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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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Arrangement of the mitochondrial genome of Meloidogyne graminicola.Gene scaling is only approximate. All genes are coding by the same DNA strand, and the arrow indicates the direction of transcription. All protein-coding genes have standard nomenclature. All tRNA genes follow the one-letter amino acid code; L1/L2 and S1/S2 indicate tRNA genes for tRNALeu(CUN)/tRNALeu(UUR) and tRNASer(AGN)/tRNASer(UCN), respectively. “NCR1” refers to a small noncoding region and “NCR2” refers to a large noncoding region.
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pone-0098558-g001: Arrangement of the mitochondrial genome of Meloidogyne graminicola.Gene scaling is only approximate. All genes are coding by the same DNA strand, and the arrow indicates the direction of transcription. All protein-coding genes have standard nomenclature. All tRNA genes follow the one-letter amino acid code; L1/L2 and S1/S2 indicate tRNA genes for tRNALeu(CUN)/tRNALeu(UUR) and tRNASer(AGN)/tRNASer(UCN), respectively. “NCR1” refers to a small noncoding region and “NCR2” refers to a large noncoding region.

Mentions: The complete mtDNA sequence of M. graminicola is 19,589 bp in length (Figure 1) and has been deposited into GenBank (Accession number KJ139963). The mt genome of M. graminicola is larger than those of four PPNs reported to date, i.e., X. americanum (12,626 bp) [24], B. mucronatus (14,583 bp) [26], B. xylophilus (14,778 bp) [17] and R. similis (16,791 bp) [25] but slightly smaller than the mt genome of P. vulnus (21,656 bp) [17]. The larger sizes of the mt genomes of M. graminicola and P. vulnus are partly due to the presence of long noncoding regions.


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)

Arrangement of the mitochondrial genome of Meloidogyne graminicola.Gene scaling is only approximate. All genes are coding by the same DNA strand, and the arrow indicates the direction of transcription. All protein-coding genes have standard nomenclature. All tRNA genes follow the one-letter amino acid code; L1/L2 and S1/S2 indicate tRNA genes for tRNALeu(CUN)/tRNALeu(UUR) and tRNASer(AGN)/tRNASer(UCN), respectively. “NCR1” refers to a small noncoding region and “NCR2” refers to a large noncoding region.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0098558-g001: Arrangement of the mitochondrial genome of Meloidogyne graminicola.Gene scaling is only approximate. All genes are coding by the same DNA strand, and the arrow indicates the direction of transcription. All protein-coding genes have standard nomenclature. All tRNA genes follow the one-letter amino acid code; L1/L2 and S1/S2 indicate tRNA genes for tRNALeu(CUN)/tRNALeu(UUR) and tRNASer(AGN)/tRNASer(UCN), respectively. “NCR1” refers to a small noncoding region and “NCR2” refers to a large noncoding region.
Mentions: The complete mtDNA sequence of M. graminicola is 19,589 bp in length (Figure 1) and has been deposited into GenBank (Accession number KJ139963). The mt genome of M. graminicola is larger than those of four PPNs reported to date, i.e., X. americanum (12,626 bp) [24], B. mucronatus (14,583 bp) [26], B. xylophilus (14,778 bp) [17] and R. similis (16,791 bp) [25] but slightly smaller than the mt genome of P. vulnus (21,656 bp) [17]. The larger sizes of the mt genomes of M. graminicola and P. vulnus are partly due to the presence of long noncoding regions.

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