Access to this full-text is provided by MDPI.
Content available from Insects
This content is subject to copyright.
insects
Article
Comparative Mitogenomic Analysis of Two Longhorn Beetles
(Coleoptera: Cerambycidae: Lamiinae) with Preliminary
Investigation into Phylogenetic Relationships of Tribes
of Lamiinae
Yifang Ren 1,† , Huanhuan Lu 2, † , Longyan Chen 1, Simone Sabatelli 3, Chaojie Wang 1, Guanglin Xie 1,
Ping Wang 1, Meike Liu 1,* , Wenkai Wang 1, * and Paolo Audisio 3
Citation: Ren, Y.; Lu, H.; Chen, L.;
Sabatelli, S.; Wang, C.; Xie, G.; Wang,
P.; Liu, M.; Wang, W.; Audisio, P.
Comparative Mitogenomic Analysis
of Two Longhorn Beetles (Coleoptera:
Cerambycidae: Lamiinae) with
Preliminary Investigation into
Phylogenetic Relationships of Tribes
of Lamiinae. Insects 2021,12, 820.
https://doi.org/10.3390/
insects12090820
Academic Editor: Teiji Sota
Received: 23 August 2021
Accepted: 8 September 2021
Published: 12 September 2021
Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations.
Copyright: © 2021 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/).
1Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China;
201973050@yangtzeu.edu.cn (Y.R.); clylyly@126.com (L.C.); 202071670@yangtzeu.edu.cn (C.W.);
xieguanglin@yangtzeu.edu.cn (G.X.); wangping1992@yangtzeu.edu.cn (P.W.)
2Chongqing Key Laboratory of Vector Insects, College of Life Sciences, Chongqing Normal University,
Chongqing 401331, China; 2019110513046@stu.cqnu.edu.cn
3Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Universitàdi Roma,
Viale dell’Università32, I-00185 Rome, Italy; simone.sabatelli@uniroma1.it (S.S.);
paolo.audisio@uniroma1.it (P.A.)
*Correspondence: liumk2009@126.com (M.L.); wwk@yangtzeu.edu.cn (W.W.)
† These authors have equally contributed in this study.
Simple Summary:
Many species of Cerambycidae are important pests in the agriculture, forestry, and
fruit industries, and which have research significance. The subfamily Lamiinae is the most taxonomically
diverse subfamily of Cerambycidae, but relationships between the tribes of Lamiinae are still unresolved.
In order to provide a new perspective on the phylogenetic relationships among the tribes of Lamiinae, the
mitogenomes of two species representing two tribes, Agapanthia amurensis (Agapanthiini) and Moechotypa
diphysis (Ceroplesini), were sequenced. We present annotated, complete mitogenomes of these two
species, and the results of a comparative analysis of both mitogenomes. The two new mitogenomes
were found to be highly conservative, as found in other Cerambycidae. We also reconstructed the
phylogenetic trees using mitogenomes of 38 species/subspecies of Lamiinae. Overall, this study
explores the phylogenetic position between some tribes based on mitogenomic data and provides a
further basis for studying the evolution of Lamiinae.
Abstract:
The subfamily Lamiinae is the most taxonomically diverse subfamily of Cerambycidae,
but relationships between tribes of Lamiinae are still unresolved. In order to study the characteristics
of the mitogenomes of Lamiinae and the tribal-level phylogenetic relationships, we sequenced
the mitogenomes of two species representing two tribes, Agapanthia amurensis (Agapanthiini) and
Moechotypa diphysis (Ceroplesini), with a total length of 15,512 bp and 15,493 bp, respectively. The
gene arrangements of these two new mitogenomes were consistent with the inferred ancestral
insect mitogenomes. Each species contained 37 typical mitochondrial genes and a control region
(A + T-rich region), including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and
two ribosomal RNA genes (rRNAs). All PCGs initiated with the standard start codon ATN, and
terminated with the complete stop codons of TAA and TAG, or incomplete stop codon T. All tRNAs
could be folded into a clover-leaf secondary structure except for trnS1, in which the dihydrouridine
(DHU) arm was reduced. Moreover, we studied the phylogenetic relationships between some tribes
of Lamiinae based in mitochondrial PCGs in nucleotides; our results show that the relationships
were as follows: (Onciderini + ((Apomecynini + Acanthocinini) + ((Ceroplesini + Agapanthiini)
+ ((Mesosini + Pteropliini) + ((Dorcaschematini + (Saperdini 1 + (Phytoeciini + Saperdini 2))) +
(Batocerini + Lamiini)))))).
Keywords: molecular; mitochondrial genome; genome structure; phylogenetic analysis
Insects 2021,12, 820. https://doi.org/10.3390/insects12090820 https://www.mdpi.com/journal/insects
Insects 2021,12, 820 2 of 13
1. Introduction
The family Cerambycidae is one of the largest families of the superfamily Chrysomeloidea
(Coleoptera: Polyphaga), consisting of a little less than 40,000 species, among which Lami-
inae have about 20,000 species [
1
]. Thus, some species of Cerambycidae are important
pests in the agriculture, forestry, and fruit industries. Some are also important quarantine
pests. For example, some Monochamus species are the main transmission vectors of the
pine wood nematode Bursaphelenchus xylophilus (Aphelenchoidae) [
2
,
3
]. However, adults
of many species of Lepturinae in the Cerambycidae family have flower-visiting behaviors
and help plants to pollinate [
4
]. All in all, Cerambycidae is believed to have great potential
for applications in forest health and ecological biodiversity assessment [5–7].
As the most taxonomically diverse subfamily in Cerambycidae, the monophyly of
Lamiinae is supported based on morphology and/or molecule studies [
8
–
13
]. However, the
phylogenetic relationships of tribes among Lamiinae are controversial. Latreille (1825) pro-
posed a modern classification of Cerambycidae, first using the term Lamiaires, which later
became Lamiinae [
14
]. Blanchard (1845) proposed names for suprageneric groups of Lami-
inae and recognized seven groups (Acanthocinites, Lamiites, Mesosites, Petrognathites,
Saperdites, Stellognathites and Tetraophtalmites) [
15
]. Then, Thomson (1860) proposed an
eight-rank taxonomic system (in French: Famille, Tribu, Sous-Tribu, Groupe, Sous-groupe,
Division, Genre, Espèce), and recorded 17 groups of Lamiinae, which later increased to
33 groups in 1864 [
16
,
17
]. This laid a foundation for the later taxonomic study of tribes
among Lamiinae. Aurivillius (1922, 1923) compiled a catalogue of Lamiinae and divided it
into 96 tribes, which was the first comprehensive summary of Lamiinae [
18
,
19
]. Breuning
(1958–1969) significantly reduced the tribes to 58 by synonymizing some controversial
tribes [
20
–
31
], but this system was not fully accepted by subsequent researchers. More re-
cently, Bouchard et al. (2011) synthesized the data of all known extant and fossil Coleoptera
for the first time, and recognized 80 tribes of Lamiinae [
32
]. Souza et al. (2020) performed a
study on the tribal classification of Lamiinae by molecular phylogenetic assessment [
13
].
They confirmed the monophyly of Lamiinae, and suggested some synonyms for its tribes
based on the fragments of two mitochondrial genes (cytochrome c oxidase subunit 1 and
large ribosomal RNA subunit) and three nuclear genes (wingless, carbamoyl-phosphate
synthase domain of the CAD locus, and large ribosomal rRNA subunit).
Insect mitogenomes present unique features, such as maternal inheritance, low molec-
ular weight, low recombination level, and fast evolutionary rate. Thus, they are widely
used as molecular markers in studies of classification, genetic evolution, and phylogenetic
analysis [
33
–
35
]. Insect mitogenomes consist of 37 genes, including 13 protein-coding genes
(PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control
region (A + T-rich region) [
33
]. With the rapid development of next-generation sequencing,
about 40,000 mitogenomes of animals have been published in the NCBI datasets [
36
]. How-
ever, few studies have been proposed based on molecular methods at the tribal level of
Lamiinae. In this study, mitogenomes of two species of Lamiinae representing two tribes,
Agapanthia amurensis Kraatz, 1879 (Agapanthiini) and Moechotypa diphysis (Pascoe, 1871)
(Ceroplesini), were sequenced and analyzed. Of these, M. diphysis was the first complete
mitogenome of Ceroplesini. In addition, we used the available and annotated mitogenomes
from NCBI and two newly sequenced mitogenomes to infer the phylogenetic relationships
between some tribes among Lamiinae.
2. Materials and Methods
2.1. Sample Preparation and DNA Extraction
Specimens of Agapanthia amurensis Kraatz, 1879 and Moechotypa diphysis
(Pascoe, 1871)
were collected from Enshi Tujia and Miao Autonomous Prefecture, Hubei Province, China
(May 2020). The latitude and longitude of the collection sites are 30
◦
36
0
18.6” N and
110
◦
4
0
6.8” E. All specimens were identified by Prof. Guanglin Xie based on morpho-
logical characteristics. All specimens were immediately preserved in 100% ethanol and
stored at
−
20
◦
C in the Entomological Museum of Yangtze University
(No. A.amurensis
Insects 2021,12, 820 3 of 13
YZU20200507134 and No. M.diphysis YZU20200507216). Then, total genomic DNA was
extracted from the thoracic muscle tissues using a DNeasy DNA Blood & Tissue Kit
(Qiagen, Beijing, China).
2.2. Sequence Analysis
Two mitogenome sequences were generated using the Illumina HiSeq platform with
paired ends of 2
×
251 bp at Biomarker Technologies Co. Ltd. (Beijing, China). Raw
reads were filtered, and quality was assessed using Fast-QC (http://www.bioinformatics.
babraham.ac.uk/projects/fastqc, accessed on 01 July 2021) based on Q20 (>95%) and Q30
(>90%). After quality trimming, the reads were assembled by Geneious v8.1.3 (Biomatters,
Auckland, New Zealand) [
37
] with default parameters and using the mitogenome of Aromia
bungii (Faldermann, 1835) (GenBank accession no. MT371041) as reference [
38
]. All PCGs
of two mitogenomes were identified based on finding the open reading frames (ORFs) and
translated by Geneious v8.1.3 according to the invertebrate mitochondrial genetic code. The
secondary structures of the tRNAs were identified by the MITOS Web Server [
39
] and drawn
in Adobe Illustrator CC2019. The positions of rRNAs and control region were predicted
by adjacent genes and homology alignment with A.bungii. The mitogenome maps were
drawn using CGView Server [
40
]. Nucleotide composition, AT or GC skews, and relative
synonymous codon usage (RSCU) were analyzed by PhyloSuite v1.2.2 [
41
]. The tandem
repeats of the control region were predicted by the Tandem Repeats Finder online server
(http://tandem.bu.edu/trf/trf.basic.submit.html, accessed on 01 July 2021) [42].
2.3. Phylogenetic Analysis
Two newly sequenced mitogenomes and 36 species/subspecies of Lamiinae were
selected from the NCBI, representing 12 tribes (Acanthocinini, Agapanthiini, Apome-
cynini, Batocerini, Ceroplesini, Dorcaschematini, Lamiini, Mesosini, Onciderini, Phy-
toeciini, Pteropliini, Saperdini). In addition, two species (Chrysomela vigintipunctata and
Plagiodera versicolora
) of Chrysomelidae were selected as outgroups (Supplementary Ma-
terials Table S1). The 13PCGs were aligned by MAFFT v7.0 [
43
]. Then, poorly aligned
positions and high divergence regions were removed by Gblocks v0.91b in PhyloSuite.
The potential index of substitution saturation (Iss) of each codon position of each nucleic
acid sequence was analyzed by DAMBE v7.2.1 based on default parameters. [
44
]. Phy-
logenetic analyses were conducted using two datasets: 13PCGs (nucleotides sequences
for protein-coding genes; including all codon positions) and 13PCGs_AA (amino acids of
13PCGs). The phylogenetic analyses were reconstructed by the Bayesian inference (BI) and
the Maximum likelihood (ML) methods based on these two datasets. The best evolutionary
model of BI was inferred by PartitionFinder v2.1.1 [
45
] using the greedy search algorithm
with branch lengths linked and Bayesian information criterion (BIC) in PhyloSuite. The
best fit model of ML was selected using ModelFind in IQ-TREE. ML analysis was con-
ducted by IQ-TREE [
46
], and node supports were computed via 1000 ultrafast bootstrap
replicates. BI analysis was conducted by MrBayes v3.2.6 [
47
] under four Markov chain
Monte Carlo (MCMC) chains of 1 million generations twice, sampled every 1000 genera-
tions, with the first 25% of generations removed as burn-in. MCMC analysis was stopped
when the average standard deviation of the split frequency was below 0.01. Additionally,
PhyloBayes analysis based on the CAT-GTR model was conducted by PhyloBayes v1.5a
on CIPRES [
12
,
48
]. Two chains were run until the likelihood had satisfactorily converged
(maxdiff < 0.2, minimum effective size > 50). The phylogenetic tree was displayed and
edited by Tree of Life (iTOL, http://itol.embl.de, accessed on 01 July 2021) [49].
3. Results and Discussion
3.1. General Features of the Mitogenomes of Agapanthia amurensis and Moechotypa diphysis
The complete mitogenomes of Agapanthia amurensis (GenBank accession number:
MW617354) and Moechotypa diphysis (MW617356) were 15,512 bp and 15,493 bp in length,
respectively (Table S1). Both mitogenomes included 37 typical mitogenomic genes and a
Insects 2021,12, 820 4 of 13
control region. In these two mitogenomes, most genes (nine PCGs and 14 tRNAs) were
concentrated on the J strand, and others (four PCGs, eight tRNAs, and two rRNAs) on the
N strand (Figures 1a and 2a, Table S2). Aside from the control region, six intergenic regions
were found in the mitogenomes of both A.amurensis (35 bp total) and M.diphysis (31 bp
total), and the longest region was detected between trnS2 and nad1. Sixteen overlapping
regions were found in the mitogenomes of both A.amurensis (50 bp total) and M.diphysis
(45 bp total) (Table S3). The base composition of A.amurensis was A (38.5%), T (36.7%),
G (9.3%), and C (15.5%), and the base composition of M.diphysis was A (37.6%), T (38.0%),
G (9.5%), and C (14.9%). Both sequences displayed a high AT nucleotide bias, with
A + T%
of the whole sequence of 75.2% in A.amurensis and 75.6% in M.diphysis; these were similar
to other sequenced Lamiinae species (Table S4). The composition skew analysis showed
that the two new mitogenomes presented a negative GC skew. For AT skew, the value
for A.amurensis was 0.024 and for M.diphysis was
−
0.005 (Table S4). Circular maps of the
mitogenomes of these two new sequences were visualized in Figures 1a and 2a.
Figure 1. Complete mitogenome of Agapanthia amurensis. (A) Circular map. (B) Organization of the
A + T-rich regions.
Insects 2021,12, 820 5 of 13
Figure 2.
Complete mitogenome of Moechotypa diphysis. (
A
) Circular map. (
B
) Organization of the
A + T-rich regions.
3.2. Genome Structure
3.2.1. Protein-Coding Genes
The PCGs ranged from 156 bp (atp8) to 1714 bp (nad5) in A.amurensis, and 156 bp
(atp8) to 1720 bp (nad5) in M.diphysis (Table S4). A.amurensis and M.diphysis exhibited
similar start and stop codons. All PCGs started with the typical ATN codon, and most
PCGs ended with TAA or TAG, while three PCGs (cox1,cox2, and nad5) in A.amurensis and
four PCGs (cox1,cox2,nad4, and nad5) in M.diphysis ended with incomplete stop codon T.
In all 38 species/subspecies of Lamiinae, the termination TAA occurred more frequently
than TAG (Table S2).
Research on relative synonymous codon usage (RSCU) showed that the frequency of
A or T is higher than that of G or C in the third codon position (Figure 3). For example,
the third codon position of the seven most used codons (TTA, TCT, AGA, CCT, GTA, ACT,
and TGT) in the mitogenome of M.diphysis was A or T, whereas codons with G or C in the
third position (GCG, CCG, CGC, and GGC) were seldom presented in the mitogenome of
M.diphysis (Table S5).
3.2.2. Transfer and Ribosomal RNA Genes
Both new mitogenomes included 22 typical tRNAs genes. The size of these genes
ranged from 64 bp (trnE,trnG,trnL1, and trnP) to 70 bp (trnK, and trnY) in A. amurensis,
and from 61 bp (trnC) to 70 bp (trnK) in M. diphysis (Table S2). The whole tRNA region of
these two mitogenomes was 1462 bp in A. amurensis and 1435 bp in M. diphysis
(Table S4)
.
Insects 2021,12, 820 6 of 13
Except for trnS1, which lacked a dihydrouracil (DHU) arm and formed a simple loop,
other tRNAs could be folded into the classic clover-leaf secondary structure (Figure 4a,b).
This phenomenon often occurs in the mitogenomes of Cerambycidae [
50
,
51
]. Based on the
secondary structure of tRNAs, we found five types of mismatched bases (U-U, G-U, A-G,
A-C, and A-A) in A.amurensis, and three types (U-U, G-U, and A-G) in M.diphysis.
Figure 3.
Relative synonymous codon usage (RSCU) of PCGs in mitogenomes of Lamiinae. X- and Y-axis represent codon
type and species name, respectively.
Int. J. Environ. Res. Public Health 2021, 18, x. https://doi.org/10.3390/xxxxx www.mdpi.com/journal/ijerph
(A)
Figure 4. Cont.
Insects 2021,12, 820 7 of 13
(B)
Figure 4.
(
A
) Secondary structures of tRNAs in mitogenome of Agapanthia amurensis; bonds of A-U, G-C are marked with
purple and red lines, and G-U mismatched bases with green lines and solid dots. (
B
) Secondary structures of tRNAs in
mitogenome of Moechotypa diphysis; bonds of A-U, G-C are marked with purple and red lines, and G-U mismatched bases
with green lines and solid dots.
There were two rRNAs in both new mitogenome sequences: rrnL (16SrRNA) was
located between trnL and trnV, and rrnS (12SrRNA) was located between trnV and the
control region. The length of rrnL was 1281 bp in A.amurensis and 1280 bp in M.diphysis,
and the length of rrnS was 781 bp (A.amurensis) and 777 bp (M.diphysis), respectively
(Table S2). These two rRNAs displayed a heavy AT nucleotide bias, with A + T content of
78.7% in A.amurensis and 80.4% in M.diphysis. Both rRNAs showed a negative AT skew
and a positive GC skew in these two new sequences (Table S4).
3.2.3. Control Region
The control region is normally the largest non-coding region in insect mitogenomes,
also known as the A + T-rich region owing to the high AT content. This region was thought
to have a function in regulating the transcription and replication of insect genes [
52
–
54
].
Insects 2021,12, 820 8 of 13
Tandem repeats in the control region were considered as the sequences that mainly affect the
size of the mitogenome [
52
,
55
]. In this study, the control region of both new mitogenomes
was located between rrnS and trnI, and the size was 857 bp in A.amurensis and 874 bp in
M.diphysis (Table S2). One tandem repeat-like region was found in the control region of
each. One Poly (A) was found in the non-repeat region of each. Three Poly (T) were found
in non-repeat regions of M.diphysis (Figures 1b and 2b); Poly (T) stretch was considered as
an origin of transcription and replication [52].
3.3. Phylogenetic Analysis
The substitution saturation analyses (Table S6) showed that the index of substitu-
tion saturation (Iss) was less than Iss.cSym (p<0.05) regardless of whether datasets were
trimmed by Gblocks. This result suggested that all nucleotide positions of PCGs could pro-
vide useful information for the phylogenetic analysis. Based on the 13PCGs and 13PCGs_AA
datasets, the phylogenetic relationships between the 12 tribes of Lamiinae were inferred
from ML and BI analyses. The best model of the phylogenetic relationship is presented
in Table S7. Inconsistent topologies were generated by ML and BI analyses based on the
13PCGs_AA dataset (Supplementary Materials Figure S1). The positions of some tribes
(Agapanthiini, Acanthocinini, Onciderini, Apomecynini, and Phytoeciini) in ML and BI
trees were different, and there were some clade nodes had low support values
(Figure S1)
.
It may require more mitogenomes and other molecular evidence of Lamiinae to solve
these problems [
56
,
57
]. Except for the position of Psacothea hilaris, the ML (Figure 5a)
and Bl (Figure 5b) analyses based on the 13PCGs dataset produced basically consistent
topologies, and the support value of the BI tree was generally higher than that of the
ML tree. They all indicated that the relationships among the 12 tribes of Lamiinae were:
(Onciderini + ((Apomecynini + Acanthocinini) + ((Ceroplesini + Agapanthiini) + ((Mesosini
+ Pteropliini) + ((Dorcaschematini + (Saperdini 1 + (Phytoeciini + Saperdini 2))) + (Bato-
cerini + Lamiini)))))). Due to the heterogeneity in base composition and evolutionary
rates, phylogenetics research based on mitogenomes is still controversial [
58
–
60
]. Previ-
ous studies argued that using a CAT-GTR model in PhyloBayes was more suitable than
other methods to reconstruct relationships at the subfamily level and above [
12
,
59
,
60
].
In this study, the PhyloBayes analysis based on the 13PCGs_AA dataset (Figure S2) us-
ing the CAT-GTR model produced almost congruent topologies with the phylogenetic
tree based on the 13PCGs. The only differences were the position of clades Onciderini
and
(Mesosini + Pteropliini)
. Therefore, only the phylogenetic trees constructed using the
13PCGs dataset are shown in this paper (Figure 5a,b).
In this study, the monophyly of Lamiinae was highly supported, which had been
confirmed in previous studies [
8
–
13
,
51
,
61
]. We also studied the phylogenetic relationships
between some tribes among Lamiinae, and the monophyly of Lamiini was supported
(BS = 100; PP = 1)
. The boundary of Lamiini is controversial; some researchers have sup-
ported the retention of Lamiini and Monochamini [
32
,
62
,
63
], while others have proposed
that the tribe Monochamini should be included in Lamiini [
64
–
66
]. Souza et al. (2020)
proposed that Monochamini is a synonym of Lamiini based on the fragments of two mito-
chondrial genes (cox1 and rrnL) and three nuclear genes (Wg,CPS, and LSU) [
13
], which
is also supported by our present result. Moreover, in our study, the monophyly of the
tribe Saperdini was not supported as Phytoeciini was nested within the Saperdini clade
(BS = 76.7; PP = 1). Based on this result, we considered that Phytoeciini should be included
in Saperdini. Souza et al. (2020), who performed the first, relatively dense phylogenetic
systematic assessment of Lamiinae, supported Phytoeciini as a synonym of Saperdini [
13
].
Further, the phylogenetic tree (Figure 3in Zhang et al. (2021)) of 30 species of Lamiinae
based on the nucleotide dataset of the 13PCGs of mitogenomes showed the same result [
61
].
Insects 2021,12, 820 9 of 13
Figure 5. Cont.
Figure 5.
(
A
) Maximum likelihood (ML) phylogenetic tree based on 13PCGs dataset. Numbers on
branches are bootstrap values. (
B
) Bayesian inference (BI) phylogenetic tree based on 13PCGs dataset.
Numbers on branches are Bayesian posterior probabilities.
4. Conclusions
This study describes two complete mitogenomes of Agapanthia amurensis and
Moechotypa diphysis in Lamiinae. The gene arrangements of these new mitogenomes
were consistent with other longhorn beetles. Each species contained 37 typical mitochon-
drial genes and a control region. All tRNAs could be folded into a clover-leaf secondary
structure except for trnS1, in which the dihydrouridine (DHU) arm was reduced. In all
38 species/subspecies of Lamiinae in this study, the termination TAA occurred more than
Insects 2021,12, 820 10 of 13
TAG. Our phylogenetic tree inferences of Lamiinae based on mitogenomes confirm the
monophyly of Lamiinae. Regarding the relationships between the tribes among Lami-
inae, our results support Lamiini being monophyletic and Phytoeciini as a synonym of
Saperdini. In this study, the Bayesian analysis based on the 13PCGs dataset is better than
other analyses, which of course requires more samples and studies to verify. All in all, in
order to better understand the phylogenetic relationships between tribes among Lamiinae,
more mitochondrial datasets and other molecular evidence are still needed. Using more
taxon samples and molecular markers may help to determine the higher-level relationships
among Cerambycidae.
Supplementary Materials:
The following are available online at https://www.mdpi.com/article/
10.3390/insects12090820/s1. Figure S1: Phylogenetic relationship of ML and Bl trees based on
13PCGs_AA dataset. Figure S2: Phylogenetic relationship of PhyloBayes tree based on 13PCGs_AA
dataset. Table S1: Summary of mitogenome data used in this study. Table S2: Comparison of
annotated mitogenomes of Lamiinae. Table S3: Intergenic region statistics of mitogenomes of
Lamiinae. Table S4: Nucleotide composition of mitogenomes of Agapanthia amurensis and Moechotypa
diphysis. Table S5: Relative synonymous codon usage (RSCU) of PCGs in mitogenomes. Table S6:
Saturation substitution tests for 13PCGs dataset. Table S7: Best model of phylogenetic relationships.
Author Contributions:
Conceptualization, M.L., W.W., Y.R., and P.A.; methodology, Y.R., H.L., M.L.,
L.C. and S.S.; validation, M.L., W.W. and P.A.; formal analysis, H.L. and S.S.; investigation, Y.R., H.L.,
and M.L.; resources, C.W., G.X. and P.W.; data curation, C.W., G.X. and P.W.; writing—original draft
preparation, Y.R., H.L., L.C. and C.W.; writing—review and editing, M.L., W.W., S.S. and P.A.; funding
acquisition, W.W. All authors have read and agreed to the published version of the manuscript.
Funding:
This research was funded by the National Natural Science Foundation of China (31672327).
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement:
All mitogenomic sequences in this study are available in the Gen-
Bank database (https://www.ncbi.nlm.nih.gov/nuccore, accessed on 01 July 2021), and the newly
generated sequences are deposited in GenBank with accession numbers MW617354 and MW617356.
Acknowledgments:
The authors greatly appreciate the valuable comments on an earlier version of
this manuscript received from Professor Alessandro Bruno Biscaccianti (Laboratorio di Entomologia
ed Ecologia Applicata, UniversitàMediterranea di Reggio Calabria, Dipartimento PAU, Repubblica
Italiana), and other anonymous reviewers.
Conflicts of Interest: All authors declare no conflict of interest.
References
1.
Tavakilian, G.L.; Chevillotte, H. Titan: Base de données internationales sur les Cerambycidae ou Longicornes. Version 3.0.
Available online: http://titan.gbif.fr/index.html (accessed on 1 May 2021).
2.
Ikeda, T.; Oda, K. The occurrence of attractiveness for Monochamus alternatus Hope (Coleoptera: Cerambycidae) in nematode-
infected pine trees. J. Jpn. For. Soc. 1980,62, 432–434. [CrossRef]
3.
Evans, H.F.; McNamara, D.G.; Braasch, H.; Chadoeuf, J.; Magnusson, C. Pest risk analysis (PRA) for the territories of the European
Union (as PRA area) on Bursaphelenchus xylophilus and its vectors in the genus Monochamus.EPPO Bull.
1996
,26, 199–249.
[CrossRef]
4.
Jiang, S.N. Coleoptera, Fauna Sinica Insecta.Vol 21 Coleoptera Cerambycidae Lepturinae; Science Press: Beijing, China, 2001; pp. 1–299.
ISBN 7-03-008163-3/Q934.
5.
Allison, J.D.; Borden, J.H.; Seybold, S.J. A review of the chemical ecology of the Cerambycidae (Coleoptera). Chemoecology
2004
,
14, 123–150. [CrossRef]
6.
Raje, K.R.; Abdel-Moniem, H.E.M.; Farlee, L.; Ferris, V.B.; Holland, J.D. Abundance of pest and benign Cerambycidae both
increase with decreasing forest productivity. Agric. For. Entomol. 2012,14, 165–169. [CrossRef]
7.
Karpi´nski, L.; Maák, I.; Wegierek, P. The role of nature reserves in preserving saproxylic biodiversity: Using longhorn beetles
(Coleoptera: Cerambycidae) as bioindicators. Eur. Zool. J. 2021,88, 487–504. [CrossRef]
Insects 2021,12, 820 11 of 13
8.
Napp, D.S. Phylogenetic relationships among the subfamilies of Cerambycidae (Coleoptera, Chrysomeloidea). Rev. Bras. Entomol.
1994,38, 265–419.
9.
Marvaldi, A.E.; Duckett, C.N.; Kjer, K.M.; Gillespie, J.J. Structural alignment of 18S and 28S rDNA sequences provides insights
into the phylogeny of Phytophaga (Coleoptera: Curculionoidea and Chrysomeloidea). Zool. Scripta 2008,38, 63–77. [CrossRef]
10.
Wang, B.; Ma, J.Y.; McKenna, D.D.; Yan, E.V.; Zhang, H.C.; Jarzembowski, E.A. The earliest known longhorn beetle (Cerambycidae:
Prioninae) and implications for the early evolution of Chrysomeloidea. J. Syst. Palaeontol. 2013,12, 565–574. [CrossRef]
11.
Haddad, S.; Shin, S.; Lemmon, A.R.; Lemmon, E.M.; Svacha, P.; Farrell, B.; ´
Slipi´nski, A.; Windsor, D.; Mckenna, D.D. Anchord
hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae). Syst. Entomol.
2017,43, 68–89. [CrossRef]
12.
Nie, R.E.; Vogler, A.P.; Yang, X.K.; Lin, M.Y. Higher-level phylogeny of longhorn beetles (Coleoptera: Chrysomeloidea) inferred
from mitochondrial genomes. Syst. Entomol. 2020,46, 56–70. [CrossRef]
13.
Souza, D.D.S.; Marinoni, L.; Monné, M.L.; Gómez-Zurita, J. Molecular phylogenetic assessment of the tribal classification of
Lamiinae (Coleoptera: Cerambycidae). Mol. Phylogenetics Evol. 2020,145, 106736. [CrossRef]
14.
Latreille, P.A. Familles Naturelles du Règne Animal, Exposées Succinctement et Dans un Ordre Analytique, Avec l’Indication de Leurs
Genres; Imprimerie DE J.: Paris, France, 1825; pp. 1–570.
15.
Blanchard, C.É.Histoire dês Insectes, Traitant de Leurs Moeurs et Leurs Métamorphoses em General et Comprenant une Nouvelle
Classification Fondée sur Leurs Rapports Naturels; Hymenoptères et Coléoptères; Librairie de Firmin Didot Frères: Paris, France,
1845; pp. 154–161.
16.
Thomson, J. Essai d’Une Classification de la Famille des Cérambycides et Matériaux pour Servir a Une Monographie de Cette Famille;
Bouchard-Huzard: Paris, France, 1860; pp. 1–128.
17.
Thomson, J. Systema Cerambycidarum ou Exposéde Tous les Genres Compris Dans La famille dês Cérambycides et Familles Limitrophes;
Sociétéroyale des sciences de Liège: Paris, France, 1864; pp. 1–540.
18. Aurivillius, C. Coleopterorum Catalogus, Pars 73, Cerambycidae: Lamiinae, I; W, Junk: Berlin, Germany, 1922; pp. 1–322.
19. Aurivillius, C. Coleopterorum Catalogus, Pars 74, Cerambycidae: Lamiinae II; W, Junk: Berlin, Germany, 1923; pp. 322–704.
20.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 1; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1958;
pp. 1–48.
21.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 2.; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1959;
pp. 109–182.
22.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 3.; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1960;
pp. 183–284.
23. Breuning, S. Révision des Pteropliini (Col. Cerambycidae). Pesquisas Zoologia 1961,9, 5–60.
24.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 4; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1961;
pp. 287–382.
25.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 5; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1961;
pp. 387–459.
26.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 6; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1962;
pp. 463–555.
27.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 7; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1963;
pp. 49–107.
28.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 8; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1965;
pp. 559–655.
29.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 9; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1966;
pp. 659–765.
30.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 10; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1967;
pp. 771–864.
31.
Breuning, S. Catalogue des Lamiaires du Monde (Col. Céramb.). 11; Verlag des Museum, G. Frey: Tutzing bei Munich, Germany, 1969;
pp. 865–1069.
32.
Bouchard, P.; Bousquet, Y.; Davies, A.; Alonso-Zarazaga, M.A.; Lawrence, J.F.; Lyal, C.H.C.; Newton, A.F.; Reid, C.A.M.; Schmitt,
M.; ´
Slipi´nski, S.A.; et al. Family-group names in Coleoptera (Insecta). ZooKeys 2011,88, 1–972. [CrossRef] [PubMed]
33.
Saccone, C.; Giorgi, C.D.; Gissi, C.; Pesole, G.; Reyes, A. Evolutionary genomics in Metazoa: The mitochondrial DNA as a model
system. Gene 1999,238, 195–209. [CrossRef]
34.
Abascal, F.; Posada, D.; Knight, R.D.; Zardoya, R. Parallel evolution of the genetic code in arthropod mitochondrial genomes.
PLoS Biol. 2006,4, e127. [CrossRef] [PubMed]
35.
Simon, C.; Buckley, T.R.; Frati, F.; Stewart, J.B.; Beckenbach, A.T. Incorporating molecular evolution into phylogenetic analysis,
and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu. Rev. Ecol. Evol.
Syst. 2006,37, 545–579. [CrossRef]
36.
Tan, M.H.; Gan, H.M.; Lee, Y.P.; Poore, G.C.; Austin, C.M. Digging deeper: New gene order rearrangements and distinct patterns
of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda). PeerJ
2017,5, e2982. [CrossRef]
Insects 2021,12, 820 12 of 13
37.
Kearse, M.; Moir, R.; Wilson, A.; Stones-Havas, S.; Cheung, M.; Sturrock, S.; Buxton, S.; Cooper, A.; Markowitz, S.; Duran, C.; et al.
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data.
Bioinformatics 2012,28, 1647–1649. [CrossRef]
38.
Li, R.M.; Song, X.; Du, Y.M. Mitochondrial genome of Aromia bungii (Coleoptera: Chrysomeloidea: Cerambycidae) and phyloge-
netic analysis. Mitochondrial DNA Part B 2021,6, 71–72. [CrossRef] [PubMed]
39.
Bernt, M.; Donath, A.; Jühling, F.; Externbrink, F.; Florentz, C.; Fritzsch, G.; Pütz, J.; Middendorf, M.; Stadler, P.F. MITOS:
Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 2012,69, 313–319. [CrossRef]
40.
Grant, J.R.; Stothard, P. The CGView Server: A comparative genomics tool for circular genomes. Nucleic Acids Res.
2008
,36,
181–184. [CrossRef]
41.
Zhang, D.; Gao, F.L.; Jakovli´c, I.; Zou, H.; Zhang, J.; Li, W.X.; Wang, G.T. PhyloSuite: An integrated and scalable desktop platform
for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Resour.
2019
,20,
348–355. [CrossRef] [PubMed]
42.
Benson, G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res.
1999
,27, 573–580. [CrossRef]
[PubMed]
43.
Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability.
Mol. Biol. Evol. 2013,30, 772–780. [CrossRef]
44.
Xia, X. DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Mol. Biol. Evol.
2018
,35,
1550–1552. [CrossRef]
45.
Lanfear, R.; Frandsen, P.B.; Wright, A.M.; Senfeld, T.; Calcott, B. Partition finder 2: New Methods for selecting partitioned models
of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 2016,34, 772–773. [CrossRef]
46.
Nguyen, L.T.; Schmidt, H.A.; Von Haeseler, A.; Minh, B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating
maximum-likelihood phylogenies. Mol. Biol. Evol. 2015,32, 268–274. [CrossRef]
47.
Ronquist, F.; Teslenko, M.; Van Der Mark, P.; Ayres, D.L.; Darling, A.; Höhna, S.; Larget, B.; Liu, L.; Suchard, M.A.; Huelsenbeck,
J.P. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol.
2012
,61,
539–542. [CrossRef]
48.
Timmermans, M.J.; Barton, C.; Haran, J.; Ahrens, D.; Culverwell, C.L.; Ollikainen, A.; Vogler, A.P. Family-level sampling of
mitochondrial genomes in Coleoptera: Compositional heterogeneity and phylogenetics. Genome Biol. Evol.
2016
,8, 161–175.
[CrossRef]
49.
Letunic, I.; Bork, P. Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees.
Nucleic Acids Res. 2016,44, 242–245. [CrossRef]
50.
Liu, Y.Q.; Chen, D.B.; Liu, H.H.; Hu, H.L.; Bian, H.X.; Zhang, R.S.; Yang, R.S.; Jiang, X.F.; Shi, S.L. The complete mitochondrial
genome of the longhorn Beetle Dorysthenes paradoxus (Coleoptera: Cerambycidae: Prionini) and the implication for the
phylogenetic relationships of the Cerambycidae species. J. Insect Sci. 2018,18, 1–8. [CrossRef] [PubMed]
51.
Wang, J.; Dai, X.Y.; Xu, X.D.; Zhang, Z.Y.; Zhang, J.Y. The complete mitochondrial genomes of five longicorn beetles (coleoptera:
Cerambycidae) and phylogenetic relationships within cerambycidae. PeerJ 2019,7, e7633. [CrossRef] [PubMed]
52.
Zhang, D.X.; Hewitt, G.M. Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary
studies. Biochem. Syst. Ecol. 1997,25, 99–120. [CrossRef]
53. Boore, J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999,27, 1767–1780. [CrossRef]
54.
Cameron, S.L. Insect mitochondrial genomics: Implications for evolution and phylogeny. Annu. Rev. Èntomol.
2014
,59, 95–117.
[CrossRef]
55. Rand, D.M. Endotherms, ectotherms, and mitochondrial genome size variation. J. Mol. Evol. 1993,37, 281–295. [CrossRef]
56. Rydin, C.; Källersjö, M. Taxon sampling and seed plant phylogeny. Cladistics 2002,18, 485–513. [CrossRef]
57. Sanderson, M.J.; Donoghue, M.J. Patterns of variation in levels of homoplasy. Evolution 1989,43, 1781–1795. [CrossRef]
58.
Cai, C.; Tihelka, E.; Pisani, D.; Donoghue, P.C. Data curation and modeling of compositional heterogeneity in insect phylogenomics:
A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga). Mol. Phylogenetics Evol. 2020,147, 106782. [CrossRef]
59.
Ai, D.; Peng, L.; Qin, D.; Zhang, Y. Characterization of three complete mitogenomes of Flatidae (Hemiptera: Fulgoroidea)
and compositional heterogeneity analysis in the Planthoppers’ mitochondrial phylogenomics. Int. J. Mol. Sci.
2021
,22, 5586.
[CrossRef]
60.
Nie, R.E.; Andújar, C.; Gómez-Rodríguez, C.; Bai, M.; Xue, H.J.; Tang, M.; Vogler, A.P. The phylogeny of leaf beetles (Chrysomeli-
dae) inferred from mitochondrial genomes. Syst. Entomol. 2020,45, 188–204. [CrossRef]
61.
Zhang, Z.Y.; Guan, J.Y.; Cao, Y.R.; Dai, X.Y.; Storey, K.B.; Yu, D.N.; Zhang, J.Y. Mitogenome analysis of four lamiinae species
(Coleoptera: Cerambycidae) and gene expression responses by monochamus alternatus when infected with the parasitic
nematode, bursaphelenchus mucronatus. Insects 2021,12, 453. [CrossRef] [PubMed]
62.
Cherepamov, A.I.; Zolotarenko, G.S.; Kothekar, V.S. Cerambycidae of Northern Asia. Vollume 3, Lamiinae, Part 1 (English Edition);
Amerind Publishing: New Delhi, India, 1990; pp. 1–300.
63.
Löbl, I.; Smetana, A. Catalogue of Palaearctic Coleoptera, Vol. 6: Chrysomeloidae; Apollo Books: Stenstrup, Denmark, 2010; pp. 1–924.
64.
Gressitt, J.L. Longicorn Beetles of China. Longicornia, Études et Notes sur les Longicornes; Paul Lechevalier: Paris, Germany, 1951;
pp. 1–667. Volume 2.
Insects 2021,12, 820 13 of 13
65. Ohbayashi, N.; Niisato, T. Longicorn Beetles of Japan; Tokai University Press: Kanagawa, Japan, 2007; pp. 1–818.
66.
Toki, W.; Kubota, K. Molecular phylogeny based on mitochondrial genes and evolution of host plant use in the long-horned
beetle tribe Lamiini (Coleoptera: Cerambycidae) in Japan. Environ. Entomol. 2010,4, 1336–1343. [CrossRef] [PubMed]
Content uploaded by Huanhuan Lu
Author content
All content in this area was uploaded by Huanhuan Lu on Feb 17, 2025
Content may be subject to copyright.
Content uploaded by Sabatelli Simone
Author content
All content in this area was uploaded by Sabatelli Simone on Sep 12, 2021
Content may be subject to copyright.
