Chloroplast genomes of seven species of Coryloideae (Betulaceae): structures and comparative analysis

Genome ◽  
2020 ◽  
Vol 63 (7) ◽  
pp. 337-348
Author(s):  
Guanglong Hu ◽  
Lili Cheng ◽  
Wugang Huang ◽  
Qingchang Cao ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Information ◽  
Molecular Breeding ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Mutational Hotspots ◽  
The Family ◽  
Identification Of Species

Coryloideae is a subfamily in the family Betulaceae consisting of four extant genera: Carpinus, Corylus, Ostrya, and Ostryopsis. We sequenced the plastomes of six species of Corylus and one species of Ostryopsis for comparative and phylogenetic analyses. The plastomes are 159–160 kb long and possess typical quadripartite cp architecture. The plastomes show moderate divergence and conserved arrangement. Five mutational hotspots were identified by comparing the plastomes of seven species of Coryloideae: trnG-atpA, trnF-ndhJ, accD-psaI, ndhF-ccsA, and ycf1. We assembled the most complete phylogenomic tree for the family Betulaceae using 68 plastomes. Our cp genomic sequence phylogenetic analyses placed Carpinus, Ostrya, and Ostryopsis in a clade together and left Corylus in a separate clade. Within the genus Corylus, these analyses indicate the existence of five subclades reflecting the phylogeographical relationships among the species. The data offer significant genetic information for the identification of species of the Coryloideae, taxonomic and phylogenetic studies, and molecular breeding.

scholarly journals Complete chloroplast genomes of Impatiens cyanantha and Impatiens monticola: Insights into genome structures, mutational hotspots, comparative and phylogenetic analysis with its congeneric species

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0248182
Author(s):  
Chao Luo ◽  
Yang Li ◽  
Roshani Budhathoki ◽  
Jiyuan Shi ◽  
Huseyin Yer ◽  
...  
Keyword(s):  
Sister Relationship ◽  
Protein Coding ◽  
Important Species ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Mutational Hotspots ◽  
Identification Of Species ◽  
The Comparative Study ◽  
Rna Genes ◽  
Different Altitudes

Impatiens L., the largest genus in the family Balsaminaceae with approximately 1000 species, is a controversial and complex genus that includes many economically important species well known for medicinal and ornamental values. However, there is limited knowledge of molecular phylogeny and chloroplast genomics, and uncertainties still exist at a taxonomic level. In this study, we have assembled four chloroplast genomics specimens of Impatiens cyanantha and Impatiens monticola, which are found at the different altitudes of Guizhou and Yunnan in China, and compared them with previously published three wild Balsaminaceae species (Impatiens piufanensis, Impatiens glandlifera, and Hydrocera triflora). The complete chloroplast genome sequences ranged from 152,236 bp (I. piufanensis) to 154,189 bp (H. triflora) and encoded 115 total distinct genes, of which 81 were protein-coding, 30 were distinct transfer RNA genes(tRNA), and 4 were ribosomal RNA genes (rRNA). A comparative analysis of I. cyanantha (Guizhou) vs. I. cyanantha (Yunnan) and I. monticola (Guizhou) vs. I. monticola (Yunnan) revealed minor changes in lengths; however, similar gene contents, gene orders, and GC contents existed among them. Interestingly, highly coding and non-coding genes, and regions matK, psbK, atpH-atpI, trnC-trnT, petN, psbM, atpE, rbcL, accD, psaL, rps3-rps19, ndhG-ndhA,rpl16, rpoB, ndhB, ndhF, ycf1, and ndhH were found, which could be suitable for identification of species and phylogenetic studies. During the comparison between I. cyanantha (Guizhou) and I. cyanantha (Yunnan), we observed that the rps4, ycf2, ndhF, ycf1, and rpoC2 genes underwent positive selection. Meanwhile, in the comparative study of I. monticola (Guizhou) vs. I. monticola (Yunnan), The accD and ycf1 genes were positively selected. Additionally, phylogenetic relationships based on maximum likelihood (ML) and Bayesian inference (BI) among whole chloroplast genomes showed that a sister relationship with I. monticola (Guizhou) and I. monticola (Yunnan) formed a clade with I.piufanensis proving their close connection. Besides, I.cyanantha (Guizhou) and I. cyanantha (Yunnan) formed a clade with I. glandlifera. Along with the findings and the results, the current study might provide valuable significant genomic resources for systematics and evolution of the genus impatiens in different altitudes of regions.

scholarly journals The genus Microniphargus (Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer from Niphargidae to Pseudoniphargidae

2021 ◽  
Vol 151 ◽  
Author(s):  
Dieter Weber ◽  
Fabio Stoch ◽  
Lee R.F.D. Knight ◽  
Claire Chauveau ◽  
Jean-François Flot
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Phylogenetic Analyses ◽  
Ribosomal Gene ◽  
Phylogenetic Position ◽  
Mitochondrial Cytochrome ◽  
Monotypic Genus ◽  
Centre Of Origin ◽  
Phylogenetic Studies ◽  
The Family

Microniphargus leruthi Schellenberg, 1934 (Amphipoda: Niphargidae) was first described based on samples collected in Belgium and placed in a monotypic genus within the family Niphargidae. However, some details of its morphology as well as recent phylogenetic studies suggest that Microniphargus may be more closely related to Pseudoniphargus (Amphipoda: Pseudoniphargidae) than to Niphargus. Moreover, M. leruthi ranges over 1,469 km from Ireland to Germany, which is striking since only a few niphargids have confirmed ranges in excess of 200 km. To find out the phylogenetic position of M. leruthi and check whether it may be a complex of cryptic species, we collected material from Ireland, England and Belgium then sequenced fragments of the mitochondrial cytochrome c oxidase subunit 1 gene as well as of the nuclear 28S ribosomal gene. Phylogenetic analyses of both markers confirm that Microniphargus is closer to Pseudoniphargus than to Niphargus, leading us to reallocate Microniphargus to Pseudoniphargidae. We also identify three congruent mito-nuclear lineages present respectively in Ireland, in both Belgium and England, and in England only (with the latter found in sympatry at one location), suggesting that M. leruthi is a complex of at least three species with a putative centre of origin in England.

scholarly journals Characterization and Comparative Analysis of Two Rheum Complete Chloroplast Genomes

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Kaihui Zhao ◽  
Lianqiang Li ◽  
Yazhou Lu ◽  
Junbo Yang ◽  
Zhirong Zhang ◽  
...  
Keyword(s):  
Economic Value ◽  
Evolutionary Analysis ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Circular Structure ◽  
Mutational Hotspots ◽  
Single Clade ◽  
History Of ◽  
History Of Use ◽  
Genome Scale

Rheum species present a significant economic value. Traditional Chinese medicine rhubarb is an important medicinal material in China. It has a long history of use, with a record of use as early as two thousand years ago. Here, we determined the complete chloroplast genome sequences of Rheum nobile and Rheum acuminatum and comprehensively compared them to two other available Rheum cp genomes at the genome scale. The results revealed cp genomes ranging in size from 159,051 to 161,707 bp with a similar typical quadripartite and circular structure. The genome organization, gene numbers, gene order, and GC contents of these four Rheum cp genomes were similar to those of many angiosperm cp genomes. Repeats and microsatellites were detected in the R. nobile and R. acuminatum cp genomes. The Mauve alignment revealed that there were no rearrangements in the cp genomes of the four Rheum species. Thirteen mutational hotspots for genome divergence were identified, which could be utilized as potential markers for phylogenetic studies and the identification of Rheum species. The phylogenetic relationships of the four species showed that the members of Rheum cluster into a single clade, indicating their close relationships. Our study provides valuable information for the taxonomic, phylogenetic, and evolutionary analysis of Rheum.

scholarly journals Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6032 ◽  
Author(s):  
Zhenyu Zhao ◽  
Xin Wang ◽  
Yi Yu ◽  
Subo Yuan ◽  
Dan Jiang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Genomic Resources ◽  
Chloroplast Genomes ◽  
The Family ◽  
Small Single Copy

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.

scholarly journals Comparison and Phylogenetic Analyses of Nine Complete Chloroplast Genomes of Zingibereae

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 710
Author(s):  
Heng Liang ◽  
Juan Chen
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
The Family ◽  
Phylogenomic Analyses ◽  
Close Relatives ◽  
Rna Genes ◽  
Insight Into ◽  
Simple Sequence

Zingibereae is a large tribe in the family Zingiberaceae, which contains plants with important medicinal, edible, and ornamental values. Although tribes of Zingiberaceae are well circumscribed, the circumscription of many genera within Zingibereae and the relationships among them remain elusive, especially for the genera of Boesenbergia, Curcuma, Kaempferia and Pyrgophyllum. In this study, we investigated the plastome variation in nine species representing five genera of Zingibereae. All plastomes showed a typical quadripartite structure with lengths ranging from 162,042 bp to 163,539 bp and contained 132–134 genes, consisting of 86–88 coding genes, 38 transfer RNA genes and eight ribosomal RNA genes. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were detected. In addition, we conducted phylogenomic analyses of the Zingibereae and related taxa with plastomes data from additional 32 species from Genbank. Our results confirmed that Stahlianthus is closely related to Curcuma, supporting the idea of merging it into Curcuma. Kaempferia, Boesenbergia and Zingiber were confirmed as close relatives and grouped together as the Kaempferia group. Pyrgophyllum is not allied with the Curcuma clade but instead is embedded within the Hedychium clade. Our results demonstrate the power of plastid phylogenomics in improving the phylogenetic relationships within Zingibereae and provide a new insight into plastome evolution in Zingibereceae.

scholarly journals Mutational Dynamics of Aroid Chloroplast Genomes II

2021 ◽  
Vol 11 ◽  
Author(s):  
Abdullah ◽  
Claudia L. Henriquez ◽  
Thomas B. Croat ◽  
Peter Poczai ◽  
Ibrar Ahmed
Keyword(s):  
Correlation Coefficients ◽  
Large Family ◽  
Nucleotide Polymorphisms ◽  
Strong Correlations ◽  
Crown Group ◽  
Sequence Alignments ◽  
Chloroplast Genomes ◽  
Basal Group ◽  
Mutational Hotspots ◽  
The Family

The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.

scholarly journals Title: The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species

2021 ◽  
Author(s):  
Mahtab Moghaddam ◽  
Atsushi Ohta ◽  
Motoki Shimizu ◽  
Ryohei Terauchi ◽  
Shahrokh Kazempour-Osaloo
Keyword(s):  
Comparative Analysis ◽  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Paired End Sequencing

Abstract Plastid genome sequences provide valuable markers for surveying the evolutionary relationships and population genetics of plant species. In the present study, the complete plastid genome of Onobrychis gaubae, endemic to Iran, was sequenced using Illumina paired-end sequencing and was compared with previously known genomes of the IRLC species of legumes. The O. gaubae plastid genome was 123,645 bp in length and included a large single-copy (LSC) region of 81,034 bp, a small single-copy (SSC) region of 13,788 bp and one copy of the inverted repeat (IRb) of 28,823 bp. The genome encoded 110 genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes and possessed 89 simple sequence repeats (SSRs) and 28 repeated structures with the highest proportion in the LSC. Comparative analysis of the chloroplast genomes across IRLC revealed three hotspot genes (ycf1, ycf2, clpP) which could be used as molecular markers for resolving phylogenetic relationships and species identification. IRLC plastid genomes also showed multiple gene losses and inversions. Phylogenetic analyses revealed that O. gaubae is closely related to Hedysarum. The complete O. gaubae genome is a valuable resource for investigating evolution of Onobrychis species and can be used to identify related species.

scholarly journals Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Forests ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 861
Author(s):  
Huijuan Zhou ◽  
Xiaoxiao Gao ◽  
Keith Woeste ◽  
Peng Zhao ◽  
Shuoxin Zhang
Keyword(s):  
Comparative Analysis ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Species Hybrids ◽  
Rna Genes

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

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