SSR identification and phylogenetic analysis in four plant species based on complete chloroplast genome sequences

Zhu, Yueyi; Zhang, Xianwen; Yan, Shufeng; Chen, Feng; Wang, Dongfang; Yang, Wei; Daud, Muhammad; Xiang, Jingjing; Mei, Lei

doi:10.1016/j.plasmid.2023.102670

Cited by 11 publications

(5 citation statements)

References 33 publications

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“…Nuclear SSR markers showed greater polymorphism whereas only one mitochondrial SSR marker showed polymorphism in our study. It was reported earlier that mitochondria and chloroplast SSRs in rice accession exhibited polymorphism [8,9]. The lack of polymorphism in our study may be explained by the same maternal origin of the genotypes under study or there may be technical difficulty to resolve small differences of PCR amplified products in agarose gel that we have used in gel electrophoresis.…”

Section: Discussionmentioning

confidence: 54%

Study of Genetic Diversity and Drought-Tolerance Characteristics of Few Rice Varieties Using Morphological and Molecular Markers

Kalita,

Saharia,

Thakur

et al. 2024

IJPSS

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Rice (Oryza sativa L.) is one of the most important cereal crops. Increasing rice production is constrained by various stresses and drought is one of the major limiting factors. For future food security, assessments of genetic resources are necessary. Indigenous varieties contain a high level of genetic diversity and can serve as potential genetic resources for improving yield, and resistance to various biotic and abiotic stress conditions. The present investigation was conducted in the Biotech Hub, Biswanath College of Agriculture, AAU, Biswanath Chariali during 2022-23. In this study, the genetic diversity of 27 indigenous rice germplasm using SSR markers was assessed. Out of the total 28 SSR markers screened, 17 were found polymorphic across twenty-seven genotypes with PIC values ranging from 0.076 to 0.499. The genetic diversity was estimated by the Jaccard dissimilarity coefficient. The phylogenetic tree, using unweighted neighbor-joining (UPGMA) drawn from the analysis divides 27 genotypes into 3 clusters. Nine genotypes were further characterized by exposure to drought stress compared to the control condition. Plants were grown in PVC pipes and subjected to drought by withdrawing water at 45 days after showing (DAS) for 25 days. A comparative study was done for a few morphophysiological parameters i.e. root length, root biomass, root-shoot ratio, root length density, chlorophyll content etc. It was observed that genotype Dehangi followed by N22 and Shahabhagi showed the best performance for all parameters under drought stress. This information will help in the selection of varieties with better root characteristics for drought tolerance in future breeding programs.

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Section: Discussionmentioning

confidence: 54%

Study of Genetic Diversity and Drought-Tolerance Characteristics of Few Rice Varieties Using Morphological and Molecular Markers

Kalita,

Saharia,

Thakur

et al. 2024

IJPSS

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“… 2021 ), Plectranthus barbatus (ON641315.1), Coleus hadiensis (OP611428.1), Hanceola exserta (MW238418.1; Zhu et al. 2023 ), Isodon serra (MT317099.1; Zhang et al. 2020 ), Siphocranion macranthum (MT473779.1; Zhao et al.…”

Section: Resultsmentioning

confidence: 99%

Chloroplast genome of Ocimum basilicum var. purpurascens Bentham 1830 (Lamiaceae)

Venkatesan,

Balaji,

Tanuja

et al. 2024

Mitochondrial DNA Part B

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Ocimum basilicum var. purpurascens Bentham 1830 (Red Rubin Basil) is an aromatic herb belonging to the family Lamiaceae and is known for its medicinal uses. It is commonly used in traditional medicine to treat cardiovascular diseases and obesity. It possesses anti-inflammatory, antioxidant, antifungal, and anti-spasmodic properties. In our recent study, we assembled the chloroplast genome sequence of O. basilicum var. purpurascens using Illumina paired-end sequencing technology. The assembled chloroplast genome was 152,407 base pairs (bp), inclusive of a large single-copy (LSC) region accounting for 83,409 bp and a small single-copy (SSC) region spanning 17,604 bp. Two inverted repeats (IRs) interspersed these regions, each 25,697 bp long. The chloroplast genome harbored 132 genes, comprising 88 protein-coding genes, 36 transfer RNA (tRNA), and eight rRNA genes. Among these, nine genes encompassed a single intron, two presented with two introns, with the remaining devoid of any introns. The overall GC content of the chloroplast genome was determined to be 38%. The GC content in the LSC, SSC, and IR regions was 35.9%, 31.6%, and 43.1%, respectively. Our phylogenetic exploration of the chloroplast genomes elucidated that O. basilicum var. purpurascens exhibits close genetic affinity with O. basilicum var. basilicum and other constituents of the Ocimum genus within the Lamiaceae family.

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“… 2023 ), Skapanthus oreophilus NC067672, Hanceola exserta NC056915 (Zhu et al. 2023 ), Gomphostemma lucidum MT473764, Leonurus japonicus NC038062 (Yang et al. 2006 ), Leonurus sibiricus NC 067787, Leonurus cardiaca NC058592 (Sun et al.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome of Leonurus sibiricus Linnaeus (Labiatae, Leonurus Miller)

Huang,

Men,

Bian

et al. 2024

Mitochondrial DNA Part B

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Leonurus sibiricus Linnaeus 1753, an annual or biennial herb found in northern China, Mongolia, and Russia, typically grows in stony, sandy grasslands, and pine forests. This study sequenced and reported the complete chloroplast genome of L. sibiricus for the first time. The entire circular genome measures 151,689 bp in length, with a GC content of 38.4%. A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNAs, and eight rRNAs. The genome exhibits a typical quadripartite structure, comprising a large single-copy (LSC 82,820 bp) region, a small single-copy (SSC 17,619 bp) region, and a pair of inverted repeat (IR 25,625 bp each) regions. Phylogenetic analysis using the maximum-likelihood method indicates that L. sibiricus is most closely related to L. japonicus Houttuyn. This study provides valuable genomic resources for further research on the phylogenetics and biodiversity of the genus Leonurus.

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SSR identification and phylogenetic analysis in four plant species based on complete chloroplast genome sequences

Cited by 11 publications

References 33 publications

Study of Genetic Diversity and Drought-Tolerance Characteristics of Few Rice Varieties Using Morphological and Molecular Markers

Study of Genetic Diversity and Drought-Tolerance Characteristics of Few Rice Varieties Using Morphological and Molecular Markers

Chloroplast genome of Ocimum basilicum var. purpurascens Bentham 1830 (Lamiaceae)

The complete chloroplast genome of Leonurus sibiricus Linnaeus (Labiatae, Leonurus Miller)

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