Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Hand, Melanie L., Spangenberg, German C., Forster, John W., Cogan, Noel O. I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618348/
https://www.ncbi.nlm.nih.gov/pubmed/23550121
http://dx.doi.org/10.1534/g3.112.005264
_version_ 1782265406412554240
author Hand, Melanie L.
Spangenberg, German C.
Forster, John W.
Cogan, Noel O. I.
author_facet Hand, Melanie L.
Spangenberg, German C.
Forster, John W.
Cogan, Noel O. I.
author_sort Hand, Melanie L.
collection PubMed
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.
format Online
Article
Text
id pubmed-3618348
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Genetics Society of America
record_format MEDLINE/PubMed
spelling 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. G3 (Bethesda) 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.
spellingShingle Investigations
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
title 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_short 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
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618348/
https://www.ncbi.nlm.nih.gov/pubmed/23550121
http://dx.doi.org/10.1534/g3.112.005264
work_keys_str_mv AT handmelaniel plastomesequencedeterminationandcomparativeanalysisformembersoftheloliumfestucagrassspeciescomplex
AT spangenberggermanc plastomesequencedeterminationandcomparativeanalysisformembersoftheloliumfestucagrassspeciescomplex
AT forsterjohnw plastomesequencedeterminationandcomparativeanalysisformembersoftheloliumfestucagrassspeciescomplex
AT cogannoeloi plastomesequencedeterminationandcomparativeanalysisformembersoftheloliumfestucagrassspeciescomplex