The annotated mitogenomic sequence was submitted to GenBank with the accession number MZ913437. The complete mitogenome of M. gongshanensis was a closed loop with the length of 15,154 bp (Fig. 1). The figure was drawn using the CGView online server (http://cgview.ca/) with default parameters [22]. Differing from other Thrips [23–27], gene rearrangement occurred in the mitochondrial genome sequence of M. gongshanensis. Two repetitive tRNA genes (tRNA-Asn and tRNA-Ile) were contained in this genome sequence besides the 37 typical mitochondrial genes (13 PCGs, 22 tRNAs, two rRNAs). Meanwhile, two A + T-rich regions (D-loop) were detected, which is similar to Neohydatothrips samayunkur [27], Thrips imaginis [25], and T. palmi [26], but less than Frankliniella intonsa [24] and F. occidentalis [25]. As seem as other Thrips [23, 25–26], 3 PCGs (nad4L, nad4 and nad5) and 3 tRNAs (tRNA-His, tRNA-Tyr and tRNA-Pro) were encoded on the light (L)-strand, while the rest genes were encoded on the heavy (H)-strands (Table 1). Within the complete mitochondrial genome of M. gongshanensis, 19 small non-coding portions (intergenic spacers) were found and a total of 18 bp overlaps were identified at 10 gene junctions, and two large non-coding regions were identified with 202 and 149 bp in length, respectively (Table 1). The nucleotide composition was AT-biased (5.20%), with the respectively proportion as follow: A = 40.64% (6159), C = 12.67% (1920), G = 10.06% (1525) and T = 36.62% (5550) (Table 2).
The PCGs, ranging from 196 bp (atp8) to 1689 bp (nad 5), with the total length of 10,985 bp (Table 2). All of the PCGs were initiated with typical start codons ATN (N, any nucleotide) and terminated with typical stop codons TAA or TAG, except for atp8 started with GTG and terminated with incomplete stop codon T. The AT skew of the PCGs nucleotide composition was 4.71%, slightly lower than that of the whole mitochondrial genome. And the A, T, G, C proportion were 39.99%, 36.39%, 10.00%, 13.62%, respectively (Table 2).
The tRNAs, ranging from 60 bp (Ile, Trp, Ser, Val) to 69 bp (Pro and Gln), with the total length of 1576 bp. All tRNAs have the conserved triple nucleotides recognizing corresponding codon. The nucleotide composition was AT-biased, with the ratio of 4.11% (Table 2).
The length of 16S rRNA and 12S rRNA gene are 1096 bp and 717 bp, respectively (Table 1). The AT skew of the rRNAs was 15.19%, higher than that of PCGs and tRANs obviously (Table 2).
As the A + T richest region, the proportion of control regions can reach 88.60%. Distinct to the genes, the AT skew of control regions was negative (Table 2).
Table 1
Annotations of the complete mitochondrial genome of Mycterothrips gongshanensis
Gene | Position | Size | Codon | Anticodon | Stranda | IGSb (bp) |
Start | End | Start | Stop |
nad4 | 1 | 1320 | 1320 | ATT | TAA | | L | 0 |
nad4L | 1314 | 1580 | 267 | ATG | TAG | | L | -7 |
tRNA-Cys | 1652 | 1715 | 64 | | | GCA | H | 71 |
nad6 | 1721 | 2215 | 495 | ATC | TAA | | H | 5 |
tRNA-Val | 2241 | 2300 | 60 | | | TAC | H | 25 |
16S rRNA | 2301 | 3396 | 1096 | | | | H | 0 |
tRNA-Ser | 3397 | 3462 | 66 | | | TGA | H | 0 |
cox1 | 3477 | 5018 | 1542 | ATG | TAA | | H | 14 |
nad3 | 5018 | 5371 | 354 | ATG | TAA | | H | -1 |
tRNA-Leu | 5375 | 5440 | 66 | | | TAA | H | 3 |
cox2 | 5441 | 6103 | 663 | ATA | TAA | | H | 0 |
tRNA-Asp | 6114 | 6178 | 65 | | | GTC | H | 10 |
tRNA-Arg | 6179 | 6243 | 65 | | | TCG | H | 0 |
tRNA-Gly | 6244 | 6309 | 66 | | | TCC | H | 0 |
tRNA-Lys | 6316 | 6378 | 63 | | | TTT | H | 6 |
cox3 | 6411 | 7205 | 795 | ATA | TAA | | H | 32 |
tRNA-Asn | 7294 | 7360 | 67 | | | GTT | H | 88 |
tRNA-Ile | 7378 | 7444 | 67 | | | GAT | H | 17 |
CRc1 | 7445 | 7646 | 202 | | | | | 0 |
tRNA-Trp | 7647 | 7713 | 67 | | | TCA | H | 0 |
nad1 | 7714 | 8640 | 927 | ATA | TAA | | H | 0 |
tRNA-Met | 8637 | 8701 | 65 | | | CAT | H | -4 |
tRNA-Ala | 8702 | 8766 | 65 | | | TGC | H | 0 |
tRNA-Phe | 8767 | 8833 | 67 | | | GAA | H | 0 |
12S rRNA | 8834 | 9550 | 717 | | | | H | 0 |
atp8 | 9551 | 9746 | 196 | GTG | T | | H | 0 |
atp6 | 9764 | 10417 | 654 | ATT | TAA | | H | 17 |
tRNA-Ser | 10431 | 10490 | 60 | | | TCT | H | 13 |
tRNA-Leu | 10491 | 10557 | 67 | | | TAG | H | 0 |
tRNA-Thr | 10565 | 10630 | 66 | | | TGT | H | 7 |
tRNA-Pro | 10634 | 10702 | 69 | | | TGG | L | 3 |
tRNA-Gln | 10714 | 10782 | 69 | | | TTG | H | 11 |
tRNA-Glu | 10806 | 10871 | 66 | | | TTC | H | 23 |
cytb | 10917 | 12026 | 1110 | ATA | TAG | | H | 45 |
tRNA-Tyr | 12024 | 12090 | 67 | | | GTA | L | -3 |
nad2 | 12123 | 13103 | 981 | ATT | TAA | | H | 32 |
tRNA-Asn-2 | 13104 | 13170 | 67 | | | GTT | H | 0 |
tRNA-Ile-2 | 13188 | 13254 | 67 | | | GAT | H | 17 |
CRc2 | 13255 | 13403 | 149 | | | | | 0 |
nad5 | 13404 | 15092 | 1689 | ATT | TAA | | L | 0 |
tRNA-His | 15090 | 15154 | 65 | | | GTG | L | -3 |
aH heavy strand, L light strand; bIGS denotes the length of the intergenic spacer region, for which negative numbers indicate nucleotide overlapping between adjacent genes; cCR control region. |
Table 2
Nucleotide composition of the complete mitochondrial genome of Mycterothrips gongshanensis
Gene sequnences | Size(bp) | A% | G% | T% | C% | AT% | GC% | AT skew(%) | GC skew(%) |
Whole genome | 15154 | 40.64 | 10.06 | 36.62 | 12.67 | 77.27 | 22.73 | 5.20 | -11.48 |
Protein coding genes | 10985 | 39.99 | 10.00 | 36.39 | 13.62 | 76.38 | 23.62 | 4.71 | -15.33 |
tRNA genes | 1576 | 41.18 | 10.34 | 38.07 | 10.41 | 79.25 | 20.75 | 3.92 | -0.34 |
rRNA genes | 1813 | 44.73 | 11.69 | 32.93 | 10.65 | 77.66 | 22.34 | 15.19 | 4.66 |
Control regions | 351 | 37.32 | 5.13 | 51.28 | 6.27 | 88.60 | 11.40 | -15.76 | 10.00 |
The phylogenetic analysis indicated that Sericothripini and Dendrothripini were monophyletic with most nodes received high support (Bayesian posterior probability (PP) ≥ 0.96). Within the tribe of Sericothripini, the phylogenetic relationship indicated that M. gongshanensis was sister group relationship with the genus Thrips, and the genus Frankliniella was recovered as a sister group with the clade that Scirtothrips dorsalis and Neohydatothrips samayunkur formed (Fig. 2). Compared with the previous studies based on the mitochondrial genome of Thripdae [25–28], more mitochondrial genome sequences were selected to construct the phylogenetic tree in this study. While the generic relationship within Thripdae remained questionable, which was not consistent with previous studies. To clarify the phylogenetic and evolutionary relationships within Thripdae, further studies with more taxon samples are much needed.