Ian Max Møller

The genome and transcriptome of perennial ryegrass mitochondria

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Standard

The genome and transcriptome of perennial ryegrass mitochondria. / Islam, Md. Shofiqul; Studer, Bruno; Byrne, Stephen; Farrell, Jacqueline Danielle; Panitz, Frank; Bendixen, Christian; Møller, Ian Max; Asp, Torben.

I: B M C Genomics, Bind 14, Nr. 202, 23.03.2013.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Harvard

APA

CBE

MLA

Vancouver

Islam MS, Studer B, Byrne S, Farrell JD, Panitz F, Bendixen C o.a. The genome and transcriptome of perennial ryegrass mitochondria. B M C Genomics. 2013 mar 23;14(202). https://doi.org/10.1186/1471-2164-14-202

Author

Islam, Md. Shofiqul ; Studer, Bruno ; Byrne, Stephen ; Farrell, Jacqueline Danielle ; Panitz, Frank ; Bendixen, Christian ; Møller, Ian Max ; Asp, Torben. / The genome and transcriptome of perennial ryegrass mitochondria. I: B M C Genomics. 2013 ; Bind 14, Nr. 202.

Bibtex

@article{490d27123f7c4a34943417c1c5be9283,
title = "The genome and transcriptome of perennial ryegrass mitochondria",
abstract = "Background: Perennial ryegrass (Lolium perenne L.) is one of the most important forage and turf grass species of temperate regions worldwide. Its mitochondrial genome is inherited maternally and contains genes that can influence traits of agricultural importance. Moreover, the DNA sequence of mitochondrial genomes has been established and compared for a large number of species in order to characterize evolutionary relationships.Therefore, it is crucial to understand the organization of the mitochondrial genome and how it varies between and within species. Here, we report the first de novo assembly and annotation of the complete mitochondrial genome from perennial ryegrass. Results: Intact mitochondria from perennial ryegrass leaves were isolated and used for mtDNA extraction. The mitochondrial genome was sequenced to a 167-fold coverage using the Roche 454 GS-FLX Titanium platform, and assembled into a circular master molecule of 678,580 bp. A total of 34 proteins, 14 tRNAs and 3 rRNAs are encoded by the mitochondrial genome, giving a total gene space of 48,723 bp (7.2{\%}). Moreover, we identified 149 open reading frames larger than 300 bp and covering 67,410 bp (9.93{\%}), 250 SSRs, 29 tandem repeats, 5 pairs of large repeats, and 96 pairs of short inverted repeats. The genes encoding subunits of the respiratory complexes – nad1 to nad9, cob, cox1 to cox3 and atp1 to atp9 – all showed high expression levels both in absolute numbers and after normalization. Conclusions: The circular master molecule of the mitochondrial genome from perennial ryegrass presented here constitutes an important tool for future attempts to compare mitochondrial genomes within and between grass species. Our results also demonstrate that mitochondria of perennial ryegrass contain genes crucial for energy production that are well conserved in the mitochondrial genome of monocotyledonous species. The expression analysis gave us first insights into the transcriptome of these mitochondrial genes in perennial ryegrass.",
keywords = "De novo assembly, Mitochondrial gene expression, Mitochondrial genome, Next-generation sequencing, Perennial ryegrass (Lolium perenne L.)",
author = "Islam, {Md. Shofiqul} and Bruno Studer and Stephen Byrne and Farrell, {Jacqueline Danielle} and Frank Panitz and Christian Bendixen and M{\o}ller, {Ian Max} and Torben Asp",
year = "2013",
month = "3",
day = "23",
doi = "10.1186/1471-2164-14-202",
language = "English",
volume = "14",
journal = "B M C Genomics",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",
number = "202",

}

RIS

TY - JOUR

T1 - The genome and transcriptome of perennial ryegrass mitochondria

AU - Islam, Md. Shofiqul

AU - Studer, Bruno

AU - Byrne, Stephen

AU - Farrell, Jacqueline Danielle

AU - Panitz, Frank

AU - Bendixen, Christian

AU - Møller, Ian Max

AU - Asp, Torben

PY - 2013/3/23

Y1 - 2013/3/23

N2 - Background: Perennial ryegrass (Lolium perenne L.) is one of the most important forage and turf grass species of temperate regions worldwide. Its mitochondrial genome is inherited maternally and contains genes that can influence traits of agricultural importance. Moreover, the DNA sequence of mitochondrial genomes has been established and compared for a large number of species in order to characterize evolutionary relationships.Therefore, it is crucial to understand the organization of the mitochondrial genome and how it varies between and within species. Here, we report the first de novo assembly and annotation of the complete mitochondrial genome from perennial ryegrass. Results: Intact mitochondria from perennial ryegrass leaves were isolated and used for mtDNA extraction. The mitochondrial genome was sequenced to a 167-fold coverage using the Roche 454 GS-FLX Titanium platform, and assembled into a circular master molecule of 678,580 bp. A total of 34 proteins, 14 tRNAs and 3 rRNAs are encoded by the mitochondrial genome, giving a total gene space of 48,723 bp (7.2%). Moreover, we identified 149 open reading frames larger than 300 bp and covering 67,410 bp (9.93%), 250 SSRs, 29 tandem repeats, 5 pairs of large repeats, and 96 pairs of short inverted repeats. The genes encoding subunits of the respiratory complexes – nad1 to nad9, cob, cox1 to cox3 and atp1 to atp9 – all showed high expression levels both in absolute numbers and after normalization. Conclusions: The circular master molecule of the mitochondrial genome from perennial ryegrass presented here constitutes an important tool for future attempts to compare mitochondrial genomes within and between grass species. Our results also demonstrate that mitochondria of perennial ryegrass contain genes crucial for energy production that are well conserved in the mitochondrial genome of monocotyledonous species. The expression analysis gave us first insights into the transcriptome of these mitochondrial genes in perennial ryegrass.

AB - Background: Perennial ryegrass (Lolium perenne L.) is one of the most important forage and turf grass species of temperate regions worldwide. Its mitochondrial genome is inherited maternally and contains genes that can influence traits of agricultural importance. Moreover, the DNA sequence of mitochondrial genomes has been established and compared for a large number of species in order to characterize evolutionary relationships.Therefore, it is crucial to understand the organization of the mitochondrial genome and how it varies between and within species. Here, we report the first de novo assembly and annotation of the complete mitochondrial genome from perennial ryegrass. Results: Intact mitochondria from perennial ryegrass leaves were isolated and used for mtDNA extraction. The mitochondrial genome was sequenced to a 167-fold coverage using the Roche 454 GS-FLX Titanium platform, and assembled into a circular master molecule of 678,580 bp. A total of 34 proteins, 14 tRNAs and 3 rRNAs are encoded by the mitochondrial genome, giving a total gene space of 48,723 bp (7.2%). Moreover, we identified 149 open reading frames larger than 300 bp and covering 67,410 bp (9.93%), 250 SSRs, 29 tandem repeats, 5 pairs of large repeats, and 96 pairs of short inverted repeats. The genes encoding subunits of the respiratory complexes – nad1 to nad9, cob, cox1 to cox3 and atp1 to atp9 – all showed high expression levels both in absolute numbers and after normalization. Conclusions: The circular master molecule of the mitochondrial genome from perennial ryegrass presented here constitutes an important tool for future attempts to compare mitochondrial genomes within and between grass species. Our results also demonstrate that mitochondria of perennial ryegrass contain genes crucial for energy production that are well conserved in the mitochondrial genome of monocotyledonous species. The expression analysis gave us first insights into the transcriptome of these mitochondrial genes in perennial ryegrass.

KW - De novo assembly

KW - Mitochondrial gene expression

KW - Mitochondrial genome

KW - Next-generation sequencing

KW - Perennial ryegrass (Lolium perenne L.)

U2 - 10.1186/1471-2164-14-202

DO - 10.1186/1471-2164-14-202

M3 - Journal article

C2 - 23521852

VL - 14

JO - B M C Genomics

JF - B M C Genomics

SN - 1471-2164

IS - 202

ER -