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The two complete plastomes from Scrophularia (Scrophulariaceae): Scrophularia buergeriana and S. takesimensis.

ABSTRACT: The plastome sequences of Scrophularia buergeriana and S. takesimensis are completed in family Scrophulariaceae. The structure of two Scrophularia plastomes shows similar characteristic with the typical plastome of angiosperm. The lengths of two plastomes are 153,631bp and 152,436bp, respectively. They are divided into LSC region (84,454bp and 83,542bp) and SSC region (17,929bp and 17,938bp) by two IR regions (25,624bp and 25,478bp). Both plastomes contain 113 genes including 79 protein coding genes, 30 tRNA genes and 4 rRNA genes. Eight protein-coding, seven tRNA and four rRNA genes are duplicated in the IR regions. Eighteen genes have one or two intron(s). The overall A-T contents of two genomes are 62.0% and 61.9%, respectively. The A-T content in the non-coding (both 64.5%) is higher than in the coding (60.2% and 60.1%) region. Forty-four and forty-one simple sequence repeat (SSR) loci are identified in the S. buergeriana and S. takesimensis plastomes, respectively. In phylogenetic analysis, the genus Scrophularia shows closed relationship with Plantaginaceae.

SUBMITTER: Yi DK

PROVIDER: S-EPMC7800856 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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The two complete plastomes from Scrophularia (Scrophulariaceae): Scrophularia buergeriana and S. takesimensis.

Yi Dong-Keun DK Kim Ki-Joong KJ

Mitochondrial DNA. Part B, Resources 20160918 1

The plastome sequences of Scrophularia buergeriana and S. takesimensis are completed in family Scrophulariaceae. The structure of two Scrophularia plastomes shows similar characteristic with the typical plastome of angiosperm. The lengths of two plastomes are 153,631bp and 152,436bp, respectively. They are divided into LSC region (84,454bp and 83,542bp) and SSC region (17,929bp and 17,938bp) by two IR regions (25,624bp and 25,478bp). Both plastomes contain 113 genes includin ...[more]

PMID: 33473602

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Project description:BackgroundDomestic cultivation of medicinal plants is an important strategy for protecting these species from over harvesting. Some species of medicinal plants have been brought into cultivation for more than hundreds years. Concerns about severe loss of genetic diversity and sustainable cultivation can potentially limit future use of these valuable plants. Genetic studies with comprehensive sampling of multiple medicinal species by molecular markers will allow for assessment and management of these species. Here we examine the population genetic consequences of cultivation and domestication in Scrophularia ningpoensis Hemsl. We used chloroplast DNA and genomic AFLP markers to clarify not only the effects of domestication on genetic diversity, but also determine the geographic origins of cultivars and their genetic divergence from native populations. These results will allow both better management of cultivated populations, but also provide insights for crop improvement.ResultsTwenty-one cpDNA haplotypes of S. ningpoensis were identified. Wild populations contain all haplotypes, whereas only three haplotypes were found in cultivated populations with wild populations having twice the haplotype diversity of cultivated populations. Genetic differentiation between cultivated populations and wild populations was significant. Genomic AFLP markers revealed similar genetic diversity patterns. Furthermore, Structure analysis grouped all wild populations into two gene pools; two of which shared the same gene pool with cultivated S. ningpoensis. The result of Neighbor-Joining analysis was consistent with the structure analysis. In principal coordinate analysis, three cultivated populations from Zhejiang Province grouped together and were separated from other cultivated populations.ConclusionsThese results suggest that cultivated S. ningpoensis has experienced dramatic loss of genetic diversity under anthropogenic influence. We postulate that strong artificial selection for medicinal quality has resulted in genetic differentiation between cultivated and wild populations. Furthermore, it appears that wild populations in Jiangxi-Hunan area were involved in the origin of cultivated S. ningpoensis.

Project description:BackgroundSpiraea is a genus of deciduous shrubs that contains 80-120 species, is mainly distributed in the Northern Hemisphere and has diversified in East Asia. Spiraea species are cultivated as ornamental plants and some are used in traditional herbal medicine. Based on morphological characteristics and genetic markers, phylogenetic classification exhibits low discriminatory power.ResultsIn present study, we assembled and characterized the chloroplast (cp) genomes of ten Spiraea species and comparatively analysed with five reported cp genomes of this genus. The cp genomes of the fifteen Spiraea species, ranging from 155,904 to 158,637 bp in length, were very conserved and no structural rearrangements occurred. A total of 85 protein-coding genes (PCGs), 37 tRNAs and 8 rRNAs were annotated. We also examined 1,010 simple sequence repeat (SSR) loci, most of which had A/T base preference. Comparative analysis of cp genome demonstrated that single copy and non-coding regions were more divergent than the inverted repeats (IRs) and coding regions and six mutational hotspots were detected. Selection pressure analysis showed that all PCGs were under purifying selection. Phylogenetic analysis based on the complete cp genome data showed that Spiraea formed a monophyletic group and was further divided into two major clades. Infrageneric classification in each clade was supported with a high resolution value. Moreover, the phylogenetic trees based on each individual mutational hotspot segment and their combined dataset also consisted of two major clades, but most of the phylogenetic relationships of interspecies were not well supported.ConclusionsAlthough the cp genomes of Spiraea species exhibited high conservation in genome structure, gene content and order, a large number of polymorphism sites and several mutation hotspots were identified in whole cp genomes, which might be sufficiently used as molecular markers to distinguish Spiraea species. Phylogenetic analysis based on the complete cp genome indicated that infrageneric classification in two major clades was supported with high resolution values. Therefore, the cp genome data of the genus Spiraea will be effective in resolving the phylogeny in this genus.

Dataset Information

The two complete plastomes from Scrophularia (Scrophulariaceae): Scrophularia buergeriana and S. takesimensis.

Publications

The two complete plastomes from <i>Scrophularia</i> (Scrophulariaceae): <i>Scrophularia buergeriana</i> and <i>S. takesimensis</i>.

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