Cargando…

Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

BACKGROUND: The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurb...

Descripción completa

Detalles Bibliográficos
Autores principales: Rodríguez-Moreno, Luis, González, Víctor M, Benjak, Andrej, Martí, M Carmen, Puigdomènech, Pere, Aranda, Miguel A, Garcia-Mas, Jordi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175227/
https://www.ncbi.nlm.nih.gov/pubmed/21854637
http://dx.doi.org/10.1186/1471-2164-12-424
_version_ 1782212135618609152
author Rodríguez-Moreno, Luis
González, Víctor M
Benjak, Andrej
Martí, M Carmen
Puigdomènech, Pere
Aranda, Miguel A
Garcia-Mas, Jordi
author_facet Rodríguez-Moreno, Luis
González, Víctor M
Benjak, Andrej
Martí, M Carmen
Puigdomènech, Pere
Aranda, Miguel A
Garcia-Mas, Jordi
author_sort Rodríguez-Moreno, Luis
collection PubMed
description BACKGROUND: The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits. RESULTS: The nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively. CONCLUSIONS: Whereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non-conserved structure both in gene number and organisation, as well as in the features of the noncoding DNA. The transfer of nuclear DNA to the melon mitochondrial genome and the high proportion of repetitive DNA appear to explain the size of the largest mitochondrial genome reported so far.
format Online
Article
Text
id pubmed-3175227
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-31752272011-09-18 Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin Rodríguez-Moreno, Luis González, Víctor M Benjak, Andrej Martí, M Carmen Puigdomènech, Pere Aranda, Miguel A Garcia-Mas, Jordi BMC Genomics Research Article BACKGROUND: The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits. RESULTS: The nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively. CONCLUSIONS: Whereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non-conserved structure both in gene number and organisation, as well as in the features of the noncoding DNA. The transfer of nuclear DNA to the melon mitochondrial genome and the high proportion of repetitive DNA appear to explain the size of the largest mitochondrial genome reported so far. BioMed Central 2011-08-20 /pmc/articles/PMC3175227/ /pubmed/21854637 http://dx.doi.org/10.1186/1471-2164-12-424 Text en Copyright ©2011 Rodríguez-Moreno et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Rodríguez-Moreno, Luis
González, Víctor M
Benjak, Andrej
Martí, M Carmen
Puigdomènech, Pere
Aranda, Miguel A
Garcia-Mas, Jordi
Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin
title Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin
title_full Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin
title_fullStr Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin
title_full_unstemmed Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin
title_short Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin
title_sort determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of dna having a nuclear origin
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175227/
https://www.ncbi.nlm.nih.gov/pubmed/21854637
http://dx.doi.org/10.1186/1471-2164-12-424
work_keys_str_mv AT rodriguezmorenoluis determinationofthemelonchloroplastandmitochondrialgenomesequencesrevealsthatthelargestreportedmitochondrialgenomeinplantscontainsasignificantamountofdnahavinganuclearorigin
AT gonzalezvictorm determinationofthemelonchloroplastandmitochondrialgenomesequencesrevealsthatthelargestreportedmitochondrialgenomeinplantscontainsasignificantamountofdnahavinganuclearorigin
AT benjakandrej determinationofthemelonchloroplastandmitochondrialgenomesequencesrevealsthatthelargestreportedmitochondrialgenomeinplantscontainsasignificantamountofdnahavinganuclearorigin
AT martimcarmen determinationofthemelonchloroplastandmitochondrialgenomesequencesrevealsthatthelargestreportedmitochondrialgenomeinplantscontainsasignificantamountofdnahavinganuclearorigin
AT puigdomenechpere determinationofthemelonchloroplastandmitochondrialgenomesequencesrevealsthatthelargestreportedmitochondrialgenomeinplantscontainsasignificantamountofdnahavinganuclearorigin
AT arandamiguela determinationofthemelonchloroplastandmitochondrialgenomesequencesrevealsthatthelargestreportedmitochondrialgenomeinplantscontainsasignificantamountofdnahavinganuclearorigin
AT garciamasjordi determinationofthemelonchloroplastandmitochondrialgenomesequencesrevealsthatthelargestreportedmitochondrialgenomeinplantscontainsasignificantamountofdnahavinganuclearorigin