Complete mitochondrial genome of Gynaikothrips ficorum (Thysanoptera: Phlaeothripidae)

Abstract

Gynaikothrips ficorum (Marchal 1908) is a major pest of bonsai ficus and poses a considerable economic threat to gardening industry. The mitochondrial genome of G. ficorum was sequenced and annotated in this study. Its whole mitogenome was 15,313 bp in length, including 37 typical genes in animal mitogenomes. ATN was used as start codon in most of the PCGs except for nad4l, which used TTG. All PCGs used TAA as termination codon except atp8 and atp6 which were ended with an incomplete T and TAG, respectively. A phylogenetic tree based on complete mitochondrial genomes of 17 species (15 Thysanoptera species and two outgroups) showed that the monophyly of Phlaeothripidae was supported and G. ficorum and G. uzeli formed a sister group.

Keywords:

• Thysanoptera
• mitochondrial genome
• phylogeny

A major pest of bonsai ficus, Gynaikothrips ficorum (Marchal 1908) preferentially feeds on tender young leaves and induces leaf-fold galls on Ficus microcarpa (Okajima 2006). The infested trees will not be killed, but the ornamental value and quality of the plants are reduced markedly (Han 1997). In this study, the samples of G. ficorum were collected from F. microcarpa located beside the road at Yibin City in Sichuan Province, China (104°60′04″E, 28°75′14″N) in 2015. Fresh specimens were preserved in 95% ethanol for slide mounting and DNA extraction. Voucher specimens (JM2015051) were identified by morphology, and deposited in Qinba Biological Museum, Shaanxi University of Technology, Hanzhong, China (QBM). The genomic DNA extraction of G. ficorum is used by the DNeasy kit (Qiagen, Hilden, Germany). The paired end libraries were constructed and sequenced (2 × 150bp) using the Illumina HiSeq 4000 platform by Nextomics Bioscience Company (Wuhan, China). The complete mitogenome for this species was assembled and annotated by MITOZ (Meng et al. 2019).

The complete mitogenome of G. ficorum is a typical circular double-stranded DNA molecule of 15,313 bp in length (GenBank accession no. MT892761). It consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes in which trnM and trnY are duplicated, two ribosomal RNA genes and one control region (d-loop). Twenty-four genes (4 PCGs, 18 tRNA and 2 rRNA genes) are transcribed on the majority strand (J-strand), with the remaining genes being located on the minority strand (N-strand). The overall nucleotide composition of the G. ficorum mitogenome is 42.8% T, 8.6% C, 40.3% A and 8.3% G, with a strong bias toward A + T (83%), AT- and GC- skew of the whole mitogenome of G. ficorum is −0.029 and −0.017, respectively. Most PCGs start with ATN codon, expect nad4l, which starts with TTG codon. Most PCGs were ended with TAA codon expect atp8 and atp6 which are ended with an incomplete T and TAG, respectively. A single putative control region, rather than two or more in some other thrips species (Yan et al. 2012; Shao and Baker 2003; Yan et al. 2014; Dickey et al. 2015; Chakraborty et al. 2018; Kumar et al. 2019), is found in the mt genome of G. ficorum. The unique control region is 251 bp in length and located between nad5 and trnF. The secondary structure of tRNA were predicted by MITOS (Bernt et al. 2013) and found that except trnS1 loses a dihydrouridine (DHU) arm, all others form a typical clover-leaf structure.

Comparing the arranged mitochondrial genes of G. ficorum with inferred insect ancestral arrangement, we found severe rearrangements in the G. ficorum mitochondrial genome. Most genes arranged irregularly but two gene clusters (atp8-atp6-cox3 and nad4-nad4L) conserved. The mt genes of this target species arranged in cox1-trnQ-cox2-atp8-atp6-cox3-nad3-trnN-trnS1-trnE-nad5-trnF-trnH -trnS-trnC-nad4-nad4L-trnT-nad6-cytb-trnR-trnA-trnY2-rrnS-trnD-trnG-trnL1-trnW-trnM1-trnY1-trnM2-trnV-trnK-trnI-nad2-trnL2-rrnL-trnP-nad1.

A phylogenetic tree was constructed based on the complete mitochondrial genomes of 15 Thysanoptera species together with two species Aphis gossypii and Alloeorhynchus bakeri as outgroups using the maximum-likelihood (ML) method with 1000 bootstrap replicates by MEGA7.0 (Sudhir et al. 2016) (Figure 1). The phylogenetic relationships indicated by the tree supported completely their taxonomic relationships based on morphological characteristic (ThripsWiki 2020), in which G. ficorum and G. uzeli were clustered into a clade, and they formed a sister clade to H. aculeatus. The result showed the three species belonging to two genera have close relationships, and it supported the monophyly of Phlaeothripidae.

Figure 1. The maximum-likelihood (ML) phylogenetic tree of Thysanoptera.

Disclosure statement

The authors declare that they have no conflict of interest.

Data availability statement

The data that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov/genbank/, reference number MT892761. The associated SRA, BioProject and Bio-Sample numbers are as follows: SRR14205964, PRJNA721109, and SAMN18700104.

Additional information

Funding

This work was supported by National Natural Sciences Foundation of China [No. 31702042, 31900345], a Young Talent Fund of University Association for Science and Technology in Shaanxi, China [20180209], and the Foundation of Shaanxi University of Technology [SLGKY2001].