Characterization of the complete chloroplast genome of the ornamental plant  Osmanthus cooperi

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Abstract

Osmanthus cooperi is an evergreen ornamental plant belonging to the olive family. In this study, its complete chloroplast genome was assembled from the whole genome Illumina sequencing data. The circular genome is 155,262 bp long, and comprises a pair of inverted repeat regions (IRs, 25,685 bp each), a large single-copy region (LSC, 86,525 bp), and a small single-copy region (SSC, 17,367 bp). It encodes 132 genes, including 8 rRNA genes, 36 tRNAs genes, and 88 protein-coding genes. The GC content of O. cooperi cp genome is 37.8%. Phylogenetic analysis indicates that O. cooperi is close to O. fragrans in Oleaceae.

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CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

Chang Liu, Linchun Shi, Yingjie Zhu … (2012)

Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.

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Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution

Wan-Lin Dong, Ruo-Nan Wang, Na-Yao Zhang … (2018)

Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: Cremastra appendiculata, Calanthe davidii, Epipactis mairei, and Platanthera japonica. The size of the chloroplast genome ranged from 153,629 bp (C. davidi) to 160,427 bp (E. mairei). The gene order, GC content, and gene compositions are similar to those of other previously-reported angiosperms. We identified that the genes of ndhC, ndhI, and ndhK were lost in C. appendiculata, in that the ndh I gene was lost in P. japonica and E. mairei. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in orchid species. E. mairei had the highest number of repeats (81), while C. davidii had the lowest number (57). The total number of Simple Sequence Repeats is at least 50 in C. davidii, and, at most, 78 in P. japonica. Interestingly, we identified 16 genes with positive selection sites (the psbH, petD, petL, rpl22, rpl32, rpoC1, rpoC2, rps12, rps15, rps16, accD, ccsA, rbcL, ycf1, ycf2, and ycf4 genes), which might play an important role in the orchid species’ adaptation to diverse environments. Additionally, 11 mutational hotspot regions were determined, including five non-coding regions (ndhB intron, ccsA-ndhD, rpl33-rps18, ndhE-ndhG, and ndhF-rpl32) and six coding regions (rps16, ndhC, rpl32, ndhI, ndhK, and ndhF). The phylogenetic analysis based on whole cp genomes showed that C. appendiculata was closely related to C. striata var. vreelandii, while C. davidii and C. triplicate formed a small monophyletic evolutionary clade with a high bootstrap support. In addition, five subfamilies of Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae, formed a nested evolutionary relationship in the phylogenetic tree. These results provide important insights into the adaptive evolution and phylogeny of Orchidaceae.

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Plastid phylogenomics resolves infrafamilial relationships of the Styracaceae and sheds light on the backbone relationships of the Ericales.

Aiping Meng, Tao Feng, Michael Moore … (2018)

Relationships among the genera of the small, woody family Styracaceae and among families of the large, diverse order Ericales have resisted complete resolution with sequences from one or a few genes. We used plastome sequencing to attempt to resolve the backbone relationships of Styracaceae and Ericales and to explore plastome structural evolution. Complete plastomes for 23 species are newly reported here, including 18 taxa of Styracaceae and five of Ericales (including species of Sapotaceae, Clethraceae, Symplocaceae, and Diapensiaceae). Combined with publicly available complete plastome data, this resulted in a data set of 60 plastomes, including 11 of the 12 genera of Styracaceae and 12 of 22 families of Ericales. Styracaceae plastomes were found to possess the quadripartite structure typical of angiosperms, with sizes ranging from 155 to 159 kb. Most of the plastomes were found to possess the full complement of typical angiosperm plastome genes. Unusual structural features were detected in plastomes of Alniphyllum and Bruinsmia, including the presence of a large 20-kb inversion (14 genes) in the Large Single-Copy region, the loss or pseudogenization of the clpP and accD genes in Bruinsmia, and the loss of the first exon of rps16 in B. styracoides. Likewise, the second intron from clpP was found to be lost in Alniphyllum and Huodendron. Phylogenomic analyses including all 79 plastid protein-coding genes provided improved resolution for relationships among the genera of Styracaceae and families of Ericales. Styracaceae was strongly supported as monophyletic, with Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia successively sister to the remainder of the family, all with strong support. All genera of Styracaceae were recovered as monophyletic, except for Halesia and Pterostyrax, which were each recovered as polyphyletic with strong support. Within Ericales, all families were recovered as monophyletic with strong support, with Balsaminaceae sister to remaining Ericales. Most relationships recovered in plastome analyses are congruent with previous analyses based on smaller data sets. Our results demonstrate the power of plastid phylogenomics to improve phylogenetic hypotheses among genera and families, and provide new insight into plastome evolution across Ericales.

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Author and article information

Journal

Journal ID (nlm-ta): Mitochondrial DNA B Resour

Journal ID (iso-abbrev): Mitochondrial DNA B Resour

Title: Mitochondrial DNA. Part B, Resources

Publisher: Taylor & Francis

ISSN (Electronic): 2380-2359

Publication date (Electronic, pub): 11 July 2019

Publication date (Electronic, collection): 2019

Volume: 4

Issue: 2

Pages: 2314-2315

Affiliations

[a ]Department of Bioengineering, Huangshan Vocational and Technical College , Huangshan, Anhui, China;

[b ]Nanjing Foreign Language School , Nanjing, Jiangsu, China;

[c ]International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University , Nanjing, Jiangsu, China;

[d ]Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University , Nanjing, Jiangsu, China

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CONTACT Yifan Duan yifan419@ 123456hotmail.com International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University , Nanjing, Jiangsu, 210037, China

[*]

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Article

Publisher ID: 1627951

DOI: 10.1080/23802359.2019.1627951

PMC ID: 7687408

SO-VID: 6a4fc75b-49f0-4936-af00-2ae4b8d19953

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This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Characterization of the complete chloroplast genome of the ornamental plant Osmanthus cooperi

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CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution

Plastid phylogenomics resolves infrafamilial relationships of the Styracaceae and sheds light on the backbone relationships of the Ericales.

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