Genetic diversity and genetic structure of Acer monspessulanum L. across Zagros forests of Iran using molecular markers

Motahari, Behnaz; Shabanian, Naghi; Rahmani, Mohammad-Shafie; Mohammad-Hasani, Farshad

doi:10.1016/j.gene.2020.145245

Cited by 13 publications

(7 citation statements)

References 39 publications

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“…The study demonstrated that palindromic (P) and forward (F) repeats were the most abundant in all dispersed repeats, and most of them were 30-40 bp in length, similar to previous studies [33,[87][88][89]. Simple sequence repeats (SSRs) were widely used as a molecular marker for studies of genetic diversity and population structure [90][91][92]. We observed five and four types of SSRs in H. bodinieri and E. cavaleriei cp genomes, respectively.…”

Section: Features Of Complete Chloroplast Genome and Comparativesupporting

confidence: 86%

Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales

Yang

2022

BMC Genomics

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Background Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. Results The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. Conclusion This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.

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Section: Features Of Complete Chloroplast Genome and Comparativesupporting

confidence: 86%

Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales

Yang

2022

BMC Genomics

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“…Mountains and rivers function as natural geographical barriers affecting gene ow in plants [6][7][8]. Moreover, human disturbances, such as road or bridge construction and mining, can signi cantly increase geographical isolation and habitat fragmentation of populations, resulting in reduced gene ow and genetic diversity of populations, thus affecting the genetic structure and population dynamics of the species [9][10][11][12]. Even forest park tourism and farming, which have recently become popular in China, pose a threat to rare species.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing

Wu¹,

Dong

Zhao³

et al. 2022

Preprint

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Background: Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos isone of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified. Results: Here, 99 individuals of C. macranthos from north and northeastChina were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gbhigh-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant “Isolation by Distance” between populations. Conclusions: Our study demonstrates that the present genetic diversity andgenetic structure of C. macranthos populations weremainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.

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“…Particularly, members of section Acer (SeriesMonspessulana ) were diverged from north and undergone recent diversification in western and southern Anatolia in Pliocene (5.33 Ma). The distribution of series Monspessulana continues from southern Türkiye to Zagros Mountains (Motahari et al 2021). In conclusion, all molecular dating analysis imply that the geographic barriers, mountain ranges (Hypothetical Anatolian diagonal barrier, Colchic and Zagros mountains) (Bilgin 2011;Gao et al 2020) and the last glacial period acting as glacial cover for forest biodiversity (Ledig 1998) have an effect on shaping the current composition of Acer native to Türkiye.…”

Section: Molecular Datingmentioning

confidence: 83%

New insight into molecular phylogeny and morphology of the genus Acer L. (Sapindaceae) native to Türkiye

ACAR,

Seki,

Bani

et al. 2024

Preprint

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This study examined phylogenetic relationship, the taxonomic status and numerical morphometric analysis of 21 taxa of the genus Acer L. naturally found in Türkiye using the DNA sequence data of cpDNA ndhF, trnL-F and nrDNA ITS gene regions and 18 elucidative morphological characters. To date, no comprehensive molecular and morphological study dealing with the genus in Türkiye. Selected morphological traits of Dim1 (Leaf length, Leaf width, Petiole length, Loculus length, Loculus width, Fruit wing length and Fruit length) and Dim2 (Pubescence of leaf beneath, Margin, Latex and Form of nutles) are highly distinctive characters for the Acer genus in series and sectional levels. The nuclear (ITS) and chloroplast (trnL-F) gene regions were also found as quite diverse and informative. The results of phylogenetic and morphometric analysis revealed a relieable taxonomic clarification for the species Acer tauricolum, A. divergens (endemic to Türkiye), A. orthocampestre and A. cappadocicum subsp. cappadocicum. Chloroplast lineage of Acer species native to Türkiye appears to be originated in Oligocene and diversified mainly in Miocene. The majority of Acer speciation events in Türkiye is likely to be regulated by the habitats created by the by northern mountain ranges. Phylogenetically, the Acer species of Türkiye seemed to be closely related to the taxa from Asia and Europe.

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Genetic diversity and genetic structure of Acer monspessulanum L. across Zagros forests of Iran using molecular markers

Cited by 13 publications

References 39 publications

Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales

Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales

Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing

New insight into molecular phylogeny and morphology of the genus Acer L. (Sapindaceae) native to Türkiye

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