Comparative analysis of the Liriomyza chinensis mitochondrial genome with other Agromyzids reveals conserved genome features

Abstract

Liriomyza chinensis is a serious pest of onions in many countries, especially in East Asia. We sequenced the complete mitochondrial genome of this species and compared it with five other Agromyzidae species. The L. chinensis mitogenome is a double-stranded 16,175 bp circular molecule with an A + T content of 78.3%. It contains 37 genes and a control region as do the sequenced Liriomyza species. The mitogenomes of L. chinensis and other Agromyzidae species showed a clear bias in nucleotide composition with a positive AT-skew. Most PCGs used standard ATN as start codons, and TAN as termination codons. The tRNAs exhibited the typical clover-leaf structure, except for tRNASer(AGN) and the two rRNA genes are conserved with those of other Agromyzids. The L. chinensis mitogenome control region included several conserved regions, including a poly-T, two (TA)n and one poly-A stretch, which are considered important replication and transcription. The 13 PCGs were used to study the phylogeny of L. chinensis and five related Agromyzids. Analysis by maximum likelihood, Bayesian inference and genetic distance suggest congruent phylogenetic relationships in Liriomyza spp. and provide a useful supplement to taxonomic classification by morphology.

Simplified rapid differentiation of Liriomyza chinensis Kato (Diptera; Agromyzidae) genotypes A and B using PCR‐RFLP

“…Previously, 38 samples of genotype A and 199 samples of genotype B collected from eight prefectures in Japan perfectly matched each genotype via their mtCOI nucleotide sequences (Uesugi, unpublished data). Additionally, nucleotide sequences corresponding to genotype A were submitted to GenBank (NCBI) from the Philippines () (Scheffera et al., 2007) and Japan (‐) (Nakamura et al., 2013), and these were identical to our sequences, and genotype B sequences have been reported from China () (Chen et al., 2018), which were also identical to the sequences in this study. These data suggest that our method may be useful in other countries, although it is necessary to survey the sequence and mode of feeding for some samples.…”

“…These characteristics decelerate the growth and deteriorate the quality of Allium spp. and, thus, make L. chinensis a pest of economic importance (Chen et al., 2018; Nakamura et al., 2013; Tokumaru, 2019). However, from spring to autumn, the onion thrips Thrips tabaci is an equal or even more severe threat to A. fistulosum cultivation than L. chinensis , as T. tabaci is known to have low susceptibility to many pesticides registered in Japan (Galina et al., 2012; Takeda, 2014).…”

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

“…The CR is prone to high mutation, yet the substitution rate is low due to high A + T content and directional mutation pressure 144 , 154 . This part of the mitogenome differs significantly in length among insects, ranging from 70 bp to 13 kb, and it accounts for most of the variation in mitogenome size 153 . We noted that the CR size of 36 Oestroidea flies ranges from 89 to 1750 bp, of which 16, 12, and 8 species can be categorized as large (> 800 bp), medium (200–800 bp), and small (< 200 bp) CR respectively, and Blepharipa sp (168 bp) falls under the small category (see Fig.…”

Species Identity Dominates over Environment in Driving Bacterial Community Assembly in Wild Invasive Leaf Miners

“…Among this group, three highly polyphagous species, L. trifolii , L. huidobrensis , and L. sativae , which originated in the Americas, have now spread to multiple regions of China where they are causing severe yield losses of numerous ornamental and vegetable crops ( 46 , 47 ). An oligophagous species L. chinensis is a native leaf miner found in a few regions of China ( 46 , 48 ). To our knowledge, there have been no reports the microbiome of these important plant pests.…”