ISSR-based genetic diversity assessment of five populations of Juniperus polycarpos K. Koch in southern habitats of Iran

Boogar, Abdolrahman Rahimian; Sher, Hassan

doi:10.52547/flowerjournal.6.1.1

Cited by 2 publications

(2 citation statements)

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“…The genetic diversity of the species in the genus has been thoroughly studied using different types of DNA markers. In particular, markers such as random amplified polymorphic DNA (RAPD) [17][18][19][20], inter-simple sequence repeats (ISSR) [19,21,22], amplified fragment length polymorphisms (AFLP) [23][24][25], and single-nucleotide polymorphisms (SNP) [26] have been widely used to evaluate the genetic diversity of Juniperus. In the last 20 years, simple sequence repeats (SSRs), or microsatellites, have become the most popular marker; these are extensively employed in the population genetics of Juniperus species [27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Almerekova,

Yermagambetova,

Jumanov

et al. 2024

PLoS ONE

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Juniperus species are shrubs or trees in the family Cupressaceae that play an important role in forest ecosystems. In this study, we report the complete sequences of the plastid (pt) genomes of five Juniperus species collected in Kazakhstan (J. communis, J. sibirica, J. pseudosabina, J. semiglobosa, and J. davurica). The sequences of the pt genomes of the five species were annotated in addition to two full pt genome sequences from J. sabina and J. seravschanica, which we have previously reported. The pt genome sequences of these seven species were compared to the pt genomes of Juniperus species available in the public NCBI database. The total length of the pt genomes of Juniperus species, including previously published pt genome data, ranged from 127,469 bp (J. semiglobosa) to 128,097 bp (J. communis). Each Juniperus plastome consisted of 119 genes, including 82 protein-coding genes, 33 transfer RNA and 4 ribosomal RNA genes. Among the identified genes, 16 contained one or two introns, and 2 tRNA genes were duplicated. A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. A phylogenetic tree of 26 Juniperus species based on the 82 protein-coding genes separated the Juniperus samples into two major clades, corresponding to the Juniperus and Sabina sections. The analysis of pt genome sequences indicated that accD and ycf2 were the two most polymorphic genes. The phylogenetic evaluation of 26 Juniperus species using these two genes confirmed that they can be efficiently used as DNA barcodes for phylogenetic analyses in the genus. The sequenced plastomes of these Juniperus species have provided a large amount of genetic data that will be valuable for future genomic studies of this genus.

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Section: Introductionmentioning

confidence: 99%

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Almerekova,

Yermagambetova,

Jumanov

et al. 2024

PLoS ONE

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“…However, the genetic diversity of J. seravschanica has only been assessed using a few types of DNA markers. For example, Adams [ 15 ], Sultangaziev, et al [ 5 ], and Rahimian Boogar and Salehi [ 43 ] studied selected populations of the species using RAPD, PCR-RFLP, and ISSR markers, respectively. Naturally, assessing these populations using different types of DNA markers cannot provide a comprehensive platform for evaluating genetic diversity in Central Asia.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia

Yermagambetova

Almerekova

Turginov³

et al. 2023

Plants

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Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub–forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. A comprehensive study of the species’ genetic diversity and population structure is a basic approach to understanding the current status of J. seravschanica resources for the development of future conservation strategies. Samples from 15 populations of J. seravschanica were collected from the mountain ranges of Uzbekistan, Kyrgyzstan, and Kazakhstan. The genetic diversity and population structure of 15 Central Asian populations of J. seravschanica were assessed using 11 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including the number of alleles (na), the effective number of alleles (ne), Shannon’s information index (I), the percentage of polymorphic loci (PPL), Nei’s genetic diversity index (Nei), principal coordinate analysis (PCoA), etc., were evaluated. The analysis of 15 J. seravschanica populations based on 11 polymorphic SSRs detected 35 alleles. The average PIC value was 0.432, and the highest value (0.662) was found in the JT_40 marker. Nei’s genetic diversity index for the J. seravschanica populations was 0.450, ranging from 0.407 (population 14) to 0.566 (population 4). The analysis of molecular variance (AMOVA) showed that 90.3% of total genetic variation is distributed within the population. Using the alleles of all the populations, the gene flow (Nm) was found to be 4.654. Population structure analysis revealed poor clustering in the studied populations and confirmed our AMOVA results. The output of this work can be efficiently used for the maintenance of the species across the Central Asian region.

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ISSR-based genetic diversity assessment of five populations of Juniperus polycarpos K. Koch in southern habitats of Iran

Cited by 2 publications

References 40 publications

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia

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