The mitochondrial gene order in Thysanoptera is notably distinct and highly rearranged, with each species exhibiting its own unique arrangement. To elucidate the relationship between gene rearrangements and phylogeny, the complete mitochondrial genome (mitogenome) of the wheat pest, Aptinothrips stylifer, was sequenced and assembled, spanning a total length of 16,033 bp. Compared with the ancestral arthropod mitogenome, significant rearrangement differences were evident in A. stylifer, whereas the gene order between A. stylifer and Anaphothrips obscurus was similar. Phylogenetic trees were reconstructed based on all 13 protein-coding gene sequences using Bayesian inference and maximum-likelihood methods, both yielding similar topological structures. Notably, A. stylifer was robustly clustered with A. obscurus, affirming its classification within Anaphothrips genus group. This exemplifies the potential correlation between gene rearrangements and phylogeny in the Thripidae family. Additionally, the mitogenome of A. stylifer exhibited several atypical features, including: (1) Three putative control regions (CRs) in close proximity, with CR2 and CR3 displaying partial similarity, and CR1 differing in base composition; (2) Two transfer RNAs (tRNAs), trnS1 and trnV, lacking the DHU arm; (3) Two ribosomal RNA (rRNA) genes inverted and positioned distant from each other; (4) Negative AT and GC skew (AT skew = −0.001, GC skew = −0.077); (5) One transposition (nad6), one inverse transposition (trnQ), four inversions (trnF, trnH, trnC, and gene block nad1-trnL1-rrnL-trnV-rrnS), and four tandem duplication random loss events; and (6) Two protein-coding genes, nad2 and atp8, terminated with an incomplete stop codon “T”.

中文翻译：

---

小麦害虫Aptinothrips stylifer线粒体基因组的非凡重排和蓟马科（缨翅目）线粒体系统发育

缨翅目中的线粒体基因顺序明显不同且高度重排，每个物种都表现出自己独特的排列。为了阐明基因重排和系统发育之间的关系，对小麦害虫Aptinothrips stylifer的完整线粒体基因组（线粒体基因组）进行了测序和组装，总长度为 16,033 bp。与祖先节肢动物有丝分裂基因组相比，A. stylifer中存在明显的重排差异，而A. stylifer和Anaphothrips obscurus之间的基因顺序相似。使用贝叶斯推理和最大似然方法基于所有 13 个蛋白质编码基因序列重建系统发育树，两者都产生相似的拓扑结构。值得注意的是，A. stylifer与A. obscurus紧密地聚集在一起，证实了其属于油蓟马属组。这例证了蓟马科基因重排和系统发育之间的潜在相关性。此外， A. stylifer的线粒体基因组表现出一些非典型特征，包括：（1）三个推定的控制区（CR）非常接近，其中CR2和CR3显示出部分相似性，而CR1的碱基组成不同；(2) 两个转移RNA (tRNA)，  trnS1和trnV，缺少DHU臂；(3) 两个核糖体RNA（rRNA）基因倒置且位置彼此远离；(4) 负 AT 和 GC 偏斜（AT 偏斜 = -0.001，GC 偏斜 = -0.077）；(5) 1次转座( nad6 )、1次逆转座( trnQ )、4次倒位( trnF、trnH、trnC、基因块nad1-trnL1-rrnL-trnV-rrnS )、4次串联重复随机丢失事件；(6) 两个蛋白质编码基因nad2和atp8以不完整终止密码子“T”终止。