Chloroplast analysis of Zelkova schneideriana (Ulmaceae): genetic diversity, population structure, and conservation implications

Liu, HL; Zhang, RQ; Ml, Geng; Zhu, Jingjing; Jc, An; Jl, Ma

doi:10.4238/gmr.15017739

Cited by 8 publications

(8 citation statements)

References 23 publications

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“…Chloroplast-based genome-wide analyses can deep our understanding of plant diversity and genetic information given its highly conserved genome (Liu et al 2016). The advent of next-generation sequencing (NGS) in the twentieth century has led to rapid advances in the evolutionary analyses (Van Dijk et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Signatures of differential selection in chloroplast genome between japonica and indica

Cheng

Nam

Chu

et al. 2019

Rice

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Background The domestication process of Asian rice ( Oryza sativa L.) is complicated. It’s well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice. Results A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity ( π ) than Oryza sativa L. indica and wild rice. The fixation index values ( F ST ) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima’s D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice. Conclusions Here, we focus on the domestication of Asian rice ( indica and japonica ). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication. Electronic supplementary material The online version of this article (10.1186/s12284-019-0322-x) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Signatures of differential selection in chloroplast genome between japonica and indica

Cheng

Nam

Chu

et al. 2019

Rice

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“…In addition, Chang et al (2004) indicated that the fruit of G. microrrhynchum has no dispersal vector, and is dispersed by gravity. This restricted seed vagility might decrease gene flow between populations (Liu et al, 2016b) and expand the distributional range of local populations, leading to their restriction to local environments to which they become adapted. In addition, differentiated small local populations may exhibit increased disagreement between genetic and geographical distances due to genetic drift (Fischer and Matthies, 1998).…”

Section: Genetic Diversity and Structure Of G Microrrhynchum Populatmentioning

confidence: 99%

Conservation implications of the genetic diversity of Gymnospermium microrrhynchum in Korea

2016

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ABSTRACT. Gymnospermium microrrhynchum (Berberidaceae) is an ephemeral perennial herb with a limited distributional range in the Baekdudaegan mountain areas of the Korean Peninsula, and is designated a rare plant by the Korean Forest Service. Information about its genetic variation and structure is important for developing successful conservation strategies. To investigate the genetic variation within and among seven G. microrrhynchum populations, random amplified polymorphic DNA data were obtained for 207 individuals. The populations exhibited relatively low genetic diversity: the percentage of polymorphic bands (PPB) ranged from 32.1 to 66.7% (mean = 51.4%) and Nei's gene diversity (H E ) ranged from 0.116 to 0.248 (mean = 0.188). However, genetic diversity at the species level was relatively high (PPB = 98.7%, H E = 0.349). An analysis of molecular variance revealed high differentiation among populations (F ST = 0.6818), but the low gene flow value (N m = 0.117) suggests a low level of gene exchange occurs among populations. Principal coordinates analysis revealed that individuals were separated according to population. The high level of genetic differentiation and restricted gene flow among G. microrrhynchum populations, which resulted from their isolation in alpine areas after the Ice Age, indicates that it is essential to protect and manage all populations, rather than focus on specific populations, in order to maintain the genetic diversity of this species.

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“…Model yang memenuhi kriteria tersebut dan memiliki jumlah variabel terkecil yaitu Tamura-3-parameter (Tamura, 1992) yang mempertimbangkan perbedaan mutation rate secara transversi dan transisi serta bias kandungan GC. Dendrogram dikonstruksi menggunakan metode maximum likelihood dengan 10.000 bootstraps (Neubig, et al, 2012). Analisis jarak genetik dan konstruksi dendrogram dilakukan dengan perangkat lunak MEGA-X (Kumar, et al, 2018).…”

Section: Analisis Dataunclassified

KONFIRMASI JENIS DAN KERAGAMAN GENETIK SENGON RESISTEN DAN RENTAN INFEKSI KARAT TUMOR MENGGUNAKAN PENANDA DNA KLOROPLAS (Species confirmation and genetic diversity of Gall-rust resistant and susceptible sengon using chloroplast DNA marker)

Shabrina

Siregar

Matra

et al. 2020

Jur.pen.hut.tanaman

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Chloroplast analysis of Zelkova schneideriana (Ulmaceae): genetic diversity, population structure, and conservation implications

Cited by 8 publications

References 23 publications

Signatures of differential selection in chloroplast genome between japonica and indica

Signatures of differential selection in chloroplast genome between japonica and indica

Conservation implications of the genetic diversity of Gymnospermium microrrhynchum in Korea

KONFIRMASI JENIS DAN KERAGAMAN GENETIK SENGON RESISTEN DAN RENTAN INFEKSI KARAT TUMOR MENGGUNAKAN PENANDA DNA KLOROPLAS (Species confirmation and genetic diversity of Gall-rust resistant and susceptible sengon using chloroplast DNA marker)

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