http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1066361
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Pseudoperonospora cubensis Wei-Jia Lu1, Wen-Guo Hu2, and Guang-Peng Wang3 Lanzhou Institute of Biological Products Co., Ltd., Chengguan District, Lanzhou, China, 2Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China, and 3Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/17/15 For personal use only.
1
Abstract
Keywords
Pseudoperonospora cubensis is a species of water mould known for causing downy mildew on cucurbits. 454 GS FLX Titanium sequencing data was used to obtain its complete mitochondrial genome (38 553 bp). The mitogenome contains 60 genes, including two ribosomal RNA, 25 transfer RNA, 15 ribosomal proteins, five open reading frames (ORFs). The rps3 and rpl16 overlapped each other by 14 bp. The gene order and composition of P. cubensis was similar to that of most other oomycetes, and its GC content was 22.4%. It is the first report of the complete mitochondrial genome in the genus Pseudoperonospora. Phylogeny analysis indicates that P. cubensis has a close genetic relationship with genus Phytophthora.
Downy mildew, mitochondrion, Pseudoperonospora cubensis
Pseudoperonospora cubensis is a fungal-like organism that belongs in the Kingdom Straminipila and phylum Oomycota (Celetti et al., 2010). It is the causal agent of cucurbit downy mildew and can cause devastating losses worldwide of cucumber, cantaloupe, pumpkin, watermelon and squash (Savory et al., 2011). Phylogenetic investigations of worldwide P. cubensis species by utilizing molecular fragments indicated them paraphyltic with three main distinct linage (Fabian et al., 2011). But the complete mitochondrial of pathogen P. cubensis is still obscure. To better understand the evolutionary history of Pseudoperonospora sp., we sequenced and determined the first whole mitochondrial genome of genus Pseudoperonospora. The complete mitochondrial genome of P. cubensis (GenBank accession number: KT072718) was sequenced through 454 genome sequencing method and assembled by Newbler (Roche). The mitogenome of P. cubensis shows a total 38 553 bp of circular genome with 22.4% GC content. It contains two ribosomal RNAs for large and small subunits (rRNA), 25 transfer RNAs, 15
Correspondence: Guang-Peng Wang, Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China. E-mail: [email protected]
History Received 18 June 2015 Accepted 23 June 2015 Published online 17 July 2015
ribosomal proteins (rpl2, rpl6, rpl14, rpl16, rps2, rps3, rps4, rps8, rps10, rps11, rps12, rps14), five open reading frames (orf76, orf101, orf168, orf215, orf306) and 18 genes involved in electron transport and oxidative phosphorylation. Start codons of all protein coding genes were ATG, except rps12 (startd with codon ATT), and nad4L (startd with codon TTA). The rps3 and rpl16 overlapped each other by 14 bp. Pseudoperonospora cubensis mtDNA showed high similarity with Phytophthora mitogenomes both in size, structure and gene content. While both Phytophthora ramorum and other oomycetes mitochondrial genomes that have been reported have invert repeat sequences, which are diverse both in length and location regions. Phylogenetic tree was constructed by using 30 mt proteincoding genes (cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, nad11, atp1, atp6, atp8, atp9, rpl2, rpl6, rpl14, rpl16, rps2, rps3, rps4, rps8, rps10, rps11, rps12, rps14) with other 11 closely related algae mitochondrial genomes. Every single gene set of the 12 species was firstly aligned by Muscle in codon and then non-conserved regions were removed manually for constructing concatenated nucleotide sequences (44 610 bp of every single sequence). ML method was applied to reconstruct the phylogenetic tree by using RAxML version 8.1.12 (Stamatakis et al., 2014) with GTR + I + G model. Node confidence was calculated through 1000 bootstrap. Bootstrap analysis showed that all nodes with bootstrap values above 90 (Figure 1). Two main clades were identified distinctly from six genera: Achlya hypogyna, Thraustotheca clavata (O’Brien et al., 2014), Saprolegnia ferax (Grayburn et al., 2004) clustered in one clade and exhibited far genetic distance from other oomycetes species. Pseudoperonospora cubensis have a close genetic relationship with genus Phytophthora.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/17/15 For personal use only.
2
W.-J. Lu et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic relationships among oomycetes mt genomes. Numbers beside divergence nodes are percents of 1000 bootstrap values. The length of branch represents the divergence distance. Accession number of mitochondrial genomes used in this phylogeny analysis: Achlya hypogyna: NC_022178; Thraustotheca clavata: NC_022179; Phytophthora andina: NC_015619; Phytophthora infestans: NC_002387; Phytophthora ipomoeae: NC_015622; Phytophthora mirabilis: NC_015606; Phytophthora phaseoli: NC_015616; Phytophthora ramorum: NC_009384; Phytophthora sojae: NC_009385; Pythium ultimum: NC_014280; Saprolegnia ferax: NC_005984.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.
References Celetti M, Roddy E. (2010). Downy mildew in cucurbits. Ontario: Factsheet-Ministry of Agriculture, Food and Rural Affairs (order no. 10-065). Fabian R, Choi Y-J, Thines M. (2011). Phylogenetic investigations in the genus Pseudoperonospora reveal overlooked species and cryptic
diversity in the P. cubensis species cluster. Eur J Plant pathol 129: 135–46. Grayburn WS, Hudspeth DS, Gane MK, Hudspeth ME. (2004). The mitochondrial genome of Saprolegnia ferax: Organization, gene content and nucleotide sequence. Mycologia 96:981–9. O’Brien MA, Misner I, Lane CE. (2014). Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata. J Eukaryot Microbiol 61:146–54. Savory EA, Granke LL, Quesada-Ocampo LM, Varbanova M, Hausbeck MK, Day B. (2011). The cucurbit downy mildew pathogen Pseudoperonospora cubensis. Mol Plant Pathol 12:217–26. Stamatakis A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–13.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Pseudoperonospora cubensis Wei-Jia Lu1, Wen-Guo Hu2, and Guang-Peng Wang3 Lanzhou Institute of Biological Products Co., Ltd., Chengguan District, Lanzhou, China, 2Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China, and 3Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/17/15 For personal use only.
1
Abstract
Keywords
Pseudoperonospora cubensis is a species of water mould known for causing downy mildew on cucurbits. 454 GS FLX Titanium sequencing data was used to obtain its complete mitochondrial genome (38 553 bp). The mitogenome contains 60 genes, including two ribosomal RNA, 25 transfer RNA, 15 ribosomal proteins, five open reading frames (ORFs). The rps3 and rpl16 overlapped each other by 14 bp. The gene order and composition of P. cubensis was similar to that of most other oomycetes, and its GC content was 22.4%. It is the first report of the complete mitochondrial genome in the genus Pseudoperonospora. Phylogeny analysis indicates that P. cubensis has a close genetic relationship with genus Phytophthora.
Downy mildew, mitochondrion, Pseudoperonospora cubensis
Pseudoperonospora cubensis is a fungal-like organism that belongs in the Kingdom Straminipila and phylum Oomycota (Celetti et al., 2010). It is the causal agent of cucurbit downy mildew and can cause devastating losses worldwide of cucumber, cantaloupe, pumpkin, watermelon and squash (Savory et al., 2011). Phylogenetic investigations of worldwide P. cubensis species by utilizing molecular fragments indicated them paraphyltic with three main distinct linage (Fabian et al., 2011). But the complete mitochondrial of pathogen P. cubensis is still obscure. To better understand the evolutionary history of Pseudoperonospora sp., we sequenced and determined the first whole mitochondrial genome of genus Pseudoperonospora. The complete mitochondrial genome of P. cubensis (GenBank accession number: KT072718) was sequenced through 454 genome sequencing method and assembled by Newbler (Roche). The mitogenome of P. cubensis shows a total 38 553 bp of circular genome with 22.4% GC content. It contains two ribosomal RNAs for large and small subunits (rRNA), 25 transfer RNAs, 15
Correspondence: Guang-Peng Wang, Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China. E-mail: [email protected]
History Received 18 June 2015 Accepted 23 June 2015 Published online 17 July 2015
ribosomal proteins (rpl2, rpl6, rpl14, rpl16, rps2, rps3, rps4, rps8, rps10, rps11, rps12, rps14), five open reading frames (orf76, orf101, orf168, orf215, orf306) and 18 genes involved in electron transport and oxidative phosphorylation. Start codons of all protein coding genes were ATG, except rps12 (startd with codon ATT), and nad4L (startd with codon TTA). The rps3 and rpl16 overlapped each other by 14 bp. Pseudoperonospora cubensis mtDNA showed high similarity with Phytophthora mitogenomes both in size, structure and gene content. While both Phytophthora ramorum and other oomycetes mitochondrial genomes that have been reported have invert repeat sequences, which are diverse both in length and location regions. Phylogenetic tree was constructed by using 30 mt proteincoding genes (cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, nad11, atp1, atp6, atp8, atp9, rpl2, rpl6, rpl14, rpl16, rps2, rps3, rps4, rps8, rps10, rps11, rps12, rps14) with other 11 closely related algae mitochondrial genomes. Every single gene set of the 12 species was firstly aligned by Muscle in codon and then non-conserved regions were removed manually for constructing concatenated nucleotide sequences (44 610 bp of every single sequence). ML method was applied to reconstruct the phylogenetic tree by using RAxML version 8.1.12 (Stamatakis et al., 2014) with GTR + I + G model. Node confidence was calculated through 1000 bootstrap. Bootstrap analysis showed that all nodes with bootstrap values above 90 (Figure 1). Two main clades were identified distinctly from six genera: Achlya hypogyna, Thraustotheca clavata (O’Brien et al., 2014), Saprolegnia ferax (Grayburn et al., 2004) clustered in one clade and exhibited far genetic distance from other oomycetes species. Pseudoperonospora cubensis have a close genetic relationship with genus Phytophthora.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/17/15 For personal use only.
2
W.-J. Lu et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic relationships among oomycetes mt genomes. Numbers beside divergence nodes are percents of 1000 bootstrap values. The length of branch represents the divergence distance. Accession number of mitochondrial genomes used in this phylogeny analysis: Achlya hypogyna: NC_022178; Thraustotheca clavata: NC_022179; Phytophthora andina: NC_015619; Phytophthora infestans: NC_002387; Phytophthora ipomoeae: NC_015622; Phytophthora mirabilis: NC_015606; Phytophthora phaseoli: NC_015616; Phytophthora ramorum: NC_009384; Phytophthora sojae: NC_009385; Pythium ultimum: NC_014280; Saprolegnia ferax: NC_005984.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.
References Celetti M, Roddy E. (2010). Downy mildew in cucurbits. Ontario: Factsheet-Ministry of Agriculture, Food and Rural Affairs (order no. 10-065). Fabian R, Choi Y-J, Thines M. (2011). Phylogenetic investigations in the genus Pseudoperonospora reveal overlooked species and cryptic
diversity in the P. cubensis species cluster. Eur J Plant pathol 129: 135–46. Grayburn WS, Hudspeth DS, Gane MK, Hudspeth ME. (2004). The mitochondrial genome of Saprolegnia ferax: Organization, gene content and nucleotide sequence. Mycologia 96:981–9. O’Brien MA, Misner I, Lane CE. (2014). Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata. J Eukaryot Microbiol 61:146–54. Savory EA, Granke LL, Quesada-Ocampo LM, Varbanova M, Hausbeck MK, Day B. (2011). The cucurbit downy mildew pathogen Pseudoperonospora cubensis. Mol Plant Pathol 12:217–26. Stamatakis A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–13.
