The Complete Mitochondrial Genome of <i>Meloidogyne graminicola</i> (Tylenchina): A Unique Gene Arrangement and Its Phylogenetic Implications

<div><p><i>Meloidogyne graminicola</i> 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 <i>Pratylenchus vulnus</i> (21,656 bp). The nucleotide composition of the whole mtDNA sequence of <i>M. graminicola</i> 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 <i>M. graminicola</i> contains 36 genes (lacking <i>atp8</i>) that are transcribed in the same direction. The gene arrangement of the mt genome of <i>M. graminicola</i> is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while <i>tRNA^Ser(AGN)</i> lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by <i>tRNA^Ser(UCN)</i>. 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 <i>M. graminicola</i>, <i>P. vulnus</i>, <i>H. glycines</i> and <i>R. similis</i> from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species <i>B. xylophilus</i> and <i>B. mucronatus</i> of Aphelenchoidea. In the clade of Tylenchoidea, <i>M. graminicola</i> is sister to <i>P</i>. <i>vulnus</i>, and <i>H. glycines</i> is sister to <i>R. similis</i>, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes.</p></div

Arrangement of the mitochondrial genome of <i>Meloidogyne graminicola</i>.

<p>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 <i>tRNA^Leu(CUN)</i>/<i>tRNA^Leu(UUR)</i> and <i>tRNA^Ser(AGN)</i>/<i>tRNA^Ser(UCN)</i>, respectively. “NCR1” refers to a small noncoding region and “NCR2” refers to a large noncoding region.</p

Organization of the <i>Meloidogyne graminicola</i> mitochondrial genome.

<p>a: Indicates gap nucleotides (positive value) or overlapping nucleotides (negative value) between two adjacent genes;</p><p>NCR: Noncoding region.</p

Comparison of mitochondrial gene arrangements between <i>Meloidogyne graminicola</i> and <i>Pratylenchus vulnus</i>.

<p>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.</p

Phylogenetic tree from maximum likelihood analysis of amino sequences for 12 protein-coding genes for 50 nematode mitochondrial genomes.

<p><i>Lithobius forficatus</i> and <i>Limulus polyphemus</i> were used as the outgroups. Bootstrap percentage (BP) values are indicated at the nodes. Classification according to De Ley and Blaxter <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098558#pone.0098558-DeLey1" target="_blank">[6]</a>.</p

Supplementary_Material_(JBM) – Supplemental material for Polymorphisms in the TOX3/LOC643714 and risk of breast cancer in south China

<p>Supplemental material, Supplementary_Material_(JBM) for Polymorphisms in the TOX3/LOC643714 and risk of breast cancer in south China by Jinling Liao, Yang Chen, Jia Zhu, Qiuyan Wang and Zengnan Mo in The International Journal of Biological Markers</p

Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of <i>Meloidogyne graminicola</i>.

<p>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.</p

Phylogenetic tree from Bayesian analysis of amino sequences for 12 protein-coding genes for 50 nematode mitochondrial genomes.

<p><i>Lithobius forficatus</i> and <i>Limulus polyphemus</i> were used as the outgroups. Numbers along the branches indicate Bayesian posterior probability (BPP) values. Classification according to De Ley and Blaxter <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098558#pone.0098558-DeLey1" target="_blank">[6]</a>.</p

Additional file 1 of Carcinogenic effect of adenylosuccinate lyase (ADSL) in prostate cancer development and progression through the cell cycle pathway

Additional file 1: Figure S1. ADSL influence the human prostate cancer cells cycle confirmed with EdU staining by flow cytometry. * P < 0.05, ** P < 0.01, *** P < 0.001 comparing to control siADSL

Additional file 2 of Carcinogenic effect of adenylosuccinate lyase (ADSL) in prostate cancer development and progression through the cell cycle pathway

Additional file 2. The whole original WB blot images with ladder markers in our study