Genomic analysis and a consensus chloroplast genome sequence of Prunus yedoensis for DNA marker development

Roy, Neha Samir; Jeong, Ukhan; Na, Minho; Choi, Ik‐Young; Cheong, Eun Ju

doi:10.1007/s13580-020-00265-3

Cited by 6 publications

(7 citation statements)

References 53 publications

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“…In the cp genomes of 23 Prunus species here analyzed, mononucleotide SSRs were the most abundant, while SSRs with repeat motifs of two or more base pairs were scarce or absent, as have been reported in other angiosperms (Iram et al 2019;Niu et al 2020;Zeb et al 2020;Yik et al 2021). Among the mononucleotide SSRs, A/T repeats were found to be the most abundant, while G/C repeats were quite rare, similar to the previously reported cp genomes (Khan et al 2019;Chincoya et al 2020;Niu et al 2020;Roy et al 2020;Liu et al 2021), and this might be due to the AT-rich composition in the cp genome (Abdullah et al 2019). Most of the SSRs were located in the LSC region compared to SSC and IR regions; this result is consistent with several other studies in Artemisia scoparia (Iram et al 2019), Firmiana (Abdullah et al 2019), Lycium chinense (Yang et al 2019), Mammillaria (Chincoya et al 2020), and Olea europaea (Niu et al 2020).…”

Section: Discussionsupporting

confidence: 88%

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

Yan

et al. 2021

Tree Genetics & Genomes

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Prunus subgenus Cerasus is a large and diverse genus. Its botanical classification has long been controversial and complicated. Molecular markers derived from the chloroplast genome may provide useful tools for phylogenetic resolution and taxonomic study in Prunus species. Thus, we compared chloroplast genomes of 23 Prunus species to identify sequences with high variation levels. The repeated sequences (RSs) and two types of sequence variation, comprising divergent homologous regions and short sequence repeats (SSRs), were identified. The species with the highest number of RSs was P. emarginata (60), whereas P. campanulata contained the highest amount of SSRs (70). In contrast, P. dictyoneura and P. yedoensis contained the lowest number of RSs (37) and SSRs (46), respectively. Out of these homologous SSRs, 11 were shared in the 23 species, and seven of them showed variations. A total of 203 homologous regions were identified. Out of these, 20 regions (19 IGSs and one intron) showed a high variation from 6.75 to 19.31%. The phylogenetic tree which was inferred based on 19 highly variable regions showed a topology similar to the one obtained using the whole chloroplast genome. We conclude that the seven variable SSRs and the 20 highly variable regions may potentially be convenient as molecular markers for phylogenetic and population genetics studies in subgenus Cerasus species. In addition, the molecular phylogenetic position of P. clarofolia was inferred based on the 19 highly variable regions.

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Section: Discussionsupporting

confidence: 88%

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

Yan

et al. 2021

Tree Genetics & Genomes

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“…Furthermore, most mononucleotide and dinucleotide repeats are composed of A and T (Figure 7C,D; Table S2), which may contribute to a bias in base composition, congruent with other plastomes [71]. This indicates that the Crataegus chloroplast genome contains polyA and polyT repeats with irregular G and C repeats, similar to various other species [25,57]. In general, the SSRs in the four Crataegus plastomes examined in this study exhibit high levels of variation and can serve as potential molecular markers for future population genetic studies of Crataegus species.…”

Section: Repeat Structure and Ssr Analysis Of The Plastomes Of Crataegus Speciesmentioning

confidence: 56%

New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing

Wang

et al. 2021

Horticulturae

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Hawthorns (Crataegus L.) are one of the most important processing and table fruits in China, due to their medicinal properties and health benefits. However, the interspecific relationships and evolution history of cultivated Crataegus in China remain unclear. Our previously published data showed C. bretschneideri may be derived from the hybridization of C. pinnatifida with C. maximowiczii, and that introgression occurs between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. In the present study, chloroplast sequences were used to further elucidate the phylogenetic relationships of cultivated Crataegus native to China. The chloroplast genomes of three cultivated species and one related species of Crataegus were sequenced for comparative and phylogenetic analyses. The four chloroplast genomes of Crataegus exhibited typical quadripartite structures and ranged from 159,607 bp (C. bretschneideri) to 159,875 bp (C. maximowiczii) in length. The plastomes of the four species contained 113 genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Six hypervariable regions (ndhC-trnV(UAC)-trnM(CAU), ndhA, atpH-atpI, ndhF, trnR(UCU)-atpA, and ndhF-rpl32), 196 repeats, and a total of 386 simple sequence repeats were detected as potential variability makers for species identification and population genetic studies. In the phylogenomic analyses, we also compared the entire chloroplast genomes of three published Crataegus species: C. hupehensis (MW201730.1), C. pinnatifida (MN102356.1), and C. marshallii (MK920293.1). Our phylogenetic analyses grouped the seven Crataegus taxa into two main clusters. One cluster included C. bretschneideri, C. maximowiczii, and C. marshallii, whereas the other included C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. Taken together, our findings indicate that C. maximowiczii is the maternal origin of C. bretschneideri. This work provides further evidence of introgression between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major, and suggests that C. pinnatifida var. major might have been artificially selected and domesticated from hybrid populations, rather than evolved from C. pinnatifida.

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“…Several types of DNA-based molecular markers, such as simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), and Insertions/Deletions (InDels) have been developed and used for the identification of nucellar/zygotic individuals (Woo et al, 2019), the efficiency test of hybrid embryo rescue (Kim et al, 2020), species/cultivar identification (Woo et al, 2020;Jin et al, 2020), and phylogenetic origin analysis in citrus (Curk et al, 2016). SSRs and InDel markers from the mitochondria and/or chloroplast genomes are widely used for the identification and authentication of crop cultivars (Curk et al, 2016;Park et al, 2017;Roy et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Development of Plastid InDel Markers to Discriminate Lemons from Other Citrus Groups

Kim¹,

Kim²,

Park³

et al. 2021

HST

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Lemon (Citrus limon), an interspecific hybrid between sour orange and citron, has been widely used as a rootstock along with trifoliate orange. Though lemons are superior to trifoliate orange in terms of their high seed germination rate throughout the year, one of the obstacles to using lemons as rootstocks is the lack of reliable, lemon-specific molecular markers to discriminate buds of the micro-grafted scion from those of the lemon rootstock. In order to obtain lemon-specific molecular markers, we compared the whole-plastid genomes available from four citrus species (lemon, pummelo, sweet orange, and mandarin) and developed seven plastid insertion/deletion (InDel) markers. The plastid InDel markers were applied to 46 citrus accessions that included lemons (17 accessions), grapefruit, mandarin, pummelo, sour orange, orange, papeda, tangor, and tangelo groups. The resulting dendrogram revealed that the citrus accessions used in this analysis could be distinctly classified into seven clusters. Lemons formed a separate cluster and had identical allele sizes for each InDel locus among all accessions investigated. This set of InDel markers could be a useful molecular tool for the rapid and clear discrimination of micro-grafted scions and lemon rootstocks during the production of virus-free citrus trees. The plastid InDel markers with maternal inheritance features can also be used to analyze the phylogenetic origin of various citrus cultivars including lemons.

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Genomic analysis and a consensus chloroplast genome sequence of Prunus yedoensis for DNA marker development

Cited by 6 publications

References 53 publications

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing

Development of Plastid InDel Markers to Discriminate Lemons from Other Citrus Groups

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