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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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Comparison of mitochondrial gene arrangements between Meloidogyne graminicola and Pratylenchus vulnus.Gene and genome size are not to scale. The noncoding region (NCR) is not indicated. Arrows below the gene order map indicate the direction of transcription of genes. Genes involved in the rearrangements are shown in dashed boxes.
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pone-0098558-g002: Comparison of mitochondrial gene arrangements between Meloidogyne graminicola and Pratylenchus vulnus.Gene and genome size are not to scale. The noncoding region (NCR) is not indicated. Arrows below the gene order map indicate the direction of transcription of genes. Genes involved in the rearrangements are shown in dashed boxes.

Mentions: In contrast to Enoplean mitochondria, which show much greater variation in gene arrangement encoded by both strands, Chromadorean mitochondria share relatively conserved synteny and genes that are encoded on the same strand (Figure S1 in File S1). The most common type of gene arrangement is GA9 which has been found in 18 nematode species among 50 nematode species cited here. Compared to the GA9 type, the gene arrangement of M. graminicola shared three small blocks (nad6-nad4L, cox2-trnH-rrnL-nad3 and cob-trnL1). If tRNA genes are ignored, the gene arrangements of M. graminicola and P. vulnus are most similar; two large blocks (rrnS-nad1-nad2-cox3-nad6-nad4L-cox2 and nad4-atp6-nad5-cox1) are identical between them. Only a small block, “rrnL-nad3-cob”, was translocated into the middle of cox2 and nad4, which resulted in a novel gene order in M. graminicola (Figure 2).


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)

Comparison of mitochondrial gene arrangements between Meloidogyne graminicola and Pratylenchus vulnus.Gene and genome size are not to scale. The noncoding region (NCR) is not indicated. Arrows below the gene order map indicate the direction of transcription of genes. Genes involved in the rearrangements are shown in dashed boxes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0098558-g002: Comparison of mitochondrial gene arrangements between Meloidogyne graminicola and Pratylenchus vulnus.Gene and genome size are not to scale. The noncoding region (NCR) is not indicated. Arrows below the gene order map indicate the direction of transcription of genes. Genes involved in the rearrangements are shown in dashed boxes.
Mentions: In contrast to Enoplean mitochondria, which show much greater variation in gene arrangement encoded by both strands, Chromadorean mitochondria share relatively conserved synteny and genes that are encoded on the same strand (Figure S1 in File S1). The most common type of gene arrangement is GA9 which has been found in 18 nematode species among 50 nematode species cited here. Compared to the GA9 type, the gene arrangement of M. graminicola shared three small blocks (nad6-nad4L, cox2-trnH-rrnL-nad3 and cob-trnL1). If tRNA genes are ignored, the gene arrangements of M. graminicola and P. vulnus are most similar; two large blocks (rrnS-nad1-nad2-cox3-nad6-nad4L-cox2 and nad4-atp6-nad5-cox1) are identical between them. Only a small block, “rrnL-nad3-cob”, was translocated into the middle of cox2 and nad4, which resulted in a novel gene order in M. graminicola (Figure 2).

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