Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

Xu, Jin; Liu, Chen; Song, Yun; Li, Mingfu

doi:10.3389/fgene.2021.687844

Cited by 14 publications

(8 citation statements)

References 82 publications

(94 reference statements)

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“…The SSRs numbers in the LSC region of plastome of R. coccinea and R. philippinensis are 53 and 47, respectively. The distribution of SSR in the four species of Renanthera was consistent with that of most angiosperms (Xu et al, 2021;Sun et al, 2022;Xia et al, 2022).…”

Section: Discussionsupporting

confidence: 68%

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

Xiao

Zhang

et al. 2022

Front. Genet.

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Owing to its attractive flower shape and color, Renanthera (Orchidaceae), comprising about 19 species, has significant ornamental value as a houseplant, in floral design and in landscape gardens. Two species of Renanthera are categorized as endangered and critically endangered in China’s Red List and international trade in these orchids is currently strictly monitored by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). This paper reports on the de novo assembled and annotated plastome of four species of Renanthera; R. citrina, R. coccinea, R. imschootiana, and R. philippinensis. The length of the plastome sequences ranged from 144,673 bp (R. imschootiana) to 149,007 bp (R. coccinea) with GC content of 36.6–36.7%. The plastomes showed a typical quadripartite structure, including a large single-copy (84,241–86,404 bp), a small single-copy (11,468–12,167 bp), and a pair of inverted repeats (24,482–25,715 bp) regions. Of the 120 genes detected, 74 were protein coding, 38 were tRNA, and eight were rRNA genes. The plastome of Renanthera is rather conserved, but nucleotide variations that could distinguish them apart are noticeable—the total number of tandem repeats ranged from 62 (in R. imschootiana) to 74 (in R. citrina); while the number of long repeats ranged from 21 (in R. imschootiana and R. philippinensis) to 43 (in R. citrina). Three hypervariable regions (psbI-trnS-GCU, trnG-GCC, rpl32) were identified. Phylogenetic analyses based on the CDS using maximum likelihood (ML) and Bayesian inference (BI) revealed that Renanthera is closely related to Holcoglossum, Neofinetia, Pendulorchis, and Vanda. The relationship between the four species of Renanthera was fully resolved; a monophyletic clade was formed and R. coccinea was recorded as the first to diverge from the rest. The genetic data obtained from this study could serve as a useful resource for species identification in Renanthera as well as contribute to future research on the phylogenomics of Orchidaceae.

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Section: Discussionsupporting

confidence: 68%

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

Xiao

Zhang

et al. 2022

Front. Genet.

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“…The results of this study provide strong evidence for elucidating the evolutionary history of these species and deeply analyzing the evolutionary events of Catalpa and even Bignoniaceae. The further development of sequencing technology will help fully reveal the general characteristics and patterns of variation of the chloroplast genome and provide a foundation for resolving the differences between morphological and genetic classification and for obtaining an in-depth understanding of plant evolution ( Xu et al, 2021 ). However, due to the limited number of published chloroplast genomes of taxa within the genus Catalpa , there are still many difficulties in phylogenetic studies of this group.…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of Chloroplast Genome Structure and Phylogenetic Relationships Among Six Taxa Within the Genus Catalpa (Bignoniaceae)

et al. 2022

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Species within the Genus Catalpa are mostly semievergreen or deciduous trees with opposite or whorled leaves. C. bungei, C. fargesii f. duclouxii and C. fargesii are sources of traditional precious wood in China, known as the “kings of wood”. Due to a lack of phenotypic and molecular studies and insufficient sequence information, intraspecific morphological differences, common DNA barcodes and partial sequence fragments cannot clearly reveal the phylogenetic or intraspecific relationships within Catalpa. Therefore, we sequenced the complete chloroplast genomes of six taxa of the genus Catalpa and analyzed their basic structure and evolutionary relationships. The chloroplast genome of Catalpa shows a typical tetrad structure with a total length ranging from 157,765 bp (C. fargesii) to 158,355 bp (C. ovata). The length of the large single-copy (LSC) region ranges from 84,599 bp (C. fargesii) to 85,004 bp (C. ovata), that of the small single-copy (SSC) region ranges from 12,662 bp (C. fargesii) to 12,675 bp (C. ovata), and that of the inverted repeat (IR) regions ranges from 30,252 bp (C. fargesii) to 30,338 bp (C. ovata). The GC content of the six chloroplast genomes were 38.1%. In total, 113 unique genes were detected, and there were 19 genes in IR regions. The 113 genes included 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Five hypervariable regions (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA and rps15) were identified by analyzing chloroplast nucleotide polymorphisms, which might be serve as potential DNA barcodes for the species. Comparative analysis showed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were highly diverse in the six species. Codon usage patterns were highly similar among the taxa included in the present study. In addition to the stop codons, all codons showed a preference for ending in A or T. Phylogenetic analysis of the entire chloroplast genome showed that all taxa within the genus Catalpa formed a monophyletic group, clearly reflecting the relationships within the genus. This study provides information on the chloroplast genome sequence, structural variation, codon bias and phylogeny of Catalpa, which will facilitate future research efforts.

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“…Until now, chloroplast markers and complete chloroplast genomes of plants have been widely used and have made significant contributions to phylogeny reconstruction at different taxonomic levels in plants [31,32] including species of the genus Pulsatilla [33][34][35][36]. Plastid phylogenomic analyses, among others, showed that the species of Pulsatilla formed a monophyletic group, and should not be synonymized with the genus Anemone.…”

Section: Discussionmentioning

confidence: 99%

Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?—A Case Study of Pulsatilla patens (L.) Mill

Szandar

Sawicki

Paukszto

et al. 2022

Genes

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Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD—ccsA, rps4—rps16, and trnL(UAG)—ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes—11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset.

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Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

Cited by 14 publications

References 82 publications

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

Comparative Analysis of Chloroplast Genome Structure and Phylogenetic Relationships Among Six Taxa Within the Genus Catalpa (Bignoniaceae)

Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?—A Case Study of Pulsatilla patens (L.) Mill

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