The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L.

Guo, Xiaonong; Wang, Zhuanxia; Cai, Deyu; Song, Lei; Bai, Jialin

doi:10.1371/journal.pone.0261710

Cited by 10 publications

(7 citation statements)

References 61 publications

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“…At the same time, it is also a kind of molecular marker technology, which has been widely used in many research fields [24][25][26][27]. Due to their synchronous evolution, ITS sequences are found in many species, and there is relatively less intraspecific variation than interspecific variation [28,29]. Although the rbcL + matK composite sequence recommended by the International Plant Barcoding Working Group has a success rate of 86.3% in the identification of vascular plant taxa, there are still some taxa with a low success rate.…”

Section: Introductionmentioning

confidence: 99%

Genotypic Variation in Agronomic Traits and Molecular Markers among Chinese Luobuma (Apocynum spp.) Germplasm Accessions

Zhao,

Feng,

et al. 2024

Agriculture

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Apocynum spp., known as Chinese Luobuma species, are perennial herbaceous plants that not only have good ecological characteristics, such as drought resistance, salt resistance, freezing resistance, high-temperature resistance and wind sand resistance, but also have good medicinal and textile value. However, studies on the genetic variation in Chinese Luobuma are rare. In this study, the genotypic variation in the agronomic traits and molecular markers among eight germplasm accessions (referred to as genotypes) of Apocynum spp. was investigated. The accessions were evaluated at two locations in China, Altay and Yuzhong, during a three-year period. Analysis of the variance in yield-related traits revealed significant genotypic variation (p < 0.05) among the eight genotypes at the early flowering and full flowering stages. There were also significant (p < 0.05) genotype × year and genotype × location × year interactions for all the traits except leaf dry weight. In comparison to those evaluated at Yuzhong, the plant height, number of branches, leaf dry weight and stem dry weight at the early flowering stage were greater in Altay, with averages of 991.0 mm, 5.52, 26.41 g and 25.35 g, respectively. There were significant (p < 0.05) differences among genotypes in terms of the quality traits measured at the early and full flowering stages. The crude protein and crude fat content for each genotype at different locations at the early flowering stage in different years ranged from 8.64 to 10.07%. The average flavone (FLA) content was 2.31 mg/100 g. Principal component analysis (PCA) revealed that the G1 genotype in Altay had a higher neutral detergent fiber content and leaf dry weight, and the G2 genotype had a larger stem thickness, branch number and stem-to-leaf ratio. Five DNA sequences, ITS, matK, psbA-trnH, rbcL and trnL-F, were selected for analysis of the molecular variance in Chinese Luobuma. Analyses of molecular variance (AMOVA) based on the nuclear DNA sequences and chloroplast DNA sequences showed that most of the variation occurred within species. Our study indicated the significant genetic variation in Chinese Luobuma for future cultivar domestication. Genotypes with high leaf dry weights and many branches are beneficial for tea production, while tall plants with long internode lengths are valuable for the production of hemp.

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Section: Introductionmentioning

confidence: 99%

Genotypic Variation in Agronomic Traits and Molecular Markers among Chinese Luobuma (Apocynum spp.) Germplasm Accessions

Zhao,

Feng,

et al. 2024

Agriculture

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“…Apocynum is a perennial, persistent herb that grows mainly in harsh environments such as saline soils and deserts, and is widely used in saline land improvement, ecological restoration, textile and medicine [23][24][25][26][27][28][29]. Apocynum is divided into Apocynum venetum and Apocynum hendersonii, and these two species differ in morphological characteristics and physiological properties.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the PP2C gene family in Apocynum venetum and Apocynum hendersonii

Chen,

Wang,

et al. 2024

Preprint

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Background Protein phosphatase class 2C (PP2C) is the largest protein phosphatase family in plants, which plays an important role in plant growth and development and response to adversity stress. Apocynum is a perennial persistent herb, divided into Apocynum venetum and Apocynum hendersonii. It mainly grows in saline soil, desert and other harsh environments, and is widely used in saline soil improvement, ecological restoration, textile and medicine. It was found that Apocynum hendersonii is more tolerant of adverse conditions. The main purposeof this study was to investigate the PP2C gene family and its expression pattern under salt stress and to identify important candidate genes related to salt tolerance. Results In this study, 68 AvPP2C genes and 68 AhPP2C genes were identified from the genomes of Apocynum venetum and Apocynum hendersonii, respectively. They were classified into 13 subgroups based on their phylogenetic relationships and further analyzed for their subcellular locations, gene structures, conserved structural domains and cis-acting elements. The results of qRT-PCR analyses of seven AvPP2C genes and seven AhPP2C genes proved that they differed significantly in gene expression under salt stress. It has been observed that the PP2C genes in Apocynum venetum and Apocynum hendersonii exhibit different expression patterns. Specifically, AvPP2C2, 6, 24, 27, 41 and AhPP2C2, 6, 24, 27, 42 have shown significant differences in expression under salt stress. This indicates that these genes may play a crucial role in the salt tolerance mechanism of Apocynum venetumand Apocynum hendersonii. Conclusions In this study, we conducted a genome-wide analysis of the AvPP2C and AhPP2C gene families in Apocynum, which provided a reference for further understanding the functional characteristics of these genes.

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“…The lack of histone protection and a DNA damage repair system make the mitogenome more susceptible to mutations [11]. Additionally, assembling repetitive regions and obtaining complete mitogenome sequences are challenging tasks with shortread sequencing data from platforms like Illumina [12][13][14]. With the advent of long-read sequencing technologies by PacBio and Oxford Nanopore in recent years, sequencing plant mitogenomes has become more feasible and cost-effective [15,16].…”

Section: Introductionmentioning

confidence: 99%

The Complete Mitochondrial Genome of Paeonia lactiflora Pall. (Saxifragales: Paeoniaceae): Evidence of Gene Transfer from Chloroplast to Mitochondrial Genome

Tang,

Ni,

et al. 2024

Genes

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Paeonia lactiflora (P. lactiflora), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as well as the transference of DNA across organelle genomes. In order to investigate this matter, we sequenced and characterized the mitochondrial genome (mitogenome) of P. lactiflora. Similar to the chloroplast genome (cpgenome), the mitogenome of P. lactiflora extends across 181,688 base pairs (bp). Its unique quadripartite structure results from a pair of extensive inverted repeats, each measuring 25,680 bp in length. The annotated mitogenome includes 27 protein-coding genes, 37 tRNAs, 8 rRNAs, and two pseudogenes (rpl5, rpl16). Phylogenetic analysis was performed to identify phylogenetic trees consistent with Paeonia species phylogeny in the APG Ⅳ system. Moreover, a total of 12 MTPT events were identified and 32 RNA editing sites were detected during mitogenome analysis of P. lactiflora. Our research successfully compiled and annotated the mitogenome of P. lactiflora. The study provides valuable insights regarding the taxonomic classification and molecular evolution within the Paeoniaceae family.

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The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L.

Cited by 10 publications

References 61 publications

Genotypic Variation in Agronomic Traits and Molecular Markers among Chinese Luobuma (Apocynum spp.) Germplasm Accessions

Genotypic Variation in Agronomic Traits and Molecular Markers among Chinese Luobuma (Apocynum spp.) Germplasm Accessions

Genome-wide identification and expression analysis of the PP2C gene family in Apocynum venetum and Apocynum hendersonii

The Complete Mitochondrial Genome of Paeonia lactiflora Pall. (Saxifragales: Paeoniaceae): Evidence of Gene Transfer from Chloroplast to Mitochondrial Genome

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