Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

Zheng, Shuyu; Poczai, Péter; Hyvönen, Jaakko; Tang, Jing; Amiryousefi, Ali

doi:10.3389/fgene.2020.576124

Cited by 203 publications

(132 citation statements)

References 44 publications

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“…In addition, we used HMMER ( Wheeler and Eddy, 2013 ) and ARAGORN Version 1.2.38 ( Laslett and Canback, 2004 ) to ensure the prediction accuracy of the encoded protein and RNA genes, respectively. Finally, the resulting plastid genome maps were drawn with Chloroplot ( Zheng et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

Dong

Liu

et al. 2021

Front. Plant Sci.

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In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.

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Section: Methodsmentioning

confidence: 99%

Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

Dong

Liu

et al. 2021

Front. Plant Sci.

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“…: MT742578) on the NCBI website. The circular chloroplast genomic map of C. fargesii was drawn and visualized using Chloroplot online software (https://irscope.shinyapps.io/Chloroplot/ (accessed on 1 April 2021)) [28].…”

Section: Assembly and Annotation Of Chloroplast Genomementioning

confidence: 99%

Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

Ding

Dong

Yang

et al. 2021

Forests

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Clethra fargesii, an essential ecological and endemic woody plant of the genus Clethra in Clethraceae, is widely distributed in Central China. So far, there have been a paucity of studies on its chloroplast genome. In the present study, we sequenced and assembled the complete chloroplast genome of C. fargesii. We also analyzed the chloroplast genome features and compared them to Clethra delavayi and other closely related species in Ericales. The complete chloroplast genome is 157,486 bp in length, including a large single-copy (LSC) region of 87,034 bp and a small single-copy (SSC) region of 18,492 bp, separated by a pair of inverted repeat (IR) regions of 25,980 bp. The GC content of the whole genome is 37.3%, while those in LSC, SSC, and IR regions are 35.4%, 30.7%, and 43.0%, respectively. The chloroplast genome of C. fargesii encodes 132 genes in total, including 87 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. A total of 26,407 codons and 73 SSRs were identified in C. fargesii chloroplast genome. Additionally, we postulated and demonstrated that the structure of the chloroplast genome in Clethra species may present evolutionary conservation based on the comparative analysis of genome features and genome alignment among eight Ericales species. The low Pi values revealed evolutionary conservation based on the nucleotide diversity analysis of chloroplast genome in two Clethra species. The low selection pressure was shown by a few positively selected genes by adaptive evolution analysis using 80 coding sequences (CDSs) of the chloroplast genomes of two Clethra species. The phylogenetic tree showed that Clethraceae and Ericaceae are sister clades, which reconfirm the previous hypothesis that Clethra is highly conserved in the chloroplast genome using 75 CDSs of chloroplast genome among 40 species. The genome information and analysis results presented in this study are valuable for further study on the intraspecies identification, biogeographic analysis, and phylogenetic relationship in Clethraceae.

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“…To check the annotation results manually BLAST (v.2.8.1) and DOGMA was used [82]. A genomic map was generated by software Chloroplast [83] and inverted repeat sequences were identified through REPuter [84]. For tRNA detection tRNAscan-SE version 1.21 [85] was used.…”

Section: S Persica Chloroplast Assembly and Genome Annotationmentioning

confidence: 99%

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

et al. 2021

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Background Salvadora persica L. (Toothbrush tree – Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets available specifically on chloroplast (cp) genomics and taxonomic evolution. Herein, we have sequenced the complete chloroplast genome of S. persica for the first time and compared it with 11 related specie’s cp genomes from the order Brassicales. Results The S. persica cp genome was 153,379 bp in length containing a sizeable single-copy region (LSC) of 83,818 bp which separated from the small single-copy region (SSC) of 17,683 bp by two inverted repeats (IRs) each 25,939 bp. Among these genomes, the largest cp genome size (160,600 bp) was found in M. oleifera, while in S. persica it was the smallest (153,379 bp). The cp genome of S. persica encoded 131 genes, including 37 tRNA genes, eight rRNA genes and 86 protein-coding genes. Besides, S. persica contains 27 forward, 36 tandem and 19 palindromic repeats. The S. persica cp genome had 154 SSRs with the highest number in the LSC region. Complete cp genome comparisons showed an overall high degree of sequence resemblance between S. persica and related cp genomes. Some divergence was observed in the intergenic spaces of other species. Phylogenomic analyses of 60 shared genes indicated that S. persica formed a single clade with A. tetracantha with high bootstrap values. The family Salvadoraceae is closely related to Capparaceae and Petadiplandraceae rather than to Bataceae and Koberliniacaea. Conclusion The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, genome evolution and future genetic diversity-related studies of S. persica in complex angiosperm families.

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Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

Cited by 203 publications

References 44 publications

Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

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