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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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Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of Meloidogyne graminicola.Numbers on the Y-axis refer to the total number of codons (A) and the RSCU value (B). Codon families are provided on the X-axis. Codons that are not present in the mitochondrial genome are indicated in red at the tops of the columns.
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pone-0098558-g003: Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of Meloidogyne graminicola.Numbers on the Y-axis refer to the total number of codons (A) and the RSCU value (B). Codon families are provided on the X-axis. Codons that are not present in the mitochondrial genome are indicated in red at the tops of the columns.

Mentions: For the entire mtDNA sequence of M. graminicola, the nucleotide composition significantly favors A and T; this nucleotide bias is also reflected in codon usage (Figure 3). Excluding the stop codons, a total of 3,281 amino acids are encoded by the M. graminicola mt genome. Overall, the most frequently used amino acid is Phe (TTT), followed by Leu (TTA), Ile (ATT), Tyr (TAT), Met (ATA) and Asn (AAT). The proportion of these six amino acids is 59.8%, accounting for 1,963 amino acids; the codons encoding these amino acids are composed wholly of T and/or A, which may play an important role in the high A+T content of the entire mtDNA sequence. Three codons (GCC, GAC and CTG) were not observed in the PCGs. The absence of some codons was also reported for other PPNs [17], [25]. Analysis of the base composition at each codon position of the 12 PCGs showed that the third codon position (90.3%) is higher in A+T content than the first (80.2%) and second (79.7%) codon positions (Table S1 in File S1).


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)

Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of Meloidogyne graminicola.Numbers on the Y-axis refer to the total number of codons (A) and the RSCU value (B). Codon families are provided on the X-axis. Codons that are not present in the mitochondrial genome are indicated in red at the tops of the columns.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0098558-g003: Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of Meloidogyne graminicola.Numbers on the Y-axis refer to the total number of codons (A) and the RSCU value (B). Codon families are provided on the X-axis. Codons that are not present in the mitochondrial genome are indicated in red at the tops of the columns.
Mentions: For the entire mtDNA sequence of M. graminicola, the nucleotide composition significantly favors A and T; this nucleotide bias is also reflected in codon usage (Figure 3). Excluding the stop codons, a total of 3,281 amino acids are encoded by the M. graminicola mt genome. Overall, the most frequently used amino acid is Phe (TTT), followed by Leu (TTA), Ile (ATT), Tyr (TAT), Met (ATA) and Asn (AAT). The proportion of these six amino acids is 59.8%, accounting for 1,963 amino acids; the codons encoding these amino acids are composed wholly of T and/or A, which may play an important role in the high A+T content of the entire mtDNA sequence. Three codons (GCC, GAC and CTG) were not observed in the PCGs. The absence of some codons was also reported for other PPNs [17], [25]. Analysis of the base composition at each codon position of the 12 PCGs showed that the third codon position (90.3%) is higher in A+T content than the first (80.2%) and second (79.7%) codon positions (Table S1 in File S1).

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