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The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation

BACKGROUND: Plant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm sp...

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Autores principales: Kersten, Birgit, Rellstab, Christian, Schroeder, Hilke, Brodbeck, Sabine, Fladung, Matthias, Krutovsky, Konstantin V., Gugerli, Felix
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9703787/
https://www.ncbi.nlm.nih.gov/pubmed/36443651
http://dx.doi.org/10.1186/s12864-022-08993-9
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author Kersten, Birgit
Rellstab, Christian
Schroeder, Hilke
Brodbeck, Sabine
Fladung, Matthias
Krutovsky, Konstantin V.
Gugerli, Felix
author_facet Kersten, Birgit
Rellstab, Christian
Schroeder, Hilke
Brodbeck, Sabine
Fladung, Matthias
Krutovsky, Konstantin V.
Gugerli, Felix
author_sort Kersten, Birgit
collection PubMed
description BACKGROUND: Plant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm species that is widely distributed in Europe and occupies a large range of environmental conditions. Reference sequences of the nuclear and chloroplast genome of A. alba are available, however, the mitogenome has not yet been assembled and studied. RESULTS: Here, we used paired-end Illumina short reads generated from a single haploid megagametophyte in combination with PacBio long reads from high molecular weight DNA of needles to assemble the first mitogenome sequence of A. alba. Assembly and scaffolding resulted in 11 mitogenome scaffolds, with the largest scaffold being 0.25 Mbp long. Two of the scaffolds displayed a potential circular structure supported by PCR. The total size of the A. alba mitogenome was estimated at 1.43 Mbp, similar to the size (1.33 Mbp) of a draft assembly of the Abies firma mitogenome. In total, 53 distinct genes of known function were annotated in the A. alba mitogenome, comprising 41 protein-coding genes, nine tRNA, and three rRNA genes. The proportion of highly repetitive elements (REs) was 0.168. The mitogenome seems to have a complex and dynamic structure featured by high combinatorial variation, which was specifically confirmed by PCR for the contig with the highest mapping coverage. Comparative analysis of all sequenced mitogenomes of gymnosperms revealed a moderate, but significant positive correlation between mitogenome size and proportion of REs. CONCLUSIONS: The A. alba mitogenome provides a basis for new comparative studies and will allow to answer important structural, phylogenetic and other evolutionary questions. Future long-read sequencing with higher coverage of the A. alba mitogenome will be the key to further resolve its physical structure. The observed positive correlation between mitogenome size and proportion of REs will be further validated once available mitogenomes of gymnosperms would become more numerous. To test whether a higher proportion of REs in a mitogenome leads to an increased recombination and higher structural complexity and variability is a prospective avenue for future research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08993-9.
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spelling pubmed-97037872022-11-29 The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation Kersten, Birgit Rellstab, Christian Schroeder, Hilke Brodbeck, Sabine Fladung, Matthias Krutovsky, Konstantin V. Gugerli, Felix BMC Genomics Research BACKGROUND: Plant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm species that is widely distributed in Europe and occupies a large range of environmental conditions. Reference sequences of the nuclear and chloroplast genome of A. alba are available, however, the mitogenome has not yet been assembled and studied. RESULTS: Here, we used paired-end Illumina short reads generated from a single haploid megagametophyte in combination with PacBio long reads from high molecular weight DNA of needles to assemble the first mitogenome sequence of A. alba. Assembly and scaffolding resulted in 11 mitogenome scaffolds, with the largest scaffold being 0.25 Mbp long. Two of the scaffolds displayed a potential circular structure supported by PCR. The total size of the A. alba mitogenome was estimated at 1.43 Mbp, similar to the size (1.33 Mbp) of a draft assembly of the Abies firma mitogenome. In total, 53 distinct genes of known function were annotated in the A. alba mitogenome, comprising 41 protein-coding genes, nine tRNA, and three rRNA genes. The proportion of highly repetitive elements (REs) was 0.168. The mitogenome seems to have a complex and dynamic structure featured by high combinatorial variation, which was specifically confirmed by PCR for the contig with the highest mapping coverage. Comparative analysis of all sequenced mitogenomes of gymnosperms revealed a moderate, but significant positive correlation between mitogenome size and proportion of REs. CONCLUSIONS: The A. alba mitogenome provides a basis for new comparative studies and will allow to answer important structural, phylogenetic and other evolutionary questions. Future long-read sequencing with higher coverage of the A. alba mitogenome will be the key to further resolve its physical structure. The observed positive correlation between mitogenome size and proportion of REs will be further validated once available mitogenomes of gymnosperms would become more numerous. To test whether a higher proportion of REs in a mitogenome leads to an increased recombination and higher structural complexity and variability is a prospective avenue for future research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08993-9. BioMed Central 2022-11-28 /pmc/articles/PMC9703787/ /pubmed/36443651 http://dx.doi.org/10.1186/s12864-022-08993-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Kersten, Birgit
Rellstab, Christian
Schroeder, Hilke
Brodbeck, Sabine
Fladung, Matthias
Krutovsky, Konstantin V.
Gugerli, Felix
The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation
title The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation
title_full The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation
title_fullStr The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation
title_full_unstemmed The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation
title_short The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation
title_sort mitochondrial genome sequence of abies alba mill. reveals a high structural and combinatorial variation
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9703787/
https://www.ncbi.nlm.nih.gov/pubmed/36443651
http://dx.doi.org/10.1186/s12864-022-08993-9
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