Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex
Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid g...
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Genetics Society of America
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618348/ |
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pubmed-36183482013-04-08 Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex Hand, Melanie L. Spangenberg, German C. Forster, John W. Cogan, Noel O. I. Investigations Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. Genetics Society of America 2013-04-01 /pmc/articles/PMC3618348/ /pubmed/23550121 http://dx.doi.org/10.1534/g3.112.005264 Text en Copyright © 2013 Hand et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Hand, Melanie L. Spangenberg, German C. Forster, John W. Cogan, Noel O. I. |
| spellingShingle |
Hand, Melanie L. Spangenberg, German C. Forster, John W. Cogan, Noel O. I. Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex |
| author_facet |
Hand, Melanie L. Spangenberg, German C. Forster, John W. Cogan, Noel O. I. |
| author_sort |
Hand, Melanie L. |
| title |
Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex |
| title_short |
Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex |
| title_full |
Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex |
| title_fullStr |
Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex |
| title_full_unstemmed |
Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex |
| title_sort |
plastome sequence determination and comparative analysis for members of the lolium-festuca grass species complex |
| description |
Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. |
| publisher |
Genetics Society of America |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618348/ |
| _version_ |
1611968219580465152 |