http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.989513
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the phytopathogenic fungus Phomopsis longicolla Igor Koloniuk1, Lenka Hrabakova1,2, and Karel Petrzik1 Department of Plant Virology, BC CAS CZ, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic and 2Department of Genetics, University of South Bohemia in Ceske Budejovice, Ceske Budejovice, Czech Republic
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/19/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genome of the ascomycete fungus Phomopsis longicolla was sequenced using Illumina HiSeq platform. It consists of 53,439 bp with high (65.6%) A + T content and includes 14 conserved protein subunits of the mitochondrial oxidative phosphorylation system, two ribosomal RNAs and 25 tRNA genes. To our knowledge, this is the first complete mitochondrial genome of the Diaporthales member.
Diaporthales, mitogenome, Phomopsis
Phomopsis (Diaporthe) longicolla is a filamentous fungus and plays a major role in Phomopsis seed decay disease that reduces seeds quality and germination (Sinclair, 1993; Zhang et al., 1999). The fungus is a member of the ascomycete order Diaporthales (Sordariomycetidae, Sordariomycetes). To our knowledge, there are no available mitogenomes of the Diaporthales members at present. Fungal DNA was extracted with phenol-chloroform method (Sambrook & Russell, 2006) from mycelia of P. longicolla Hobbs, anamorph (ATCCÕ 60325Ô). The culture was kindly provided by Prof. S. A. Ghabrial, University of Kentucky, KY, USA. The sequencing library was prepared with KAPA DNA Library Preparation Kit (KAPA Biosystems, Wilmington, MA) and processed at HiSeq2500 system (Illumina, San Diego, CA) in High-output mode with TrueSeq SBS sequencing kit v.3 (Illumina, San Diego, CA) by SEQme.eu (Dobris, Czech Republic). A de novo contigs assembly was done and verified with CLC Genomic Workbench 7.5 (CLCBio, Aarhus, Denmark). Intron types and tRNAs were determined with RNAweasel and tRNAscan-SE algorithms (Lang et al., 2007; Schattner et al., 2005). Proteincoding and rRNA genes were manually annotated by sequence similarity to the mitogenomes of the ascomycetes Podospora anserina (NC_001329), Madurella mycetomatis (JQ015302),
History Received 14 November 2014 Accepted 16 November 2014 Published online 26 December 2014
Chaetomium thermophilum (JN007486), Neurospora crassa (KC683708). The complete nucleotide sequence of the P. longicolla Hobbs (ATCCÕ 60325Ô) circular mitogenome was deposited in Genbank under accession number KP137411. An A + T content of the 53,439 bp genome is 65.6%. It encodes 25 tRNA genes (Table 1) with three copies of tRNA-Met and two of each tRNA with anticodons for arginine, serine and leucine. All genes are encoded on the forward strand (Table 1). Codon usage shows strong bias towards codons ending with A/T(U) across all codon families. Long (41kbp), self-splicing group I introns interrupt five of the genes (cox1, cox2, nad1, nad5 and atp6) and contain a total of nine GIY-YIG and LAGLIDADG homing endonucleases. Some of their ORFs are in phase with upstream exons. The search of the highest G/C bias, which is a hallmark of replication origin region, revealed G predominance over C after 45,000 bp position. While the mitogenomic organization P. longicolla resembles that of other Sordariomycetes, there are certain rearrangements of both tRNA and protein-coding genes. It supports minimum common gene organization in mtDNAs of Sordariomycetes (Kouvelis et al., 2004). Our data provide the complete mitochondrial genome of P. longicolla that will be the first one within the Diaporthales.
Correspondence: Dr Igor Koloniuk, Department of Plant Virology, BC CAS CZ, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice 37005, Czech Republic. E-mail: [email protected]
2
I. Koloniuk et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/19/15 For personal use only.
Table 1. Organization of the mitogenome in P. longicolla Hobbs, anamorph (ATCCÕ 60325Ô). Gene/CDS
Type
Start codon
Stop codon
Start
End
Length
Introns
COXI tRNA-HisGTG tRNA-MetCAT NADH-ubiquinone oxidoreductase NADH-ubiquinone oxidoreductase COXII tRNA-ArgACG NADH-ubiquinone oxidoreductase NADH-ubiquinone oxidoreductase ATP synthase protein 8 ATP synthase protein 6 rRNA Small ATP synthase protein 9 tRNA-TyrGTA tRNA-AsnGTT COXIII tRNA-TrpTCA tRNA-LysTTT tRNA-AspGTC tRNA-SerGCT tRNA-GlyTCC NADH-ubiquinone oxidoreductase tRNA-ValTAC tRNA-IleGAT tRNA-SerTGA tRNA-ProTGG rRNA Large rps3 tRNA-ThrTGT tRNA-GluTTC tRNA-MetCAT tRNA-MetCAT tRNA-LeuTAA tRNA-AlaTGC tRNA-PheGAA tRNA-LeuTAG tRNA-GlnTTG tRNA-ArgTCT NADH-ubiquinone oxidoreductase NADH-ubiquinone oxidoreductase cyt-b tRNA-CysGCA
CDS tRNA tRNA CDS CDS CDS tRNA CDS CDS CDS CDS rRNA CDS tRNA tRNA CDS tRNA tRNA tRNA tRNA tRNA CDS tRNA tRNA tRNA tRNA rRNA CDS tRNA tRNA tRNA tRNA tRNA tRNA tRNA tRNA tRNA tRNA CDS CDS CDS tRNA
ATA
TAG TAG TAA TAA
ATG ATG AAT ATG
TAA TAA TAA TAG
ATG
TAA
GTG
TAA
ATG
TAG
ATT
TAA
ATG ATG ATG
TAG TAA TAA
8142 8905 9453 11,290 11,719 14,616 14,866 15,448 18,457 19,240 21,926 25,751 26,903 27,138 27,309 28,369 29,089 29,446 30,637 31,157 31,434 32,736 32,966 33,083 33,170 33,401 39,501 38,498 39,591 39,996 40,322 40,397 40,988 41,648 42,197 42,480 42,722 43,458 46,201 47,886 52,963 53,246
1683 73 74 1686 429 759 72 270 1971 174 786 1652 225 86 72 810 72 74 74 82 72 672 73 72 87 73 3254 777 73 73 74 73 84 74 74 85 74 72 1182 1581 1161 70
5
ATG ATG ATG
130 8833 9380 9605 11,291 12,554 14,795 15,179 15,448 19,067 19,497 24,100 26,679 27,053 27,238 27,560 29,018 29,373 30,564 31,076 31,363 32,065 32,894 33,012 33,084 33,329 33,535 37,722 39,519 39,924 40,249 40,325 40,905 41,575 42,124 42,396 42,649 43,387 43,819 46,306 51,803 53,177
chain 2 chain 3 chain 4L chain 5
chain 6
chain 1 chain 4
This will be a useful resource for phylogenetic studies of the ascomycetes.
Declaration of interest This work was supported by Postdok_BIOGLOBE (CZ.1.07/2.3.00/ 30.0032), co-financed by the European Social Fund and the state budget of the Czech Republic (to I.K and K.P) and project LH-13136 Kontakt II from Ministry of educations, youth and sports of the Czech Republic (to K.P) and GAJU 143/2013/P (to L.H). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Kouvelis VN, Ghikas DV, Typas MA. (2004). The analysis of the complete mitochondrial genome of Lecanicillium muscarium
– – 1 – 1 – 1 – – –
–
1 –
1 – –
(synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: Phylogenetic implications. Fungal Genet Biol 41:930–40. Lang BF, Laforest M-J, Burger G. (2007). Mitochondrial introns: A critical view. Trends Genet 23:119–25. Sambrook J, Russell DW. (2006). Purification of nucleic acids by extraction with phenol: chloroform. Cold Spring Harbor Protoc. 2006;2006(1). doi:10.1101/pdb.prot4455. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–9. Sinclair J. (1993). Phomopsis seed decay of soybeans: A prototype for studying seed disease. Plant Dis 77:329–34. Zhang AW, Hartman GL, Curio-Penny B, Pedersen WL, Becker KB. (1999). Molecular detection of Diaporthe phaseolorum and Phomopsis longicolla from soybean seeds. Phytopathology 89: 796–804.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the phytopathogenic fungus Phomopsis longicolla Igor Koloniuk1, Lenka Hrabakova1,2, and Karel Petrzik1 Department of Plant Virology, BC CAS CZ, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic and 2Department of Genetics, University of South Bohemia in Ceske Budejovice, Ceske Budejovice, Czech Republic
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/19/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genome of the ascomycete fungus Phomopsis longicolla was sequenced using Illumina HiSeq platform. It consists of 53,439 bp with high (65.6%) A + T content and includes 14 conserved protein subunits of the mitochondrial oxidative phosphorylation system, two ribosomal RNAs and 25 tRNA genes. To our knowledge, this is the first complete mitochondrial genome of the Diaporthales member.
Diaporthales, mitogenome, Phomopsis
Phomopsis (Diaporthe) longicolla is a filamentous fungus and plays a major role in Phomopsis seed decay disease that reduces seeds quality and germination (Sinclair, 1993; Zhang et al., 1999). The fungus is a member of the ascomycete order Diaporthales (Sordariomycetidae, Sordariomycetes). To our knowledge, there are no available mitogenomes of the Diaporthales members at present. Fungal DNA was extracted with phenol-chloroform method (Sambrook & Russell, 2006) from mycelia of P. longicolla Hobbs, anamorph (ATCCÕ 60325Ô). The culture was kindly provided by Prof. S. A. Ghabrial, University of Kentucky, KY, USA. The sequencing library was prepared with KAPA DNA Library Preparation Kit (KAPA Biosystems, Wilmington, MA) and processed at HiSeq2500 system (Illumina, San Diego, CA) in High-output mode with TrueSeq SBS sequencing kit v.3 (Illumina, San Diego, CA) by SEQme.eu (Dobris, Czech Republic). A de novo contigs assembly was done and verified with CLC Genomic Workbench 7.5 (CLCBio, Aarhus, Denmark). Intron types and tRNAs were determined with RNAweasel and tRNAscan-SE algorithms (Lang et al., 2007; Schattner et al., 2005). Proteincoding and rRNA genes were manually annotated by sequence similarity to the mitogenomes of the ascomycetes Podospora anserina (NC_001329), Madurella mycetomatis (JQ015302),
History Received 14 November 2014 Accepted 16 November 2014 Published online 26 December 2014
Chaetomium thermophilum (JN007486), Neurospora crassa (KC683708). The complete nucleotide sequence of the P. longicolla Hobbs (ATCCÕ 60325Ô) circular mitogenome was deposited in Genbank under accession number KP137411. An A + T content of the 53,439 bp genome is 65.6%. It encodes 25 tRNA genes (Table 1) with three copies of tRNA-Met and two of each tRNA with anticodons for arginine, serine and leucine. All genes are encoded on the forward strand (Table 1). Codon usage shows strong bias towards codons ending with A/T(U) across all codon families. Long (41kbp), self-splicing group I introns interrupt five of the genes (cox1, cox2, nad1, nad5 and atp6) and contain a total of nine GIY-YIG and LAGLIDADG homing endonucleases. Some of their ORFs are in phase with upstream exons. The search of the highest G/C bias, which is a hallmark of replication origin region, revealed G predominance over C after 45,000 bp position. While the mitogenomic organization P. longicolla resembles that of other Sordariomycetes, there are certain rearrangements of both tRNA and protein-coding genes. It supports minimum common gene organization in mtDNAs of Sordariomycetes (Kouvelis et al., 2004). Our data provide the complete mitochondrial genome of P. longicolla that will be the first one within the Diaporthales.
Correspondence: Dr Igor Koloniuk, Department of Plant Virology, BC CAS CZ, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice 37005, Czech Republic. E-mail: [email protected]
2
I. Koloniuk et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/19/15 For personal use only.
Table 1. Organization of the mitogenome in P. longicolla Hobbs, anamorph (ATCCÕ 60325Ô). Gene/CDS
Type
Start codon
Stop codon
Start
End
Length
Introns
COXI tRNA-HisGTG tRNA-MetCAT NADH-ubiquinone oxidoreductase NADH-ubiquinone oxidoreductase COXII tRNA-ArgACG NADH-ubiquinone oxidoreductase NADH-ubiquinone oxidoreductase ATP synthase protein 8 ATP synthase protein 6 rRNA Small ATP synthase protein 9 tRNA-TyrGTA tRNA-AsnGTT COXIII tRNA-TrpTCA tRNA-LysTTT tRNA-AspGTC tRNA-SerGCT tRNA-GlyTCC NADH-ubiquinone oxidoreductase tRNA-ValTAC tRNA-IleGAT tRNA-SerTGA tRNA-ProTGG rRNA Large rps3 tRNA-ThrTGT tRNA-GluTTC tRNA-MetCAT tRNA-MetCAT tRNA-LeuTAA tRNA-AlaTGC tRNA-PheGAA tRNA-LeuTAG tRNA-GlnTTG tRNA-ArgTCT NADH-ubiquinone oxidoreductase NADH-ubiquinone oxidoreductase cyt-b tRNA-CysGCA
CDS tRNA tRNA CDS CDS CDS tRNA CDS CDS CDS CDS rRNA CDS tRNA tRNA CDS tRNA tRNA tRNA tRNA tRNA CDS tRNA tRNA tRNA tRNA rRNA CDS tRNA tRNA tRNA tRNA tRNA tRNA tRNA tRNA tRNA tRNA CDS CDS CDS tRNA
ATA
TAG TAG TAA TAA
ATG ATG AAT ATG
TAA TAA TAA TAG
ATG
TAA
GTG
TAA
ATG
TAG
ATT
TAA
ATG ATG ATG
TAG TAA TAA
8142 8905 9453 11,290 11,719 14,616 14,866 15,448 18,457 19,240 21,926 25,751 26,903 27,138 27,309 28,369 29,089 29,446 30,637 31,157 31,434 32,736 32,966 33,083 33,170 33,401 39,501 38,498 39,591 39,996 40,322 40,397 40,988 41,648 42,197 42,480 42,722 43,458 46,201 47,886 52,963 53,246
1683 73 74 1686 429 759 72 270 1971 174 786 1652 225 86 72 810 72 74 74 82 72 672 73 72 87 73 3254 777 73 73 74 73 84 74 74 85 74 72 1182 1581 1161 70
5
ATG ATG ATG
130 8833 9380 9605 11,291 12,554 14,795 15,179 15,448 19,067 19,497 24,100 26,679 27,053 27,238 27,560 29,018 29,373 30,564 31,076 31,363 32,065 32,894 33,012 33,084 33,329 33,535 37,722 39,519 39,924 40,249 40,325 40,905 41,575 42,124 42,396 42,649 43,387 43,819 46,306 51,803 53,177
chain 2 chain 3 chain 4L chain 5
chain 6
chain 1 chain 4
This will be a useful resource for phylogenetic studies of the ascomycetes.
Declaration of interest This work was supported by Postdok_BIOGLOBE (CZ.1.07/2.3.00/ 30.0032), co-financed by the European Social Fund and the state budget of the Czech Republic (to I.K and K.P) and project LH-13136 Kontakt II from Ministry of educations, youth and sports of the Czech Republic (to K.P) and GAJU 143/2013/P (to L.H). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Kouvelis VN, Ghikas DV, Typas MA. (2004). The analysis of the complete mitochondrial genome of Lecanicillium muscarium
– – 1 – 1 – 1 – – –
–
1 –
1 – –
(synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: Phylogenetic implications. Fungal Genet Biol 41:930–40. Lang BF, Laforest M-J, Burger G. (2007). Mitochondrial introns: A critical view. Trends Genet 23:119–25. Sambrook J, Russell DW. (2006). Purification of nucleic acids by extraction with phenol: chloroform. Cold Spring Harbor Protoc. 2006;2006(1). doi:10.1101/pdb.prot4455. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–9. Sinclair J. (1993). Phomopsis seed decay of soybeans: A prototype for studying seed disease. Plant Dis 77:329–34. Zhang AW, Hartman GL, Curio-Penny B, Pedersen WL, Becker KB. (1999). Molecular detection of Diaporthe phaseolorum and Phomopsis longicolla from soybean seeds. Phytopathology 89: 796–804.
