements)

References 11 publications

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“…The sequencing was carried out on HiSeq sequencing platforms at BGI‐Shenzhen (Guangdong, China). For further details on RNA extractions, transcriptome sequencing, and assembly, see Ju et al (). Then we developed primers of five species‐specific low‐copy nuclear loci (23311, 38541, 41398, 45367, and 56546) following the procedures described by Ye et al ().…”

Section: Methodsmentioning

confidence: 99%

A complex pattern of post‐divergence expansion, contraction, introgression, and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

Tian

Milne

et al. 2019

J of Sytematics Evolution

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The well-known vicariance and dispersal models dominate in understanding the allopatric pattern for related species and presume the simultaneous occurrence of speciation and biogeographic events. However, the formation of allopatry could postdate the species divergence. We examined this hypothesis using DNA sequence data from three chloroplast fragments and five nuclear loci of Dipelta floribunda Maxim. and D. yunnanensis Franch, two shrub species with the circum Sichuan Basin distribution, combining the climatic niche modeling approach. The best-fit model supported by the approximate Bayesian computation analysis indicated that D. floribunda and D. yunnanensis diverged during the mid-Pleistocene period, consistent with the largest glacial period in the Qinghai-Tibet Plateau. The historically interspecific gene flow was identified, but seemed to have ceased after the last interglacial period, when the range of D. floribunda moved northward from the south of the Sichuan Basin. Furthermore, populations of D. floribunda had expanded obviously in the north of the Sichuan Basin after the last glacial maximum (LGM). Relatively, the range of D. yunnanensis expanded before the LGM, and reduced during the post-LGM especially in the north of the Sichuan Basin, reflecting the asynchronous responses of related species to contemporary climate changes. Our results suggested that complex topography should be considered in understanding distributional patterns, even for closely related species and their demographic responses.

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Section: Methodsmentioning

confidence: 99%

A complex pattern of post‐divergence expansion, contraction, introgression, and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

Tian

Milne

et al. 2019

J of Sytematics Evolution

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“…Six highly variable pairs of EST‐SSR primers (Appendix ) were used to detected polymorphisms in B. ceiba . PCR amplification was performed according to the procedure described previously by Ju, Ma, Xin, Zhou, and Tian (). All of the high‐quality PCR products were sequenced using the amplified forward and reverse primers with an ABI 3730xl Sequence Analyzer (Life Technologies, Carlsbad, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

Effects of the Tanaka Line on the genetic structure of Bombax ceiba (Malvaceae) in dry‐hot valley areas of southwest China

Zhao

et al. 2018

Ecology and Evolution

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Southwest China is an important biodiversity hotspot. The interactions among the complex topography, climate change, and ecological factors in the dry‐hot valley areas in southwest China may have profoundly affected the genetic structure of plant species in this region. In this study, we determined the effects of the Tanaka Line on genetic variation in the wild Bombax ceiba tree in southwest China. We sampled 224 individuals from 17 populations throughout the dry‐hot valley regions. Six polymorphic expressed sequence tag–simple sequence repeat primers were employed to sequence the PCR products using the first‐generation Sanger technique. The analysis based on population genetics suggested that B. ceiba exhibited a high level of gene diversity (H E: 0.2377–0.4775; I: 0.3997–0.7848). The 17 populations were divided into two groups by cluster analysis, which corresponded to geographic characters on each side of the Tanaka Line. In addition, a Mantel test indicated that the phylogeographic structure among the populations could be fitted to the isolation‐by‐distance model (r 2 = .2553, p < .001). A barrier test indicated that there were obstacles among populations and between the two groups due to complex terrain isolation and geographic heterogeneity. We inferred that the Tanaka Line might have promoted the intraspecific phylogeographic subdivision and divergence of B. ceiba. These results provide new insights into the effects of the Tanaka Line on genetic isolation and population differentiation of plant species in southwest China.

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“…TB2013079, deposited at the Herbarium of Southwest Forestry University [SWFC], Kunming, China) and immediately frozen in liquid nitrogen, and then stored at −80°C. RNA extraction, cDNA library construction, and transcriptome sequencing were conducted following the procedures previously described by Ju et al (2015). After removing adapter sequences and low-quality sequences, a total of 86,138,489 nonredundant unigenes were assembled from 95,791,418 raw reads.…”

Section: Methods and Resultsmentioning

confidence: 99%

Development and characterization of novel EST‐SSR markers for Speranskia tuberculata (Euphorbiaceae)

et al. 2016

Appl Plant Sci

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Premise of the study:The first set of expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed and characterized for Speranskia tuberculata (Euphorbiaceae), a traditional medicinal plant endemic to northern China, to explore the effects of recent habitat fragmentation on the genetic diversity and structure of this species.Methods and Results:In this study, a total of 18 novel polymorphic microsatellite (EST-SSR) markers were developed for S. tuberculata using high-throughput transcriptome sequencing. Analysis of 24 individuals of S. tuberculata from four natural populations revealed their robust polymorphic reliability. The number of alleles per locus ranged from two to 11, while the expected and observed heterozygosity per marker varied from 0.187 to 0.827 and 0.042 to 0.917, respectively. Of these markers, 13 showed good amplification results in the closely related species S. cantonensis.Conclusions:These newly generated SSR markers are expected to provide novel tools for genetic studies of S. tuberculata, which will contribute to the conservation and sustainable use of the species’ wild genetic resources.

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Development and characterization of EST‐SSR markers in Bombax ceiba (Malvaceae)

Cited by 9 publications

References 11 publications

A complex pattern of post‐divergence expansion, contraction, introgression, and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

A complex pattern of post‐divergence expansion, contraction, introgression, and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

Effects of the Tanaka Line on the genetic structure of Bombax ceiba (Malvaceae) in dry‐hot valley areas of southwest China

Development and characterization of novel EST‐SSR markers for Speranskia tuberculata (Euphorbiaceae)

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