Chloroplast gene matK holds the barcodes for identification of Momordica (Cucurbitaceae) species from Indian subcontinent

Ramesh, Girme Aoudumbar; Mathew, Deepu; John, K. Joseph; Ravisankar, V.

doi:10.1016/j.hpj.2021.04.001

Cited by 11 publications

(5 citation statements)

References 44 publications

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“…Moreover, 13 intron-containing genes were detected in the A. argyi cp genome, all of which were located in the LSC. Among them, trnK-UUU had the largest intron, which contained matK ( Wang Y. et al, 2021 ); matK is a well-known gene that is widely used for molecular identification and analysis of genetic relationships in medicinal plants ( Hilu and Liang, 1997 ; Ramesh et al, 2022 ). Many intron-containing genes have important physiological functions; clpP is relevant to proteolysis ( Shikanai et al, 2001 ) and petB encodes the B6 protein, the core component of the cytochrome b6f complex ( Allen et al, 2011 ).…”

Section: Discussionmentioning

confidence: 99%

Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Chen

Miao²,

Luo³

et al. 2022

Front. Plant Sci.

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Artemisia argyi Levl. et Van is an important Asteraceae species with a high medicinal value. There are abundant A. argyi germplasm resources in Asia, especially in China, but the evolutionary relationships of these varieties and the systematic localization of A. argyi in the family Asteraceae are still unclear. In this study, the chloroplast (cp) genomes of 72 A. argyi varieties were systematically analyzed. The 72 varieties originated from 47 regions in China at different longitudes, latitudes and altitudes, and included both wild and cultivated varieties. The A. argyi cp genome was found to be ∼151 kb in size and to contain 114 genes, including 82 protein-coding, 28 tRNA, and 4 rRNA genes. The number of short sequence repeats (SSRs) in A. argyi cp genomes ranged from 35 to 42, and most of them were mononucleotide A/T repeats. A total of 196 polymorphic sites were detected in the cp genomes of the 72 varieties. Phylogenetic analysis demonstrated that the genetic relationship between A. argyi varieties had a weak relationship with their geographical distribution. Furthermore, inverted repeat (IR) boundaries of 10 Artemisia species were found to be significantly different. A sequence divergence analysis of Asteraceae cp genomes showed that the variable regions were mostly located in single-copy (SC) regions and that the coding regions were more conserved than the non-coding regions. A phylogenetic tree was constructed using 43 protein-coding genes common to 67 Asteraceae species. The resulting tree was consistent with the traditional classification system; Artemisia species were clustered into one group, and A. argyi was shown to be closely related to Artemisia lactiflora and Artemisia montana. In summary, this study systematically analyzed the cp genome characteristics of A. argyi and compared cp genomes of Asteraceae species. The results provide valuable information for the definitive identification of A. argyi varieties and for the understanding of the evolutionary relationships between Asteraceae species.

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Section: Discussionmentioning

confidence: 99%

Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Chen

Miao²,

Luo³

et al. 2022

Front. Plant Sci.

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“…The chloroplast genome regions (atpF-H, matK, and rbcL) have been used as candidate markers for DNA barcoding in plants to facilitate rapid identification of species [38,39]. Based on the results of mVISTA, nucleotide diversity, and comparative chloroplast genome analyses, 8 highly variable regions were identified in 50 cucumbers, including 3 intergenic regions (rbcL-accD, atpB-ycf3, and ndhF-trnN) and 5 gene regions (rbcL, psaB, clpP, accD, and ycf1).…”

Section: Discussionmentioning

confidence: 99%

Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber

Xia

Wang

Zhao

et al. 2023

IJMS

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Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616–157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339–86,883 bp), a small single copy (SSC, 18,069–18,363 bp), and two inverted repeats (IRs, 25,166–25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.

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“…Among them, the trnK-UUU gene embodied the matK genes and had the largest intron (over 2,500 bp), which has been reported in previous studies ( Li X. et al., 2019 ; Souza et al., 2020 ; Ren et al., 2022 ). matK is a well-known gene that is often used for molecular identification and analysis of genetic relationships in plants ( Hilu and Liang, 1997 ; Ramesh et al., 2022 ), including Morus ( Venkateswarlu et al., 2012 ). As a result, over one hundred matK genes of the Morus genus have been deposited in the GenBank of the NCBI.…”

Section: Discussionmentioning

confidence: 99%

Comparative and phylogenetic analyses of the chloroplast genome reveal the taxonomy of the Morus genus

et al. 2022

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Mulberry (genus Morus) is an economically important woody plant with an altered ploidy level. The variable number of Morus species recognized by different studies indicates that the genus is in need of revision. In this study, the chloroplast (CP) genomes of 123 Morus varieties were de novo assembled and systematically analyzed. The 123 varieties represented six Morus species, namely, Morus alba, Morus nigra, Morus notabilis, Morus rubra, Morus celtidifolia, and Morus serrata. The Morus CP genome was found to be 158,969~159,548 bp in size with 125 genes, including 81 protein coding, 36 tRNA, and 8 rRNA genes. The 87 out of 123 mulberry accessions were assigned to 14 diverse groups with identical CP genome, which indicated that they are maternally inherited and share 14 common ancestors. Then 50 diverse CP genomes occurred in 123 mulberry accessions for further study. The CP genomes of the Morus genus with a quadripartite structure have two inverted repeat (IR) regions (25,654~25,702 bp) dividing the circular genome into a large single-copy (LSC) region (87,873~88,243 bp) and small single-copy (SSC) region (19,740~19,994 bp). Analysis of the phylogenetic tree constructed using the complete CP genome sequences of Morus revealed a monophyletic genus and that M. alba consisted of two clades, M. alba var. alba and M. alba var. multicaulis. The Japanese cultivated germplasms were derived from M. alba var. multicaulis. We propose that the Morus genus be classified into six species, M. nigra, M. notabilis, M. serrata, M. celtidifolia, M. rubra, and M. alba with two subspecies, M. alba var. alba and M. alba var. multicaulis. Our findings provide a valuable resource for the classification, domestication, and breeding improvement of mulberry.

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Chloroplast gene matK holds the barcodes for identification of Momordica (Cucurbitaceae) species from Indian subcontinent

Cited by 11 publications

References 44 publications

Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber

Comparative and phylogenetic analyses of the chloroplast genome reveal the taxonomy of the Morus genus

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