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The complete mitochondrial genome of Meloidogyne graminicola (Tylenchina): a unique gene arrangement and its phylogenetic implications.

Sun L, Zhuo K, Lin B, Wang H, Liao J - PLoS ONE (2014)

Bottom Line: The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored.Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha.The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.

ABSTRACT
Meloidogyne graminicola is one of the most economically important plant parasitic-nematodes (PPNs). In the present study, we determined the complete mitochondrial (mt) DNA genome sequence of this plant pathogen. Compared with other PPNs genera, this genome (19,589 bp) is only slightly smaller than that of Pratylenchus vulnus (21,656 bp). The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored. The A+T content of the entire genome is 83.51%. The mt genome of M. graminicola contains 36 genes (lacking atp8) that are transcribed in the same direction. The gene arrangement of the mt genome of M. graminicola is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while tRNASer(AGN) lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by tRNASer(UCN). Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea. In the clade of Tylenchoidea, M. graminicola is sister to P. vulnus, and H. glycines is sister to R. similis, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes.

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Phylogenetic tree from maximum likelihood analysis of amino sequences for 12 protein-coding genes for 50 nematode mitochondrial genomes.Lithobius forficatus and Limulus polyphemus were used as the outgroups. Bootstrap percentage (BP) values are indicated at the nodes. Classification according to De Ley and Blaxter [6].
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pone-0098558-g005: Phylogenetic tree from maximum likelihood analysis of amino sequences for 12 protein-coding genes for 50 nematode mitochondrial genomes.Lithobius forficatus and Limulus polyphemus were used as the outgroups. Bootstrap percentage (BP) values are indicated at the nodes. Classification according to De Ley and Blaxter [6].

Mentions: We constructed phylogenetic trees to examine the relationships between 50 species of nematodes, including the newly sequenced M. graminicola, using two different methods (Bayesian inference [BI] and maximum likelihood [ML]) employing different building strategies and/or different distance models based on the combined amino acid sequences of 12 protein-encoding genes (∼2,176 amino acids each). The topologies of the Bayesian tree (Figure 4) and ML tree (Figure 5) are identical, with only small differences in Bayesian posterior probability (BPP) and bootstrap percentage (BP) of ML analyses. The two dendrograms are similar to the phylogenetic trees constructed based on previously reported mt genome analysis [17], [18]. When two Arthropod species, i.e., Lithobius forficatus and Limulus polyphemus, were used as outgroup taxa, the two resulting trees both contained two main clades that belong to the class Enoplea and the class Chromadorea, respectively.


The complete mitochondrial genome of Meloidogyne graminicola (Tylenchina): a unique gene arrangement and its phylogenetic implications.

Sun L, Zhuo K, Lin B, Wang H, Liao J - PLoS ONE (2014)

Phylogenetic tree from maximum likelihood analysis of amino sequences for 12 protein-coding genes for 50 nematode mitochondrial genomes.Lithobius forficatus and Limulus polyphemus were used as the outgroups. Bootstrap percentage (BP) values are indicated at the nodes. Classification according to De Ley and Blaxter [6].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4043755&req=5

pone-0098558-g005: Phylogenetic tree from maximum likelihood analysis of amino sequences for 12 protein-coding genes for 50 nematode mitochondrial genomes.Lithobius forficatus and Limulus polyphemus were used as the outgroups. Bootstrap percentage (BP) values are indicated at the nodes. Classification according to De Ley and Blaxter [6].
Mentions: We constructed phylogenetic trees to examine the relationships between 50 species of nematodes, including the newly sequenced M. graminicola, using two different methods (Bayesian inference [BI] and maximum likelihood [ML]) employing different building strategies and/or different distance models based on the combined amino acid sequences of 12 protein-encoding genes (∼2,176 amino acids each). The topologies of the Bayesian tree (Figure 4) and ML tree (Figure 5) are identical, with only small differences in Bayesian posterior probability (BPP) and bootstrap percentage (BP) of ML analyses. The two dendrograms are similar to the phylogenetic trees constructed based on previously reported mt genome analysis [17], [18]. When two Arthropod species, i.e., Lithobius forficatus and Limulus polyphemus, were used as outgroup taxa, the two resulting trees both contained two main clades that belong to the class Enoplea and the class Chromadorea, respectively.

Bottom Line: The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored.Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha.The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.

ABSTRACT
Meloidogyne graminicola is one of the most economically important plant parasitic-nematodes (PPNs). In the present study, we determined the complete mitochondrial (mt) DNA genome sequence of this plant pathogen. Compared with other PPNs genera, this genome (19,589 bp) is only slightly smaller than that of Pratylenchus vulnus (21,656 bp). The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored. The A+T content of the entire genome is 83.51%. The mt genome of M. graminicola contains 36 genes (lacking atp8) that are transcribed in the same direction. The gene arrangement of the mt genome of M. graminicola is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while tRNASer(AGN) lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by tRNASer(UCN). Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea. In the clade of Tylenchoidea, M. graminicola is sister to P. vulnus, and H. glycines is sister to R. similis, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes.

Show MeSH
Related in: MedlinePlus