ABSTRACT
Here, the complete mitochondrial genome of Qiongphasma jianfengense obtusicristata was sequenced and annotated from China. The circular genome has a size of 16,747 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The complete mitochondrial genome of Q. jianfengense obtusicristatai provides basic genome data for relative studies.
KEYWORDS: mitogenome, China, Necroscinae, Qiongphasma
ANNOUNCEMENT
As the southernmost island of China, Hainan Island’s isolated environment restricts gene flow (1). This drives the evolution of unique traits in its stick insects, resulting in endemic Qiongphasma species (2, 3). As a phytophagous species, the population dynamics of Q. jianfengense obtusicristata Ho, 2013, serves as a bioindicator of the health and stability of the local forest ecosystem (4, 5). Currently, there are 66 complete mitochondrial genomes available for Phasmatodea (6–10). We present one complete mitogenome of the genus Qiongphasma.
The male specimen of Q. jianfengense obtusicristata analyzed in this paper was collected from Jianfengling, Hainan, China (18.731°N 108.872°E) and preserved in anhydrous alcohol at −4°C in Guangxi Normal University. Total genomic DNA was extracted from the muscle tissue of postfemora using the genomic DNA extraction kit (TIANGEN Biochemical Technology) and sequenced using the DNBSEQ next-generation sequencing platform (Shenzhen BGI Genomics Co., Ltd.) with PE150 (paired-end 150 bp) sequencing strategy. Using SOAPnuke software (11), reads with lengths <150 bp were removed, those containing ≥0.1% N bases were eliminated, and reads with polyA/T/G/C stretches >50 bp were excluded, yielding 20,018,923 clean reads. The complete mitogenome sequence was assembled by NOVOPlasty 4.2.1 software (12) and Neohirasea hongkongensis (NC_087839.1) (13) was selected as a reference sequence. The assembled mitogenome was annotated on the MITOS webserver (14) and using MEGA v.11 (15) to examine the 13 protein-coding genes (PCGs) loci. The 13 PCGs could be correctly translated into proteins via MEGA v.11 (15). AT content, AT skew, and GC skew were calculated using PhyloSuite v1.2.3 (16). A circular mitogenome map was generated using the Chloroplot server online tool (17).
The complete mitogenome (GenBank accession number PV630663) of Q. jianfengense obtusicristata was 16,747 bp in length and contains 13 PCGs, 22 tRNAs, 2 rRNAs, and a control region (CR) (Fig. 1). The mitogenome is AT-rich (80.4%). All the 13 PCGs have a typical ATN start codon and are terminated with complete TAA, except NAD2, COX1, COX3, NAD3, and NAD5, which end with incomplete TA or T. The transcription of TA or T may involve poly(A) tail addition to compensate for the deficiency and ensure translation termination (18). The tRNAs ranged in length from 63 bp (tRNA-Pro) to 72 bp (tRNA-Leu). The lengths of 16S rRNA and 12S rRNA in Q. jianfengense obtusicristata are 1,267 bp and 766 bp (Table 1). The whole genome (0.124), J-strand tRNAs (0.08), tRNA genes (0.022), and J-strand PCGs (0.017) are AT-skewed. The GC skew of PCGs (0.018), N-strand PCGs (0.231), tRNA genes (0.157), J-strand tRNAs (0.043), N-strand tRNAs (0.327), and rRNAs (0.303) is positive. The comparative analysis revealed that the whole-genome positive AT skews (0.124) and negative GC skews (−0.164) were observed.
Fig 1.
Map of the mitochondrial genome of Q. jianfengense obtusicristata. Overlapping features are excluded for a better graphical representation of the architecture of the genome. Genes on the outside are transcribed counterclockwise, and genes on the inside are transcribed clockwise as informed by the arrows in the figure. The different colors in the outermost ring correspond to different genes.
TABLE 1.
Organization of the mitochondrial genome of Q. jianfengense obtusicristata
| Gene | Type | Start | Stop | Size (bp) | Start codon | Stop codon | Direction |
|---|---|---|---|---|---|---|---|
| tRNA-Ile | tRNA | 1 | 68 | 68 | –a | – | Forward |
| tRNA-Gln | tRNA | 71 | 139 | 69 | – | – | Reverse |
| tRNA-Met | tRNA | 140 | 208 | 69 | – | – | Forward |
| NAD2 | CDS | 209 | 1,223 | 1,015 | ATT | T | Forward |
| tRNA-Trp | tRNA | 1,224 | 1,290 | 67 | – | – | Forward |
| tRNA-Cys | tRNA | 1,283 | 1,349 | 67 | – | – | Reverse |
| tRNA-Tyr | tRNA | 1,350 | 1,414 | 65 | – | – | Reverse |
| COX1 | CDS | 1,416 | 2,949 | 1,534 | ATG | T | Forward |
| tRNA-Leu | tRNA | 2,950 | 3,013 | 64 | – | – | Forward |
| COX2 | CDS | 3,014 | 3,682 | 669 | ATA | TAA | Forward |
| tRNA-Lys | tRNA | 3,685 | 3,758 | 74 | – | – | Forward |
| tRNA-Asp | tRNA | 3,754 | 3,819 | 66 | – | – | Forward |
| ATP8 | CDS | 3,820 | 3,978 | 159 | ATT | TAA | Forward |
| ATP6 | CDS | 3,975 | 4,649 | 675 | ATG | TAA | Forward |
| COX3 | CDS | 4,649 | 5,433 | 785 | ATG | TA | Forward |
| tRNA-Gly | tRNA | 5,434 | 5,501 | 68 | – | – | Forward |
| NAD3 | CDS | 5,502 | 5,853 | 352 | ATA | T | Forward |
| tRNA-Arg | tRNA | 5,854 | 5,917 | 64 | – | – | Forward |
| tRNA-Ala | tRNA | 5,919 | 5,982 | 64 | – | – | Forward |
| tRNA-Asn | tRNA | 5,987 | 6,054 | 68 | – | – | Forward |
| tRNA-Ser | tRNA | 6,055 | 6,122 | 68 | – | – | Forward |
| tRNA-Phe | tRNA | 6,124 | 6,187 | 64 | – | – | Forward |
| tRNA-Glu | tRNA | 6,186 | 6,252 | 67 | – | – | Reverse |
| NAD5 | CDS | 6,253 | 7,975 | 1,723 | ATT | T | Reverse |
| tRNA-His | tRNA | 7,976 | 8,039 | 64 | – | – | Reverse |
| NAD4 | CDS | 8,045 | 9,376 | 1,332 | ATG | TAA | Reverse |
| NAD4L | CDS | 9,370 | 9,663 | 294 | ATG | TAA | Reverse |
| tRNA-Thr | tRNA | 9,666 | 9,729 | 64 | – | – | Forward |
| tRNA-Pro | tRNA | 9,730 | 9,792 | 63 | – | – | Reverse |
| NAD6 | CDS | 9,794 | 10,276 | 483 | ATC | TAA | Forward |
| CYTB | CDS | 10,276 | 11,412 | 1,137 | ATG | TAA | Forward |
| tRNA-Ser | tRNA | 11,425 | 11,490 | 66 | – | – | Forward |
| NAD1 | CDS | 11,484 | 12,503 | 1,020 | ATA | TAA | Reverse |
| tRNA-Leu | tRNA | 12,507 | 12,578 | 72 | – | – | Reverse |
| 16S rRNA | tRNA | 12,553 | 13,819 | 1,267 | – | – | Reverse |
| tRNA-Val | tRNA | 13,871 | 13,941 | 71 | – | – | Reverse |
| 12S rRNA | tRNA | 13,945 | 14,710 | 766 | – | – | Reverse |
| CR | – | 14,711 | 16,747 | – | – | – | – |
–, not applicable.
ACKNOWLEDGMENTS
This study was supported by the National Natural Science Foundation of China (No. 32360126).
Contributor Information
Xun Bian, Email: xunbian2010@163.com.
André O. Hudson, Rochester Institute of Technology, Rochester, New York, USA
DATA AVAILABILITY
The complete mitochondrial genome sequence of Qiongphasma jianfengense obtusicristata is available in GenBank under accession number PV630663. The associated BioProject, SRA, and BioSample numbers are PRJNA1262732, SRR33561847, and SAMN48480518, respectively. The mitochondrial genome referenced in the text is Neohirasea hongkongensis. GenBank accession number NC 087839.1.
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Associated Data
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Data Availability Statement
The complete mitochondrial genome sequence of Qiongphasma jianfengense obtusicristata is available in GenBank under accession number PV630663. The associated BioProject, SRA, and BioSample numbers are PRJNA1262732, SRR33561847, and SAMN48480518, respectively. The mitochondrial genome referenced in the text is Neohirasea hongkongensis. GenBank accession number NC 087839.1.