Genetic structure of gall oak (Quercus infectoria) characterized by nuclear and chloroplast SSR markers

Mohammad-Panah, Negar; Shabanian, Naghi; Khadivi, Ali; Rahmani, Mohammad-Shafie; Emami, Arezoo

doi:10.1007/s11295-017-1146-8

Cited by 34 publications

(26 citation statements)

References 52 publications

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“…A similar result was found in this study, with 46.9% of repeats detected in the IGS regions, followed by 34.7% in the coding regions, and the remainder in the tRNAs (Table S2). The cpSSR is an effective marker [49,50] that is widely used in population genetics, biogeographic studies, and phylogenetic evaluation [51,52]. In the cp genome of M. shiluensis, over 80% of the SSRs consisted of A or T bases, and over 80% were mononucleotide repeats.…”

Section: Discussionmentioning

confidence: 99%

Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species

Deng

Luo

et al. 2020

Forests

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Michelia shiluensis is a rare and endangered magnolia species found in South China. This species produces beautiful flowers and is thus widely used in landscape gardening. Additionally, its timber is also used for furniture production. As a result of low rates of natural reproduction and increasing levels of human impact, wild M. shiluensis populations have become fragmented. This species is now classified as endangered by the IUCN. In the present study, we characterized the complete chloroplast genome of M. shiluensis and found it to be 160,075 bp in length with two inverted repeat regions (26,587 bp each), a large single-copy region (88,105 bp), and a small copy region (18,796 bp). The genome contained 131 genes, including 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The guanine-cytosine content represented 39.26% of the overall genome. Comparative analysis revealed high similarity between the M. shiluensis chloroplast genome and those of four closely related species: Michelia odora, Magnolia laevifolia, Magnolia insignis, and Magnolia cathcartii. Phylogenetic analysis shows that M. shiluensis is most closely related to M. odora. The genomic information presented in this study is valuable for further classification, phylogenetic studies, and to support ongoing conservation efforts.

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Section: Discussionmentioning

confidence: 99%

Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species

Deng

Luo

et al. 2020

Forests

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“…Biogeographical studies of angiosperms frequently combine nuclear markers, such as SSRs, which are inherited biparentally, with chloroplast markers that are inherited matrilineally. By comparing results from both types of markers across the same sampled populations, complementary views of a species' evolution, genetic structure, differentiation, and gene flow can be obtained (McCauley, ; Mohammad‐Panah, Shabanian, Khadivi, Rahmani, & Emami, ). Here, we use a multidisciplinary approach including molecular phylogeographic, ecological niche modeling, and phylogenetic approaches to investigate the biogeography, genetic structure, and demographic history of iron walnut in China.…”

Section: Introductionmentioning

confidence: 99%

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confidence: 99%

Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China

Sun

Hou²,

Woeste

et al. 2019

Ecology and Evolution

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Southwestern (SW) China is an area of active tectonism and erosion, yielding a dynamic, deeply eroded landscape that influences the genetic structure of the resident populations of plants and animals. Iron walnut (Juglans regia subsp. sigillata) is a deciduous tree species endemic to this region of China and cultivated there for its edible nuts. We sampled 36 iron walnut populations from locations throughout the species' range in SW China and genotyped a total of 765 individuals at five chloroplast DNA regions and 22 nuclear microsatellite loci. Species distribution models were produced to predict the evolution and historical biogeography of iron walnut and to estimate the impacts of climate oscillations and orographic environments on the species' demography. Our results indicated that J. regia subsp. sigillata had relatively low genetic diversity, high interpopulation genetic differentiation, and asymmetric interpopulation gene flow. Based on DIYABC analysis, we identified two lineages of J. sigillata in southwestern China. The lineages (subpopulations) diverge during the last glacial period (~1.34 Ma). Southwestern China was a glacial refuge during the last glacial period, but increasingly colder and arid climates might have fostered the fragmentation of J. regia subsp. sigillata within this refugium. Finally, we found that recent habitat fragmentation has led to a reduction in population connectivity and increased genetic differentiation by genetic drift in isolated populations. Our results support a conclusion that geological and climatic factors since the Miocene triggered the differentiation, evolutionary origin, and range shifts of J. sigillata in the studied region.

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“…Molecular markers have been widely and effectively applied in plants for genetic diversity and association analysis [8][9][10][11][12]. Prior to this study, however, there were only six RAPD (random amplified polymorphic DNA) markers and 25 SRAP (sequence-related amplified polymorphism) markers for the genotyping of D. odorifera germplasm [7,13], and no co-dominant SSR markers have been specifically developed for this endangered tree species.…”

Section: Ssr Prediction Validation and Applicationmentioning

confidence: 99%

“…Number of sampled individuals with expected band, 2 number of alleles, 3 observed heterozygosity, 4 expected heterozygosity, 5 polymorphic information content.Forests 2019,10, 98 …”

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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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Genetic structure of gall oak (Quercus infectoria) characterized by nuclear and chloroplast SSR markers

Cited by 34 publications

References 52 publications

Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species

Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species

Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China

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

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