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The complete mitogenome of Chlorops oryzae Matsumura (Diptera: Chloropidae).

ABSTRACT: Chlorops oryzae Matsumura is an important pest of rice plants throughout Asia, and has even become a major pest in some regions. Here, we present the complete mitogenome of C. oryzae for the first time. The complete mitogenome is 17,313 bp in length and contains 37 genes (13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs) and a control region. The overall base composition is 42.04% for A, 37.18% for T, 12.59% for C, and 8.29% for G, with a bias toward A + T (79.22%). Protein-coding genes cox1 features an atypical ACG start codon and cox2, nad5, and nad4 have incomplete stop codons T or TA. All tRNA genes present the typical clover leaf secondary structure except trnS1 (AGN), where the DHU arm is replaced by a loop. Phylogeny showed that C. oryzae was placed as the basal lineage in Brachycera clade, and shared a closer relationship to Acalyptrate species.

SUBMITTER: Wang J

PROVIDER: S-EPMC8183556 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundChlorops oryzae is an important pest of rice crops. There have been frequent outbreaks of this pest in recent years and it has become the main rice pest in some regions. To elucidate the molecular mechanism of frequent C. oryzae outbreaks, we estimated the genetic diversity and genetic differentiation of 20 geographical populations based on a dataset of ISSR markers and COI sequences.ResultsISSR data revealed a high level of genetic diversity among the 20 populations as measured by Shannon's information index (I), Nei's gene diversity (H), and the percentage of polymorphic bands (PPB). The mean coefficient of gene differentiation (Gst) was 0.0997, which indicates that only 9.97% genetic variation is between populations. The estimated gene flow (Nm) value was 4.5165, indicating a high level of gene flow and low, or medium, genetic differentiation among some populations. The results of a Mantel test revealed no significant correlation between genetic and geographic distance among populations, which means there is no evidence of significant genetic isolation by distance. An UPGMA (unweighted pair-group method with arithmetic averages) dendrogram based on genetic identity, did not indicate any major geographic structure for the 20 populations examined. mtDNA COI data indicates low nucleotide (0.0007) and haplotype diversity (0.36) in all populations. Fst values suggest that the 20 populations have low, or medium, levels of genetic differentiation. And the topology of a Neighbor-Joining tree suggests that there are no independent groups among the populations examined.ConclusionsOur results suggest that C. oryzae populations have high genetic diversity at the species level. There is evidence of frequent gene flow and low, or medium, levels of genetic differentiation among some populations. There is no significant correlation between genetic and geographic distance among C. oryzae populations, and therefore no significant isolation by distance. All results are consistent with frequent gene exchange between populations, which could increase the genetic diversity, and hence, adaptability of C. oryzae, thereby promoting frequent outbreaks of this pest. Such knowledge may provide a scientific basis for predicting future outbreaks.

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The complete mitogenome of Chlorops oryzae Matsumura (Diptera: Chloropidae).

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