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Feng LY, Shi C, Gao LZ. The complete chloroplast genome sequence of Bromus catharticus Vahl. (Poaceae). Mitochondrial DNA B Resour 2021; 6:2825-2827. [PMID: 34514141 PMCID: PMC8425758 DOI: 10.1080/23802359.2021.1970646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Bromus catharticus Vahl. belongs to the Pooideae subfamily of Poaceae. In this study, we sequenced and assembled the complete chloroplast genome of B. catharticus. The complete chloroplast genome was 134,718 bp in size, including a large single-copy region of 80,540 bp, a small single-copy region of 11,806 bp and a pair of reverse repeats of 21,186 bp in size. The annotation of B. catharticus indicates that it contained 89 protein-coding genes, 47 tRNA genes and eight rRNA genes. Our phylogenetic analysis of all protein-coding genes of the 36 grass complete chroloplast genomes using Cyperus rotundus as outgroup showed that B. catharticus is closely related to the Koeleria and Avena species to form the Pooideae lineage of the grass family.
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Affiliation(s)
- Li-Ying Feng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Chao Shi
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China.,Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Chiapella JO, Barfuss MHJ, Xue ZQ, Greimler J. The Plastid Genome of Deschampsia cespitosa (Poaceae). Molecules 2019; 24:E216. [PMID: 30634385 PMCID: PMC6359331 DOI: 10.3390/molecules24020216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/28/2018] [Accepted: 01/04/2019] [Indexed: 01/03/2023] Open
Abstract
Plastid genome analysis of non-model organisms provides valuable information for basic research e.g., molecular evolutionary genomics, phylogeny and phylogeography. Deschampsia cespitosa is the most widespread species of the genus and it is a common grass that is found across Eurasia and North America. Scattered populations in regions of appropriate ecological conditions are also found in Australia, New Zealand and southern South America, where it is sympatric with D. antarctica. We analyzed the plastid genome of a sample of Deschampsia cespitosa of the Austrian Alps using high-throughput sequencing. The plastid (cp) genome shows the typical quadripartite structure with a length of 135,340 bp, comprising a large single-copy (LSC) region of 79,992 bp, a small single-copy (SSC) region of 12,572 bp and two inverted repeats (IR) regions of 21,388 bp each. It contains 115 genes, including 85 protein-coding genes, four ribosomal RNA genes and 30 transfer RNA genes. The GC content (%), number of repeats and microsatellites, RNA editing sites and codon usage were highly similar to those of D. antarctica. The results of this present study highlight the extremely conserved nature of the cp genome in this group, since the comparison involved individuals separated by about 13,000 km, from the Alps to Antarctica.
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Affiliation(s)
- Jorge O Chiapella
- Instituto Multidisciplinario de Biología Vegetal (IMBIV-CONICET), Universidad Nacional de Córdoba, POB 495, Córdoba 5000, Argentina.
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
| | - Zhi-Qing Xue
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
| | - Josef Greimler
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
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Saarela JM, Burke SV, Wysocki WP, Barrett MD, Clark LG, Craine JM, Peterson PM, Soreng RJ, Vorontsova MS, Duvall MR. A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions. PeerJ 2018; 6:e4299. [PMID: 29416954 PMCID: PMC5798404 DOI: 10.7717/peerj.4299] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
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Affiliation(s)
- Jeffery M. Saarela
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Sean V. Burke
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - William P. Wysocki
- Center for Data Intensive Sciences, University of Chicago, Chicago, IL, USA
| | - Matthew D. Barrett
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, West Perth, WA, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lynn G. Clark
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Paul M. Peterson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Robert J. Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Maria S. Vorontsova
- Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Melvin R. Duvall
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA
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Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 2016; 17:134. [PMID: 27339192 PMCID: PMC4918201 DOI: 10.1186/s13059-016-1004-2] [Citation(s) in RCA: 738] [Impact Index Per Article: 92.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming Yu
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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