Research Article |
Corresponding author: Zhonghua Wei ( wzh1164@126.com ) Academic editor: Dmitry Telnov
© 2022 Zhonghua Wei.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Wei Z (2022) The complete mitochondrial genomes of five Agrilinae (Coleoptera, Buprestidae) species and phylogenetic implications. ZooKeys 1092: 195-212. https://doi.org/10.3897/zookeys.1092.80993
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Five complete mitochondrial genomes of five species from the subfamily Agrilinae were sequenced and annotated, including Coraebus diminutus Gebhardt, 1928 (15,499 bp), Coraebus cloueti Théry, 1893 (15,514 bp), Meliboeus sinae Obenberger, 1935 (16,108 bp), Agrilus sichuanus Jendek, 2011 (16,521 bp), and Sambus femoralis Kerremans, 1892 (15,367 bp). These mitogenomes ranged from 15,367 to 16,521 bp in length and encoded 37 typical mitochondrial genes: 13 protein-coding genes (13 PCGs), 2 ribosomal RNA genes (2 rRNAs), 22 transfer RNA genes (22 tRNAs), and a control region (CR). Most of PCGs had typical ATN start codons and terminated with TAR or an incomplete stop codon T–. Among these five mitogenomes, Leu2, Ile, Phe, Ser2, Gly, Met, and Val were the seven most frequently encoded amino acids. Interestingly, in A. sichuanus, a 774 bp insertion was present at trnW and trnC junction, which is unusual in Buprestidae. Additionally, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) using Bayesian inference and maximum-likelihood methods. The results showed that the clade of Buprestidae was well separated from outgroups and all Agrilinae species formed to a single highly supported clade. The tribe Coraebini was polyphyletic, as the genus Meliboeus (Coraebini) clustered with the genus Trachys (Tracheini). The rRNA genes had important impact for the tree topology of Agrilinae. Compared to the tribes Tracheini and Agrilini, the tribe Coraebini is a younger group.
Comparative analysis, mitogenome, phylogenetic analysis
The superfamily Buprestoidea, which contains the families Buprestidae and Schizopodidae, differs from other groups of the Elateriformia by their serrate antennae, hypognathous head, transverse suture of metaventrite present, and two connate basal abdominal ventrites (
Although taxonomists have made important contributions to the buprestid classification of subfamilies and tribes based on several morphological characteristics (
In the past two decades, molecular systematic approaches have been used to resolve unsettled classification and phylogenetic relationships in Insecta (
During this time, the mitogenome emerged as a valuable source for higher-level phylogenetic analyses, evolutionary strategies, and genetic diversity analyses (
Information on the mitogenomes of Buprestidae and two outgroups used in this study.
No. | Taxa | Accession no. | Genome size (bp) | A% | A+T% | AT skew | GC skew | References |
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1 | Coraebus diminutus | OK189521 | 15,499 | 38.34 | 68.42 | 0.12 | −0.25 | This study |
2 | Coraebus cloueti | OK189520 | 15,514 | 38.53 | 69.27 | 0.11 | −0.25 | This study |
3 | Meliboeus sinae | OK189522 | 16,108 | 40.18 | 72.42 | 0.11 | −0.22 | This study |
4 | Sambus femoralis | OK349489 | 15,367 | 40.98 | 73.23 | 0.12 | −0.18 | This study |
5 | Agrilus sichuanus | OK189519 | 16,521 | 40.19 | 71.73 | 0.12 | −0.21 | This study |
6 | Agrilus planipennis | KT363854 | 15,942 | 40.25 | 71.90 | 0.12 | −0.24 |
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7 | Agrilus mali | MN894890 | 16,204 | 40.34 | 74.46 | 0.08 | −0.18 |
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8 | Coraebus cavifrons | MK913589 | 15,686 | 38.94 | 69.79 | 0.12 | −0.18 |
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9 | Trachys auricollis | MH638286 | 16,429 | 38.94 | 71.05 | 0.10 | −0.20 |
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10 | Trachys troglodytiformis | KX087357 | 16,316 | 41.03 | 74.62 | 0.10 | −0.19 | Unpublished |
11 | Trachys variolaris | MN178497 | 16,771 | 39.92 | 72.11 | 0.11 | −0.21 |
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12 | Melanophila acuminata | MW287594 | 15,853 | 38.74 | 75.66 | 0.02 | −0.25 |
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13 | Anthaxia chinensis | MW929326 | 15,881 | 40.12 | 73.61 | 0.09 | −0.29 |
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14 | Chrysochroa fulgidissima | EU826485 | 15,592 | 40.31 | 69.92 | 0.15 | −0.24 |
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15 | Acmaeodera sp. | FJ613420 | 16,217 | 38.11 | 68.41 | 0.11 | −0.25 |
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16 | Heterocerus parallelus (outgroup) | KX087297 | 15,845 | 41.90 | 74.03 | 0.13 | −0.24 | Unpublished |
17 | Dryops ernesti (outgroup) | KX035147 | 15,672 | 39.04 | 72.98 | 0.07 | −0.23 | Unpublished |
Currently, the subfamily Agrilinae contains four tribes (Agrilini, Coraebini, Aphanisticini, and Tracheini); however, the phylogenetic placement of several genera of this subfamily remains unstable. The genera in the tribes Coraebini and Agrilini were revised by
Specimens of five species were collected using an entomological net. Among them, C. diminutus, C. cloueti, M. sinae, and A. sichuanus were collected in the Dayaoshan Mountains in Guangxi Zhuang Autonomous Region, and S. femoralis was collected at Yingjiang County in Yunnan Province, China. Specimens were immediately preserved in 95% ethanol in the field after collected and then stored at –24 °C in the laboratory. The specimens were identified based on morphological characteristics under a Leica M205 FA stereomicroscope. Total DNA was extracted from muscle tissues using the Ezup Column Animal Genomic DNA Purification Kit (Shanghai, China) following the manufacturer’s instructions.
DNA sequencing and de novo assembly of each mitogenome were performed by Beijing Aoweisen Gene Technology Co. Ltd (Beijing, China). 22 tRNA genes were identified using the MITOS webserver, with the parameters of the Invertebrate Mito genetic code (
Phylogenetic trees for A. sichuanus, C. diminutus, C. cloueti, M. sinae, S. femoralis, and 10 other buprestid species belonging to four subfamilies were reconstructed by three separate datasets (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) using different best-fit models (Table
The complete mitogenomes of the buprestids A. sichuanus, C. diminutus, C. cloueti, M. sinae, and S. femoralis have the following GenBank accession numbers attributed to them: OK189519, OK189521, OK189520, OK189522, OK349489. The mitogenomes of these five species contained the 37 typical mitochondrial genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and a control region (CR) (Table
The five newly annotated Buprestidae mitogenomes. The order of these five species in the table is as follows: Agrilus sichuanus, Coraebus diminutus, Coraebus cloueti, Meliboeus sinae, and Sambus femoralis. – not determined.
Gene | Strand | Position From | To | Start codons | Stop condons | Anticodon | Intergenic nucleotides |
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trnI | J | 1/1/1/1/1 | 65/63/63/64/65 | GAT | -3/-3/-3/5-3 | ||
trnQ | N | 63/61/61/70/63 | 131/129/129/138/131 | AAG | -1/0/0/0/-1 | ||
trnM | J | 131/129/129/138/131 | 199/196/196/205/196 | CAA | 0/0/0/0/0 | ||
nad2 | J | 200/197/197/206/197 | 1222/1219/1219/1231/1210 | ATC/ATT/ATT/ATC/ATT | TAA/TAG/TAA/TAA/TAA | 1/1/-2/0/-2 | |
trnW | J | 1224/1221/1218/1232/1209 | 1293/1286/1283/1303/1273 | ACA | 774/-8/-13/13/-8 | ||
trnC | N | 2068/1279/1276/1296/1266 | 2130/1339/1336/1356/1326 | GCA | 0/2/2/0/0 | ||
trnY | N | 2131/1342/1339/1357/1327 | 2195/1404/1401/1419/1387 | GAA | 9/1/1/1/1 | ||
cox1 | J | 2205/1406/1403/1421/1389 | 3735/2936/2933/2951/2919 | –/–/–/–/– | TAA/TAA/TAA/TAA/TAA | 0/0/0/0/0 | |
trnL2 | J | 3736/2937/2934/2952/2920 | 3802/3003/3001/3016/2984 | AAG | 0/0/0/0/0 | ||
cox2 | J | 3803/3004/3002/3017/2985 | 4484/3670/3668/3698/3666 | ATT/ATA/ATA/ATC/ATT | TAA/TAA/TAA/TAA/TAA | 0/0/0/0/0 | |
trnK | J | 4485/3671/3669/3699/3667 | 4553/3740/3738/3768/3736 | CAA | 0/0/0/0/0 | ||
trnD | J | 4554/3741/3739/3769/3737 | 4618/3803/3802/3830/3798 | GAC | 0/0/0/0/0 | ||
atp8 | J | 4619/3804/3803/3831/3799 | 4777/3962/3961/3989/3954 | ATT/ATA/ATC/ATT/ATA | TAG/TAA/TAA/TAA/TAG | 0/-7/-7/-7-7 | |
atp6 | J | 4771/3956/3955/3983/3948 | 5445/4630/4629/4657/4622 | ATG/ATG/ATG/ATG/ATG | TAA/TAA/TAA/TAA/TAA | -1/-1/-1/-1/-1 | |
cox3 | J | 5445/4630/4629/4657/4622 | 6233/5416/5415/5443/5405 | ATG/ATG/ATG/ATG/ATG | TAG/TAA/TAA/TAA/TAA | 8/0/0/0/0 | |
trnG | J | 6242/5417/5416/5444/5406 | 6306/5477/5476/5509/5469 | ACC | 0/0/0/0/0 | ||
nad3 | J | 6307/5478/5477/5510/5470 | 6660/5831/5830/5863/5823 | ATT/ATT/ATT/ATT/ATT | TAG/TAG/TAG/TAG/TAG | -2/-2/-2/-2/-2 | |
trnA | J | 6659/5830/5829/5862/5822 | 6721/5890/5889/5924/5884 | AGC | 0/-1/-1/-1/0 | ||
trnR | J | 6722/5890/5889/5924/5885 | 6781/5952/5951/5988/5947 | ACG | 1/-1/-1/-1/1 | ||
trnN | J | 6783/5952/5951/5988/5949 | 6849/6017/6016/6051/6013 | GAA | 0/0/0/0/0 | ||
trnS1 | J | 6850/6018/6017/6052/6014 | 6916/6075/6074/6117/6080 | ACA | 1/0/7/-1/0 | ||
trnE | J | 6918/6076/6082/6117/6081 | 6982/6139/6143/6179/6143 | AAC | -1/-4/-4/-1/-1 | ||
trnF | N | 6982/6136/6140/6179/6143 | 7045/6198/6202/6240/6207 | GAA | 0/0/0/0/0 | ||
nad5 | N | 7046/6199/6203/6241/6208 | 8768/7915/7919/7960/7915 | ATA/ATT/ATT/ATT/ATA | TAA/TAA/TAA/TAA/TAA | 0/0/0/0/0 | |
trnH | N | 8769/7916/7920/7961/7916 | 8830/7977/7981/8026/7978 | GAG | 0/0/0/0/0 | ||
nad4 | N | 8831/7978/7982/8027/7979 | 10,166/9295/9299/9362/9308 | ATG/ATG/ATG/ATG/ATG | TAA/TAA/TAA/TAA/TAA | -7/-7/-7/-7/-7 | |
nad4L | N | 10,160/9289/9293/9356/9302 | 10,444/9576/9580/9640/9589 | ATG/ATG/ATG/ATG/ATA | TAA/TAA/TAA/TAA/TAA | 4/3/3/2/1 | |
trnT | J | 10,449/9580/9584/9643/9591 | 10,511/9642/9646/9704/9654 | AGA | -1/-1/-1/-1/-1 | ||
trnP | N | 10,511/9642/9646/9704/9654 | 10,574/9704/9708/9769/9717 | AGG | 1/1/1/1/1 | ||
nad6 | J | 10,576/9706/9710/9771/9719 | 11,079/10,185/10,189/10,259/10,192 | ATT/ATA/ATA/ATG/ATT | TAA/TAA/TAA/TAA/TAA | -1/-1/-1/-1/-1 | |
cytb | J | 11,079/10,185/10,189/10,259/10,192 | 12,224/11,327/11,331/11,401/11,334 | ATG/ATG/ATG/ATG/ATG | TAA/TAG/TAG/TAG/TAG | 8/-2/-2/-2/-2 | |
trnS2 | J | 12,233/11,326/11,330/11,400/11,333 | 12,298/11,391/11,395/11,465/11,400 | ACA | 17/9/9/19/14 | ||
nad1 | N | 12,316/11,411/11,415/11,485/11,415 | 13,266/12,361/12,365/12,432/12,365 | TTG/TTG/TTG/TTG/TTG | TAA/TAA/TAA/TAG/TAA | 1/1/1/0/1 | |
trnL1 | N | 13,268/12,363/12,367/12,433/12,367 | 13,334/12,427/12,431/12,495/12,434 | AAG | 0/0/0/0/0 | ||
rrnL | N | 13,335/12,428/12,432/12,496/12,435 | 14,605/13,693/13,697/13,757/13,692 | 0/0/0/0/0 | |||
trnV | N | 14,606/13,694/13,698/13,758/13,693 | 14,674/13,762/13,766/13,826/13,761 | AAC | 0/0/0/0/0 | ||
rrnS | N | 14,675/13,763/13,767/13,827/13,762 | 15,379/14,480/14,483/14,531/14,457 | 0/0/0/0/0 | |||
A + T rich region | 15,380/14,481/14,484/14,532/14,458 | 16,521/15,499/15,514/16,108/15,367 | 0/0/0/0/0 |
Four of the 13 PCGs (nad1, nad4L, nad4, and nad5), eight tRNAs (trnQ, trnV, trnL1, trnP, trnH, trnF, trnY, and trnC), and two rRNAS (rrnL and rrnS) are encoded on the N-strand, whereas the other 23 genes (9 PCGs and 14 tRNAs) are encoded on the J-strand. The mitogenome sequence of these five buprestid species ranged in size from 15,367 to 16,521 bp.
The mean A + T nucleotide contents of five complete mitogenomes were similar: 68.42% in C. diminutus, 69.27% in C. cloueti, 72.42% in M. sinae, 71.73% in A. sichuanus, and 73.23% in S. femoralis. The entire mitogenomes had a higher A + T contents of 68.42–73.23% (66.05–72.50% for PCGs, 70.95–74.03% for tRNA genes, 75.20–77.33% for rRNA genes, and 74.17–78.38% for the CR) than G + C contents, which is consistent with the typical base of buprestid mitogenomes. The overall AT skews in these five complete mitogenomes were 0.12, 0.11, 0.11, 0.12, and 0.12, respectively. These five species showed a positive TA skew, suggesting that a slight AT bias which are similar to those observed in other buprestid species (
The total lengths of PCGs in these five buprestid species ranged from 11,090 to 11,158 bp, accounting for 67.54–72.17% of the entire mitogenomes. Similar to the other buprestid mitogenomes, nad5 and atp8 were found to be the largest (1708–1723 bp) and smallest (156–159 bp) genes, respectively. The majority of PCGs strictly started with an ATN (ATA/ATT/ATC/ATG) start codon, except for the nad1 starting with TTG. All PCGs strictly terminated with TAR (TAG/TAA) or an incomplete stop codon T–. Similar to most previously sequenced members of Buprestidae, the AT skew (0.11–0.12) of these five PCGs (Table
Summarized mitogenomic characteristics of the five buprestid species in this study.
Species | PCGs | rRNAs | tRNA | CR | ||||||||
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Size (bp) | A+T content | AT skew | Size (bp) | A+T content | AT skew | Size (bp) | A+T content | AT skew | Size (bp) | A+T content | AT skew | |
A. sichuanus | 11,158 | 70.08 | −0.15 | 1976 | 75.96 | −0.13 | 1444 | 74.03 | −0.0009 | 1142 | 74.17 | 0.06 |
C. diminutus | 11,093 | 66.05 | −0.14 | 1984 | 75.20 | −0.11 | 1477 | 70.95 | 0.03 | 1019 | 77.72 | 0.02 |
C. cloueti | 11,093 | 67.09 | −0.15 | 1983 | 75.39 | −0.11 | 1414 | 71.22 | 0.019 | 1031 | 78.27 | 0.02 |
M. sinae | 11,135 | 70.70 | −0.15 | 1967 | 77.33 | −0.11 | 1435 | 72.13 | 0.007 | 1577 | 78.38 | 0.13 |
S. femoralis | 11,090 | 72.50 | −0.16 | 1954 | 75.69 | −0.13 | 1430 | 73.85 | 0.03 | 910 | 75.82 | 0.18 |
The nucleotide diversity (Pi) of the 13 PCGs among five species of Agrilinae is provided (Fig.
The length of rrnL genes ranged from 1258 bp (S. femoralis) to 1271 bp (A. sichuanus), whereas rrnS ranged from 696 bp (S. femoralis) to 718 bp (C. diminutus). The A + T content of the rRNA genes ranged from 75.20% (C. diminutus) to 77.33% (M. sinae) (Table
The CR, also known as the A + T-rich region (
Both ML and BI trees using three datasets produced identical topologies (Figs
In this study, five mitogenomes (15,367–16,521 bp) were newly sequenced and annotated, including representatives from the tribes Coraebini and Agrilini in subfamily Agriinae. The mitogenomes of the genera Sambus and Meliboeus are reported for the first time. These five sequences showed a positive AT skew, and the amino acids Leu, Ile, Phe, Ser2, Gly, Met, and Val were most frequently used. The secondary structures of tRNA-Ser are absent the D-arm, which is similar to other orders of Insecta. The rRNA genes are valuable for phylogenetic analyses of Agrilinae as they could affect the tree topologies. The results show that Coraebini is polyphyletic, and the genus Sambus belongs to neither Coraebini nor Agrilini. However, more mitogenome samplings are needed to resolve the phylogeny of the Buprestidae in the future to better understand the phylogenetics of jewel beetles.
I am sincerely grateful to Lanrui Wang (Qingyang, Gansu, China) and Yingqi Liu (China Agricultural University, Beijing, China) for their guidance in using the software. I also thank Dr Hui-Feng Zhao (Langfang Normal University, Hebei, China) and Menglin Wang (China West Normal University, Sichuan, China) for revising the manuscript. This work was supported by the Doctoral Scientific Research Foundation of China West Normal University (20E054).
Figures S1–S7
Data type: Images (pdf file)
Explanation note: Figure S1. The mitogenome maps of Agrilus sichuanus, Coraebus cloueti, Coraebus diminutus, Meliboeus sinae, and Sambus femoralis. Figure S2. The secondary cloverleaf structure for the tRNAs of Agrilus sichuanus. Figure S3. The secondary cloverleaf structure for the tRNAs of Coraebus cloueti. Figure S4. The secondary cloverleaf structure for the tRNAs of Coraebus diminutus. Figure S5. The secondary cloverleaf structure for the tRNAs of Meliboeus sinae. Figure S6. The secondary cloverleaf structure for the tRNAs of Sambus femoralis. Figure S7. Heterogeneous sequence divergence within datasets 13 PCGs and 2 rRNAs of Buprestidae species.