Comparative SNP Analysis of Chloroplast Genomes and 45S nrDNAs Reveals Genetic Diversity of <i>Perilla</i> Species

Cheon, Kyeong-Seong; Jeong, In-Seon; Kim, Kyung‐Hee; Lee, Myoung-Hee; Lee, Tae‐Ho; Lee, Jeong-Hee; Yoon, Ung-Han; Chandra, Romika; Lee, Yeji; Kim, Sang Woo

doi:10.9787/pbb.2018.6.2.125

Cited by 3 publications

(3 citation statements)

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“…The structure of chloroplast genomes was highly conserved in L. cardiaca, gene order and contents, while no large genome rearrangement or gene loss was detected. All genomes harbor 114 distinct genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes, which is consistent with other related species (Lukas and Novak, 2013;Qian et al, 2013;Cheon et al, 2018). The genes accD, rpl32, and ycf2 may be absent in some species, and they also do not occur in L. cardiaca (Jansen et al, 2007;Oliver et al, 2010;Wicke et al, 2011).…”

Section: Conserved Chloroplast Genome Structure Of L Cardiacasupporting

confidence: 76%

Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources

et al. 2021

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Leonurus cardiaca has a long history of use in western herbal medicine and is applied for the treatment of gynaecological conditions, anxiety, and heart diseases. Because of its botanical relationship to the primary Chinese species, L. japonicus, and extensive medical indications that go beyond the traditional indications for the Chinese species, it is a promising medicinal resource. Therefore, the features of genetic diversity and variability in the species have been prioritized. To explore these issues, we sequenced the chloroplast genomes of 22 accessions of L. cardiaca from different geographical locations worldwide using high-throughput sequencing. The results indicate that L. cardiaca has a typical quadripartite structure and range from 1,51,236 bp to 1,51,831 bp in size, forming eight haplotypes. The genomes all contain 114 distinct genes, including 80 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Comparative analysis showed abundant diversity of single nucleotide polymorphisms (SNPs), indels, simple sequence repeats (SSRs) in 22 accessions. Codon usage showed highly similar results for L. cardiaca species. The phylogenetic and network analysis indicated 22 accessions forming four clades that were partly related to the geographical distribution. In summary, our study highlights the advantage of chloroplast genome with large data sets in intraspecific diversity evaluation and provides a new tool to facilitate medicinal plant conservation and domestication.

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Section: Conserved Chloroplast Genome Structure Of L Cardiacasupporting

confidence: 76%

Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources

et al. 2021

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“…2020), 1.4 SNPs · kb ‐1 for six Perilla species (Cheon et al. 2018) or ~ 25 SNPs · kb ‐1 between 25 oat ( Avena ) species (Fu 2018). Thus, our data clearly show that foliose Ulva species are indeed separate taxa, with clear separation between species and a previously unknown high inter‐specific organellar genetic diversity (Figs.…”

Section: Discussionmentioning

confidence: 99%

Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild

Fort

McHale

Cascella

et al. 2020

Journal of Phycology

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Foliose Ulva spp. have become increasingly important worldwide for their environmental and financial impacts. A large number of such Ulva species have rapid reproduction and proliferation habits, which explains why they are responsible for Ulva blooms, known as “green tides”, having dramatic negative effects on coastal ecosystems, but also making them attractive for aquaculture applications. Despite the increasing interest in the genus Ulva, particularly on the larger foliose species for aquaculture, their inter‐ and intra‐specific genetic diversity is still poorly described. We compared the cytoplasmic genome (chloroplast and mitochondrion) of 110 strains of large distromatic foliose Ulva from Ireland, Brittany (France), the Netherlands and Portugal. We found six different species, with high levels of inter‐specific genetic diversity, despite highly similar or overlapping morphologies. Genetic variation was as high as 82 SNPs/kb between Ulva pseudorotundata and U. laetevirens, indicating considerable genetic diversity. On the other hand, intra‐specific genetic diversity was relatively low, with only 36 variant sites (0.03 SNPs/kb) in the mitochondrial genome of the 29 Ulva rigida individuals found in this study, despite different geographical origins. The use of next‐generation sequencing allowed for the detection of a single inter‐species hybrid between two genetically closely related species, U. laetevirens, and U. rigida, among the 110 strains analyzed in this study. Altogether, this study represents an important advance in our understanding of Ulva biology and provides genetic information for genomic selection of large foliose strains in aquaculture.

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“…The nrITS sequences were de novo assembled from the clean data using the GetOrganelle Toolkit ( Jin et al, 2020 ) and the annotation was carried out in Geneious by comparison with the reference sequence of Perilla frutescens (L.) Britton (GenBank accession number: KT220698 ; Cheon et al, 2018 ). For the sequences of ITS and ETS resulted from Sanger sequencing, trace files with both directions were assembled and edited using Geneious.…”

Section: Methodsmentioning

confidence: 99%

Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)

et al. 2022

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As one of the largest genera of Lamiaceae and of great medicinal importance, Isodon is also phylogenetically and taxonomically recalcitrant largely ascribed to its recent rapid radiation in the Hengduan Mountains. Previous molecular phylogenetic studies using limited loci have only successfully resolved the backbone topology of the genus, but the interspecific relationships suffered from low resolution, especially within the largest clade (Clade IV) which comprises over 80% species. In this study, we attempted to further elucidate the phylogenetic relationships within Isodon especially Clade IV using plastome sequences with a broad taxon sampling of ca. 80% species of the genus. To reduce systematic errors, twelve different plastome data sets (coding and non-coding regions with ambiguously aligned regions and saturated loci removed or not) were employed to reconstruct phylogeny using maximum likelihood and Bayesian inference. Our results revealed largely congruent topologies of the 12 data sets and recovered major lineages of Isodon consistent with previous studies, but several incongruences are also found among these data sets and among single plastid loci. Most of the shallow nodes within Clade IV were resolved with high support but extremely short branch lengths in plastid trees, and showed tremendous conflicts with the nrDNA tree, morphology and geographic distribution. These incongruences may largely result from stochasticity (due to insufficient phylogenetic signal) and hybridization and plastid capture. Therefore, the uniparental-inherited plastome sequences are insufficient to disentangle relationships within a genus which has undergone recent rapid diversification. Our findings highlight a need for additional data from nuclear genome to resolve the relationships within Clade IV and more focused studies to assess the influences of multiple processes in the evolutionary history of Isodon. Nevertheless, the morphology of the shape and surface sculpture/indumentum of nutlets is of systematic importance that they can distinguish the four major clades of Isodon.

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Comparative SNP Analysis of Chloroplast Genomes and 45S nrDNAs Reveals Genetic Diversity of Perilla Species

Cited by 3 publications

References 37 publications

Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources

Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources

Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild

Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)

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