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Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species.

ABSTRACT: The complete plastome sequences of six species were sequenced to better understand the evolutionary relationships and mutation patterns in the chloroplast genome of the genus Colobanthus. The length of the chloroplast genome sequences of C. acicularis, C. affinis, C. lycopodioides, C. nivicola, C. pulvinatus and C. subulatus ranged from 151,050 to 151,462 bp. The quadripartite circular structure of these genome sequences has the same overall organization and gene content with 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames. A total of 153 repeat sequences were revealed. Forward repeats were dominant, whereas complementary repeats were found only in C. pulvinatus. The mononucleotide SSRs composed of A/T units were most common, and hexanucleotide SSRs were detected least often. Eleven highly variable regions which could be utilized as potential markers for phylogeny reconstruction, species identification or phylogeography were identified within Colobanthus chloroplast genomes. Seventy-three protein-coding genes were used in phylogenetic analyses. Reconstructed phylogeny was consistent with the systematic position of the studied species, and the representatives of the same genus were grouped in one clade. All studied Colobanthus species formed a single group and C. lycopodioides was least similar to the remaining species.

SUBMITTER: Androsiuk P

PROVIDER: S-EPMC7359349 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species.

Androsiuk Piotr P Jastrzębski Jan Paweł JP Paukszto Łukasz Ł Makowczenko Karol K Okorski Adam A Pszczółkowska Agnieszka A Chwedorzewska Katarzyna Joanna KJ Górecki Ryszard R Giełwanowska Irena I

Scientific reports 20200713 1

The complete plastome sequences of six species were sequenced to better understand the evolutionary relationships and mutation patterns in the chloroplast genome of the genus Colobanthus. The length of the chloroplast genome sequences of C. acicularis, C. affinis, C. lycopodioides, C. nivicola, C. pulvinatus and C. subulatus ranged from 151,050 to 151,462 bp. The quadripartite circular structure of these genome sequences has the same overall organization and gene content with 73 protein-coding g ...[more]

PMID: 32661280

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Project description:BackgroundPolystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species.ResultsThe results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9-37.0%. Gene annotation revealed 106-109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust.ConclusionsOur study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae.

Project description:BackgroundBaitouweng is a traditional Chinese medicine with a long history of different applications. Although referred to as a single medicine, Baitouweng is actually comprised of many closely related species. It is therefore critically important to identify the different species that are utilized in these medicinal applications. Knowledge about their phylogenetic relationships can be derived from their chloroplast genomes and may provide additional insights into development of molecular markers.MethodsGenomic DNA was extracted from six species of Pulsatilla and then sequenced on an Illumina HiSeq 4000. Sequences were assembled into contigs by SOAPdenovo 2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the cp genomes of the six species were analyzed and compared with closely related species. Additionally, phylogenetic trees were constructed, based on single nucleotide polymorphisms (SNPs) and 51 shared protein-coding gene sequences in the cp genome among all 31 species via maximum likelihood.ResultsThe size of cp genomes of P. chinensis (Bge.) Regel, P. chinensis (Bge.) Regel var. kissii (Mandl) S. H. Li et Y. H. Huang, P. cernua (Thunb.) Bercht. et Opiz f. plumbea J. X. Ji et Y. T. zhao, P. dahurica (Fisch.) Spreng, P. turczaninovii Kryl. et Serg, and P. cernua (Thunb.) Bercht. et Opiz. were 163,851 bp, 163,756 bp, 162,481 bp, 162,450 bp, 162,795 bp, and 162,924 bp, respectively. Each species included two inverted repeat regions, a small single-copy region, and a large single-copy region. A total of 134 genes were annotated, including 90 protein-coding genes, 36 tRNAs, and eight rRNAs across all species. In simple sequence repeat analysis, only P. dahurica was found to contain hexanucleotide repeats. A total of 26, 39, 32, 37, 32 and 43 large repeat sequences were identified in the genic regions of the six Pulsatilla species. Nucleotide diversity analysis revealed that the rpl36 gene and ccsA-ndhD region have the highest Pi value. In addition, two phylogenetic trees of the cp genomes were constructed, which laced all Pulsatilla species into one branch within Ranunculaceae.ConclusionsWe identified and analyzed the cp genome features of six species of P. Miller, with implications for species identification and phylogenetic analysis.

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Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species.

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Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species.

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