Análises Comparativas de Duas Subordens Thysanoptera Eng

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Received: 27 December 2022 | Revised: 2 February 2023 | Accepted: 28 February 2023
DOI: 10.1002/arch.22010
RESEARCH ARTICLE
Comparative analysis of the two suborders

of Thysanoptera and characterization
of the complete mitochondrial genome
of Thrips parvispinus
Avas Pakrashi | Abhishek Patidar | Devkant Singha |

Vikas Kumar | Kaomud Tyagi
Molecular Systematics Division, Centre for

DNA Taxonomy, Zoological Survey of India, Abstract
Kolkata, West Bengal, India
Thrips parvispinus is a serious sucking pest on a number of
Correspondence economically important crops in the oriental region. It has
Kaomud Tyagi, Molecular Systematics
gained importance recently for its drastic range extension
Division, Centre for DNA Taxonomy,
Zoological Survey of India, Kolkata, West distribution as an invasive pest. Here, the complete
Bengal 700053, India.
mitochondrial genome (15,067 bp) of Thrips parvispinus
Email: kumud.tyagi5@gmail.com
was sequenced and characterized. It possesses 37 genes
Funding information and the putative noncoding region is duplicated. Compara-
Science and Engineering Research Board
tive analyses of nucleotide diversity, skewness, codon
usage bias, and selection pressure in mitochondrial
protein‐coding genes of the available 31 thrips mitogen-
omes (24 Terebrantia + 7 Tubulifera) were performed.
Phylogenetic analysis showed a sister relationship of T.
parvispinus to the clade (T. florum + T. hawaiiensis). Phyloge-
netic analyses formed the monophyly of subfamilies
Phlaeothripinae and Idolothripinae within the family
Phlaeothripidae (Suborder Tubulifera). Low nucleotide
diversity was indicative of reversal of strand asymmetry
in the Tubulifera. Neutrality analysis showed that direc-
tional mutation plays a major role in shaping codon usage
bias in both suborders. Principal component analysis
indicated distinct codon usage patterns in each suborder.
Our data suggested weaker selection constrains on
Terebrantia than in the Tubulifera. More tubuliferan
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https://doi.org/10.1002/arch.22010
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2 of 15 | PAKRASHI ET AL.
mitogenomes are required to resolve previous classification

hypotheses and elucidate genome evolution in these two
suborders.
KEYWORDS
comparative mitogenomics, mitogenome, Thrips parvispinus,
Thysanoptera
Research Highlights
• We sequenced and characterized the complete mito-
chondrial genome of the invasive pest species Thrips
parvispinus.
• Monophyly of subfamily Phlaeothripinae and Idolothri-
pinae under suborder Tubulifera was confirmed.
• Mitochondrial protein‐coding genes revealed low nucle-
otide diversity, indication of reversal of strand asymme-
try, disparate codon usage pattern and strong selection
pressure in Tubulifera.
1 | INTRODUCTION
Thrips (Thysanoptera) are minute, soft‐bodied fringed wing insects with asymmetrical mouthparts (Mound &
Marullo, 1996). A few species of thrips are serious sucking pests in a wide number of agroecosystems. Fifteen thrips
species are also known as the sole transmitters of plant Tospoviruses (Riley et al., 2011; Tyagi et al., 2017). A total of
180 thrips species worldwide and 60 in India are reported to act aspects of a wide variety of plants causing heavy
economic damage by their feeding and oviposition (Tyagi & Kumar, 2016).
Thrips parvispinus is known to be a major pest species commonly found in South East Asia, that has been also
reported recently from Australia (Mound & Collins, 2000), Greece (Anagnou‐Veroniki et al., 2008), Hawaii, Spain,
Tanzania, Netherlands (NPPO, 2019). A recent investigation in Indonesia (Johari et al., 2014) revealed a total yield
loss of 22.8% in chilli production due to T. parvispinus. Since its first report in India in 2015 (Tyagi et al., 2015), T.
parvispinus has been reported from Chhattisgarh and southern India from nine host plant families. Infestation results
in shedding of flowers and deformity of fruit (Rachana et al., 2018; Sridhar et al., 2021). The current study reports
the first complete mitochondrial genome of this widely distributed invasive and polyphagous pest species.
The classification of the order Thysanoptera has been questioned, with multiple classification proposed
hypotheses. The most accepted classification of the order includes two suborders (Terebrantia and Tubulifera) and
nine extant families (Mound et al., 1980; Mound & Morris, 2007). Bhatti (1988) proposed Terebrantia and
Tubulifera to be separate orders within a superorder Thysanopteroida in view of the substantial morphological and
behavioral distinctiveness. The wings of the Tubulifera were proposed to be of a primitive type than Terebrantia. In
Tubulifera, the venations are largely alacunate, with microtrichia restricted to the base whereas in Terebrantia the
venation is plesiotypically lacunate, with microtrichia present on all the veins. Therefore, a second aim of the
present study is to perform comparative analysis of thrips mitogenomic protein‐coding genes (24 Terebrantia and 7
Tubulifera) to provide insights into the evolutionary relationships between suborders of Thysanoptera.
PAKRASHI ET AL. | 3 of 15
2 | MATERIALS AND METHODS
2.1 | Collection, morphological identification, and DNA extraction
Specimens of T. parvispinus were collected with a wetted brush from chilli plants in Tamil Nadu, India
(11.008 N, 76.924 E) and transferred to absolute alcohol. Morphological identification was done by Kaomud
Tyagi with the help of available identification keys. Ethyl alcohol preserved specimens were stored at −80°C
in the Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata. For
next generation sequencing, DNA was isolated by nondestructive method (Tyagi et al., 2017) from 30
specimens individually and pooled after morphological identification of individual specimen with taxonomic
keys (Mound & Masumoto, 2005). Quantification of DNA was checked in a Qubit fluorometer (Thermo Fisher
Scientific) using the dsDNA high‐sensitivity kit with the standard protocol.
2.2 | Mitogenome sequencing, assembly, and annotation
Sequencing was performed on the Illumina platform (Illumina Hiseq. 2500) with 150 bp paired‐end read chemistry.
Paired‐end libraries were constructed with standard protocols using the TruSeq DNA Library Preparation kit.
Approximately 4–5 GB raw data was generated and NGS‐Toolkit (Patel & Jain, 2012) used for removing low‐quality
reads. For assembly from the raw data, NOVOPlasty sequence assembler (Dierckxsens et al., 2017) was used with
COI sequence of T. parvispinus as a seed. Annotation of the assembled mitogenome and estimation of gene
boundaries was done byonline MITOS web‐server (Bernt et al., 2013). Gene boundaries were confirmed manually
using BLASTn, BLASTp, and ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/) and alignment comparisons with
previously published thrips mitogenomes. The secondary structure of tRNAs was predicted using MITOS and
tRNAscan‐SE (http://lowelab.ucsc.edu/tRNAscan-SE/). The assembled mitogeome was circularized using CGView-
ServerBETA (http://cgview.ca/) with default parameters.
2.3 | Comparative analysis
Sliding window analysis of nucleotide diversity (Window size = 200 bp; step size = 20 bp) and synonymous/
nonsynonymous (Ka/Ks) substitution analysis were carried out in DnaSP6.0 (Rozas et al., 2017). Nucleotide
skew was calculated using the formula: AT skew = (A − T)/(A + T) and GC skew = (G − C)/(G + C). Nucleotide
composition and relative synonymous codon usage (RSCU) was calculated in MEGAX (Kumar et al., 2018).
The Effective Number of Codons (ENc) was determined in DAMBE ver. 7 (Xia, 2001). We used the “ggplot2”
package (Wickham et al., 2016) of R studio v.4.1.0 to prepare the GC3‐ENC and neutrality plots. The heat
map of RSCU values was plotted in “pheatmap” package (Kolde & Kolde, 2018) in RStudio v.4.1.0. Principal
component analysis (PCA) of the RSCU data set was carried out using the “FactoMineR” package (Lê
et al., 2008). Furthermore, PCA biplot with the first two components of the PCA analysis and taxonomic
group‐based clustering was performed using the “factoextra” package (Kassambara & Mundt, 2020). We
performed selection pressure analysis in EasyCodeML (Gao et al., 2019) using clade model (Bielawski &
Yang, 2004; Forsberg & Christiansen, 2003) to evaluate dN/dS (ω) ratios in two suborders of Thysanoptera.
Selection constrains in both the suborders was calculated using protein‐coding genes (PCGs), as well as the
concatenated 13 PCGs. The selected foreground lineage was compared in the model C (CmC) against a null
model 2a_rel (M2a_rel) (Weadick & Chang, 2012).
2.4 | Phylogenetic analysis
A previous study in phylogenetic analysis of 28 species of Thysanoptera (Pakrashi et al., 2022) showed the
effectiveness of first and second codon positions only PCGs data set, with GBlocks removal (PCG12 +
Gblocks) in resolving taxonomic boundaries in thrips. Here the phylogeny was constructed using 31 species
(plus outgroup Alloeorhynchus bakeri Hemiptera) with the same data set strategy (PCG12 + Gblocks: 6014 bp).
Using a codon‐based MAFFT alignment, removal of poorly aligned sites in GBlocks. PCG concatenation, and
determining the best partitioning scheme and nucleotide substitution models were carried out in Phylosuite
ver 1.2.2 (Zhang et al., 2020). Mr.Bayes ver. 3.2 (Ronquist et al., 2012) was used for BI analyses with two
MCMC runs each with four chains (three heated and one cold) run for 500,0000 generations, tree sampling
every 1000 generations and a burn‐in of 25%. The inferred tree was visualized and edited using FigTree ver
1.4.4 (Rambaut, 2018).
3 | RES UL TS AND DISC US SION
3.1 | Genome organization of T. parvispinus
The complete circular mitochondrial genome of Thrips parvispinus was 15067 bp in length (GenBank accession no:
OP910112, Figure S1). It included the typical 37 genes including 13 PCGs, 22 transfer RNAs (tRNAs), 2 ribosomal
RNAs (rRNAs), and 2 putative control regions. Mostgenes (31) were encoded on the positive strand except nad5,
nad4, nad4L, trnH, trnP, and trnY (Table 1). AT composition of the mitogenome was high (78.4%) as has previously
been reported for insect mitogenomes (Cameron, 2014). Positive overall AT skew (0.110) indicated a richness of
Adenine over Thymine. The T. parvispinus mitogenome contained four overlapping regions (7–12 bp with a total of
29 bp) and 19 intergenic spacer regions (1–71 bp with a total of 425 bp). ATN initiation codons (nine ATT, one ATG,
one with ATC, and one ATA) were observed in 12 PCGs except cox3 (TTG). Nine PCGs used complete TAA stop
codons, whereas, the incomplete termination codon T(AA) was used by nad2, nad3, nad4, and atp8. The length of
tRNAs varied form 59 bp (trnS1, trnV) to 69 bp (trnQ). All tRNAs have the typical clover leaf secondary structure
except trnS1, trnV (which lacks a DHU arm). The length of rrnL and rrnS was 1138 and 751 bp, respectively. T.
parvispinus had two distinct control regions; one at the thrips conserved position upstream of nad5 (CR1; 194 bp)
and another was between trnE and trnP (CR2; 238 bp). The sequence of CR1 was identical to that of CR2 suggesting
duplication of the control region as reported previously in thrips (Tyagi et al., 2020). Previously, four conserved
Thrips Gene Blocks (TGBs) for suborder Terebrantia were proposed (Pakrashi et al., 2022), of which only one TGB‐2
(cytb‐trnY) was not found in the T. parvispinus mitogenome. Nevertheless, the shared gene boundaries (cox2‐trnG,
atp6‐trnQ, trnQ‐trnS2, and rnL‐cox1) conserved for the genus Thrips were found as in previous studies (Pakrashi
et al., 2022; Tyagi et al., 2020).
3.2 | Comparative analysis of PCGs in Tubulifera and Terebrantia
The two suborders of order Thysanoptera can be differentiated by the following characters: Tubulifera have a
tube‐like last abdominal segment, wings without veins, three pupal stages, and oviposit eggs on the leaf
surface. In contrast, Terebrantia has a conical last abdominal segment, wings with prominent veins, a saw‐like
ovipositor, and lay egg singly within plant tissues. In view of these morphological and behavioral differences
between the suborders, we have performed comparative analyses of the PCGs to explore mitogenomic
variations between them.
TABLE 1 List of annotated mitochondrial genes of Thrips parvispinus and its characteristic features.
Name Start Stop Strand Length ovl/nc Start/stop codon
trnT 1 65 + 65 10
trnI 76 142 + 67 19
cytb 162 1256 + 1095 0 ATT/TAA
CR1 1257 1450 + 194 0
nad5 1451 3145 ‐ 1695 −12 ATT/TAA
trnH 3134 3196 ‐ 63 −10
nad4 3187 4516 ‐ 1330 −7 ATT/T(AA)
nad4l 4510 4791 ‐ 282 25 ATG/TAA
trnC 4817 4879 + 63 18
nad6 4898 5395 + 498 71 ATT/TAA
trnV 5467 5525 + 59 0
rrnL 5526 6663 + 1138 0
cox1 6664 8235 + 1572 2 ATT/TAA
nad3 8238 8586 + 349 0 ATT/T(AA)
trnL2 8587 8652 + 66 12
cox2 8665 9306 + 642 23 ATC/TAA
trnG 9330 9392 + 63 3
trnK 9396 9459 + 64 2
cox3 9462 10250 + 789 4 TTG/TAA
trnN 10255 10318 + 64 0
trnS1 10319 10377 + 59 3
trnL1 10381 10441 + 61 44
trnE 10486 10551 + 66 0
CR2 10552 10789 + 238 0
trnP 10790 10855 ‐ 66 34
trnY 10890 10953 ‐ 64 57
nad2 11011 11962 + 952 0 ATT/T(AA)
trnW 11963 12039 + 77 0
nad1 12040 12969 + 930 0 ATT/TAA
trnM 12970 13030 + 61 1
trnA 13032 13092 + 61 0
trnF 13093 13157 + 65 0
rrnS 13158 13907 + 750 0
atp8 13917 14076 + 133 41 ATA/T(AA)
(Continues)
TABLE 1 (Continued)
Name Start Stop Strand Length ovl/nc Start/stop codon
atp6 14118 14732 + 711 5 ATT/TAA
trnQ 14738 14806 + 69 59
trnS2 14866 14930 + 65 2
trnD 14933 15000 + 68 0
trnR 15001 15067 + 67 0
Note: The PCGs and rRNA genes are represented by standard nomenclature, tRNAs are represented as trn followed by the
IUPAC‐IUB single‐letter amino acid codes. (+) values in strand represent as heavy (H) and (‐) values represent as light (L).
IGN represents (+) values as intergenic nucleotides and (‐) values as overlapping regions.
Abbreviations: CR, control region; PCGs, protein‐coding genes; rRNA, ribosomal RNAs; tRNAs, transfer RNAs.
3.2.1 | Nucleotide diversity
To evaluate nucleotide diversity, sliding window analysis was performed on two separate concatenated datasets of
Terebrantia (24 species) and Tubulifera (7 species). Average nucleotide diversity value (pi) in the two suborders
were distinctly different, that is, 0.3035 in Terebrantia (range: 0.160 in cox1 to 0.456 in nad6) and 0.2063 (range:
0.092 in cox1 to 0.313 in nad2) in Tubulifera (Figure 1a). Nucleotide diversity analysis shows Terebrantia have high
genetic variability than Tubulifera.
3.2.2 | Nucleotide skewness
Positive and negative AT skew is defined as excess of A over T and T over A, respectively (Perna & Kocher, 1995). Most
insect mitogenomes have negative GC skew (more C than G) (Wei et al., 2010). In Terebrantia, the average AT skew value
was −0.167, ranging from −0.112 (Holarthrothrips indicus) to −0.224 (Anaphothrips obscurus). All Terebrantia mitogenomes
have negative GC skew except Anaphothrips obscurus that is marginally positive GC skew (0.007). Conversely, tubuliferans
have positive GC skew (range: 0.040 in Gynaikothrips uzeli to 0.063 in Psephenothrips eriobotryae) (Table S1).
Reversal of of GC skew in Tubulifera indicates the reversal of strand asymmetry in this suborder (Wei
et al., 2010) (Figure 1b). The proposed cause of asymmetry is replication processes where the lagging strand is more
prone to mutation and DNA damage during strand separation. Inversion of replication origin in the AT‐rich region
(control region), thus leads to the reversal of replication with the leading strand becoming the lagging strand and
vice versa. Further studies are necessary to know a detailed understanding of this phenomenon in thrips.
3.2.3 | Codon usage patterns
Heatmap analysis of RSCU values revealed consistent trends in each suborder, codons ending with As or Us are
much more commoner than Gs or Cs, indicating strong bias towards A/T ending codons. The codon usage bias
(CUB) dendrogram revealed distinctive CUB patterns in the suborders, both clustered separately. Nevertheless,
within suborders, relationships between families/subfamilies in the CUB‐based dendrogram were not congruent
with thrips taxonomic classifications or phylogenetic analyses (Figure 2a, Table S2).
For better insight of the potential patterns of CUB in the suborders, principal component analysis (PCA)‐ biplot
was conducted using the RSCU data set. The first two components, PC1 and PC2 explained 54.4% of the variance
(36.4% and 18%, respectively). Variability in PC1 was mostly associated with codons ending with U and C,
7 of 15
(b) AT skew versus GC skew plot of the PCGs. Terebrantia is denoted as red and Tubulifera as blue. PCGs, protein‐
F I G U R E 1 (a) Genetic diversity (Pi) of Terebrantia, and Tubulifera. Each PCGs are defined by a separating line.
|ET AL.
coding genes.
PAKRASHI
F I G U R E 2 (a) Heat map based on codon usage of the 31 studied thrips species. Codons are shown on the
x‐axis. A and U‐ending codons are shown in separate clusters. (b) Principal component analysis based on the RSCU
values of the codons. Suborders are differentiated by color as shown in the legend, the arrows show the codons
used in the analysis. RSCU, relative synonymous codon usage.
Conversely, PC2 was predominantly related to codons ending G and A. PCA analysis also showed a well‐defined
separation in CUB between two suborders. Tubuliferans have a bias towards U‐ending codons (Figure 2b).
3.2.4 | ENC‐GC3s and neutrality plot
The effective number of codons (ENC) shows the extent of amino acids codon balance. ENC values in Terebrantia
ranged from 33.31 to 45.96 and were significantly higher (t‐test, p < 0.05) than in Tubulifera (ranged from 30.90 to
32.48) (Figure 3a, Table S3). ENC suggests weaker selective constraint on Terebrantia than on Tubulifera.
Terebrantia uses a greater variety of codons to synthesize proteins potentially indicating improved translation
efficiency by lowering tRNA competition (Guan et al., 2019; Kumar et al., 2022).
To elucidate the impacts of compositional bias vs natural selection in the codon usage in the two suborders,
GC3‐ENC plot and neutrality analysis were carried out. The GC3 versus ENC plot affirmed that all species fell well
below the expected curve (Figure 3b). This clustering revealed a predominant effect of factors other than
directional mutational on in both the suborders. Moreover, the neutrality plot showed the magnitude of operational
directional mutational constraint on codon usage. The slope of the regression line in Terebrantia and Tubulifera was
0.172 and 0.212, signifying 82.2% and 78.8% due to natural selection, respectively (Figures 3c,d and 4).
F I G U R E 3 (a) Boxplot of ENC values of Terebrantia and Tubulifera; (b) ENC‐GC3 plot of 31 species of thrips;
Terebrantia is denoted in red and Tubulifera in blue; (c) Neutrality plot of 24 species of Terebrantia; (d) Neutrality
plot of seven species of Tubulifera. ENC, effective number of codons.
ET AL.
F I G U R E 4 (a) Ka/Ks plot of PCGs in suborder Terebrantia; (b) Ka/Ks plot of PCGs in suborder Tubulifera.
PAKRASHI
PCGs, protein‐coding genes.

|10 of 15
F I G U R E 5 Phylogenetic tree inferred from 13 PCGs using Bayesian inference. Posterior probabilities are
marked beside the nodes. Alloeorhynchus bakeri (Hemiptera) was used as outgroup. Families and subfamilies were
denoted by colors as denoted in the legend. PCGs, protein‐coding genes.
3.2.5 | Selection pressure analysis
Most mt genes in suborder Terebrantia are subject to purifying selection with ka/ks ratios less than 1. The average
ka/ks ratio followed the following order: cox1 < cytb < cox3 < cox2 < nad1 < nad5 < atp6 + 8 < nad3 < nad4 < nad2 <
nad4L < nad6. Conversely, all PCGs were detected to be subject to strong purifying selection in Tubulifera with
average ka/ks ratio in ascending order: cox1 < cox3 < cytb < cox2 < nad1 < atp6 + 8 < nad4 < nad5 < nad4L < nad3 <
nad2 < nad6. Each PCG had a significant difference (t‐test, p < 0.05) in Ka/Ks ratio between Tubulifera and
Terebrantia (Figure 5). To confirm the result of ka/ks ratio, dN/dS (ω) ratio analysis was carried out. dN/dS (ω) ratio
analysis revealed similar results with overall purifying selection in Thysanoptera (Tables 2 and S4). Furthermore, the
ω values for the clade of Terebrantia was higher than Tubulifera in concatenated PCGs data set and most of the
PCGs with few exceptions like cytb, nad3 and nad4L (Tables 2 and S4).
4 | PHYLOGENETIC RELATIONSHIPS
An elaborate phylogenetic analysis with varied datasets and phylogenetic methods in 28 species of thrips was
previously carried out by Pakrashi et al. in 2022. The current study defines the phylogenetic position of three newly
added species in order Thysanoptera; Bactrothrips quadrituberculatus, Psephenothrips eriobotryae, and Thrips
parvispinus. The phylogeny confirms the monophyly of subfamily Phlaeothripinae and idolothripinae under the sole
family Phlaeothripidae of Tubulifera. The genus Psephenothrips with one species is recovered as sister to the genus
T A B L E 2 Estimation of ω (d N/d S) values for the mitochondrial protein‐coding genes in suborder Terebrantia
and Tubulifera.
Terebrantia Tubulifera
Estimated Estimated
Sl No. Gene ω value 2Δl p value ω value 2Δl p value
1 atp6 0.015 29.17 0 0.004 27.82 0
2 cox1 0.067 20.56 0 0.038 20.14 0
3 cox2 0.05 5.42 0.02 0.039 0.414 0.52
4 cox3 0.053 5.56 0.018 0.035 4.56 0.033
5 cytb 0.052 0.11 0.736 0.06 1.55 0.213
6 nad1 0.067 32.38 0 0.031 24.37 0
7 nad2 0.031 185.58 0 0.028 0.35 0.554
8 nad3 0.04 0.85 0.353 0.056 1.32 0.25
9 nad4 0.029 0.57 0.447 0.027 0.37 0.002
10 nad4L 0.008 1.14 0 0.035 10.03 0.002
11 nad5 0.019 6.81 0.009 0.014 3.72 0.054
12 nad6 0.07 3.9 0.048 0.054 1.06 0.302
13 13 PCGs 0.063 202.1 0 0.034 187.38 0
Gynaikothrips with high support value. Moreover, T. parvispinus was in sister relationship to the clade of (T.
florum + T. hawaiiensis) (Figure 5).
5 | C ONC LUS I ON
This is the first mitogenomic data of the invasive pest species T. parvispinus. The current study also sheds light on
the certain distinctive genomic attributes in Terebrantia and Tubulifera. Members of Terebrantia are totally
divergent from Tubulifera in morphological, developmental, and behavioral traits. Due to these differences, multiple
classification hypotheses have been proposed (Bhatti, 1988; Bhatti, 1994, 2006; Mound & Marullo, 1996). The
current comparative study found low nucleotide diversity, reversal of strand asymmetry, disparate codon usage
patterns and strong purifying selection pressure in Tubulifera. Terebrantia are considered as more advanced and
recently diverged lineages of order Thysanoptera as compared to Tubulifera (Pakrashi et al., 2022). Additionally,
most of pest and vector thrips are terebrantians that are more active fliers than tubuliferans. Cohen et al. (2021)
linked of positive selection in nuclear PCGs to rapid adaptive evolution in a pest beetle. Mitogenomic differentiation
between Terebrantia and Tubulifera may imply a high nuclear divergence lineage between the two suborders.
However, more data of tubuliferan species and whole genomes analysis needs to be included in future studies to
resolve classification issues and get better insights into the adaptive evolution of these two suborders.
A U T H O R C O N TR I B U T I O N S
Avas Pakrashi: Data curation; formal analysis; methodology; visualization; writing—original draft; software.
Abhishek Patidar: Data curation; methodology; writing—original draft. Devkant Singha: Formal analysis; data
curation; writing—original draft. Vikas Kumar: Supervision; conceptualization; resources; project administra-
tion; writing—original draft; writing—review & editing; funding acquisition; investigation. Kaomud Tyagi:
Conceptualization; formal analysis; supervision; writing—review & editing; writing—original draft; software;
funding acquisition; validation.
A C KN O W L E D G M E N T S
The authors are thankful to the Director of Zoological Survey of India (ZSI), Ministry of Environment, Forests and
Climate Change (MoEFCC), Govt. of India for providing necessary permissions and facilities. This study was
supported by SERB funded project “Delimiting Species Boundaries in Pest and Vector thrips. (Thysanoptera:
Thripidae) from India” to V.K. and K.T.
C O NF L I C T O F I NT E R E S T S ST A T E M E N T
The authors declare that there is no conflict of interest.
D A TA A V A I L A B I L I T Y S T A T E M E N T
The data that support the findings of this study are openly available in NCBI at https://www.ncbi.nlm.nih.gov,
reference number OP910112. Annotated mitogenome assembly is deposited in NCBI GenBank under the following
accession number: OP910112.
ETHICS STATEME NT
No specific permission was needed for thrips specimen collection and experimental work as they are common pests
of agricultural fields. Sampling localities were not privately owned or naturally protected areas.
ORCID
Avas Pakrashi http://orcid.org/0000-0001-5876-0203
Abhishek Patidar http://orcid.org/0000-0003-2089-8308
Devkant Singha http://orcid.org/0000-0002-0670-520X
Vikas Kumar http://orcid.org/0000-0002-0215-0120
Kaomud Tyagi http://orcid.org/0000-0003-1064-9826
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S UP P O R T I N G I N F O R M A T I O N
Additional supporting information can be found online in the Supporting Information section at the end of this
article.
How to cite this article: Pakrashi, A., Patidar, A., Singha, D., Kumar, V. & Tyagi, K. (2023) Comparative
analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial Genome
of Thrips parvispinus. Archives of Insect Biochemistry and Physiology, e22010.
https://doi.org/10.1002/arch.22010

Análises Comparativas de Duas Subordens Thysanoptera Eng

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Comparative analysis of the two suborders

Avas Pakrashi | Abhishek Patidar | Devkant Singha |

Molecular Systematics Division, Centre for

mitogenomes are required to resolve previous classification

2 | MATERIALS AND METHODS

2.1 | Collection, morphological identification, and DNA extraction

2.2 | Mitogenome sequencing, assembly, and annotation

2.3 | Comparative analysis

2.4 | Phylogenetic analysis

3 | RES UL TS AND DISC US SION

3.1 | Genome organization of T. parvispinus

3.2 | Comparative analysis of PCGs in Tubulifera and Terebrantia

Name Start Stop Strand Length ovl/nc Start/stop codon

cytb 162 1256 + 1095 0 ATT/TAA

CR1 1257 1450 + 194 0

nad5 1451 3145 ‐ 1695 −12 ATT/TAA

trnH 3134 3196 ‐ 63 −10

nad4 3187 4516 ‐ 1330 −7 ATT/T(AA)

nad4l 4510 4791 ‐ 282 25 ATG/TAA

trnC 4817 4879 + 63 18

nad6 4898 5395 + 498 71 ATT/TAA

trnV 5467 5525 + 59 0

rrnL 5526 6663 + 1138 0

cox1 6664 8235 + 1572 2 ATT/TAA

nad3 8238 8586 + 349 0 ATT/T(AA)

trnL2 8587 8652 + 66 12

cox2 8665 9306 + 642 23 ATC/TAA

trnG 9330 9392 + 63 3

trnK 9396 9459 + 64 2

cox3 9462 10250 + 789 4 TTG/TAA

trnN 10255 10318 + 64 0

trnS1 10319 10377 + 59 3

trnL1 10381 10441 + 61 44

trnE 10486 10551 + 66 0

CR2 10552 10789 + 238 0

trnP 10790 10855 ‐ 66 34

trnY 10890 10953 ‐ 64 57

nad2 11011 11962 + 952 0 ATT/T(AA)

trnW 11963 12039 + 77 0

nad1 12040 12969 + 930 0 ATT/TAA

trnM 12970 13030 + 61 1

trnA 13032 13092 + 61 0

trnF 13093 13157 + 65 0

rrnS 13158 13907 + 750 0

atp8 13917 14076 + 133 41 ATA/T(AA)

Name Start Stop Strand Length ovl/nc Start/stop codon

atp6 14118 14732 + 711 5 ATT/TAA

trnQ 14738 14806 + 69 59

trnS2 14866 14930 + 65 2

trnD 14933 15000 + 68 0

trnR 15001 15067 + 67 0

3.2.1 | Nucleotide diversity

3.2.2 | Nucleotide skewness

3.2.3 | Codon usage patterns

3.2.4 | ENC‐GC3s and neutrality plot

PCGs, protein‐coding genes.

3.2.5 | Selection pressure analysis

1 atp6 0.015 29.17 0 0.004 27.82 0

2 cox1 0.067 20.56 0 0.038 20.14 0

3 cox2 0.05 5.42 0.02 0.039 0.414 0.52

4 cox3 0.053 5.56 0.018 0.035 4.56 0.033

5 cytb 0.052 0.11 0.736 0.06 1.55 0.213