Journal of Insect Science, (2024) 24(2): 4; 1–9

https://doi.org/10.1093/jisesa/ieae028
Research

Mitochondrial genomes of Nemourinae species

(Plecoptera: Nemouridae) and the phylogenetic
implications
Ying Wang*, Caiyue Guo, Xiaoxiao Yue, Xing Fan, Yuying Fan, Jinjun Cao
Department of Plant Protection, Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan

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Institute of Science and Technology, Hualan Road, Xinxiang 453003, China *Corresponding author, mail: wangying198586@163.com

Subject Editor: Ren-Huai Dai

Received on 30 November 2023; revised on 22 December 2023; accepted on 22 February 2024

Currently, the classification system of 2 subfamilies within Nemouridae has been widely accepted. However,
monophyly of 2 subfamilies has not been well supported by molecular evidence. To date, only mitogenomes
from genus Nemoura of the subfamily Nemourinae were used in previous phylogenetic studies and produced
conflicting results with morphological studies. Herein, we analyzed mitogenomes of 3 Nemourinae species
to reveal their mitogenomic characteristics and to examine genus-level classification among Nemouridae. In
this study, the genome organization of 3 mitogenomes is highly conserved in gene order, nucleotide compo-
sition, codon usage, and amino acid composition. In 3 Nemourinae species, there is a high variation in nucle-
otide diversity among the 13 protein-coding genes (PCGs). The Ka/Ks values for all PCGs were far lower than 1,
indicating that these genes were evolving under purifying selection. The phylogenetic analyses highly support
Nemurella as the sister group to Ostrocerca. Meanwhile, Nemoura is recovered as the sister group of Malenka;
they are grouped with other Amphinemurinae and emerged from a paraphyletic Nemourinae. More molecular
data from different taxonomic groups are needed to understand stoneflies phylogeny and evolution.

Key words: Plecoptera, Nemourinae, mitochondrial genome, phylogeny

Introduction (Sphaeronemoura, Tominemoura, Nanonemoura, and Sinonemura)

have been added, bringing the total number of genera in this family
Plecoptera, commonly known as stoneflies, is an ancient group of
to 21 (Baumann and Fiala 2001, Shimizu and Sivec 2001, Sivec and
insects with fossil records dating back to the Triassic period (Zwick
Stark 2009, Mo et al. 2020). Although Baumann (1975) proposed
2000, DeWalt et al. 2023). There are over 4,000 known species of
a widely accepted classification system for the family Nemouridae
stoneflies worldwide, distributed across most continents, with the
based on morphological data, the monophyly of 2 subfamilies has
exception of Antarctica (Zwick 2000, DeWalt et al. 2023). Stoneflies
not been well supported by molecular evidence, and conflicting
are particularly abundant in regions with cooler, clean mountain
results have been produced (Terry and Whiting 2003, Gamboa et al.
streams and rivers (Zwick 2000). Their nymphs are sensitive to
2019, South et al. 2021).
changes in water quality and habitat health, making them valuable
Insect mitochondrial genomes (mitogenomes) are of particular
bioindicators for monitoring freshwater ecosystems (Fochetti and
interest to biologists due to their compact size, rapid evolution, and
Figueroa 2008, Stewart and Stark 2008, Qian et al. 2014).
unique genetic features, making them useful tools for studying com-
Nemouridae species are commonly known as spring stoneflies
parative and evolutionary genomics, phylogenetics, and population
due to their emergence in late winter and early spring. It is one of the
genetics (Wilson et al. 2000, Lin and Danforth 2004, Gissi et al.
largest families of Plecoptera with over 600 species founded world-
2008, Salvato et al. 2008, Cameron 2014).
wide (DeWalt et al. 2023). For a long time, the classification system
To date, there are 9 complete or nearly complete Nemourinae
of Nemouridae has been in constant flux. Newman (1853) first
mitogenomes available in the NCBI database (Table 1). Most
erected Nemouridae and included most of the present Euholognatha
mitogenomes were from species of the genera Nemoura, whereas
in this family. Later, this large diverse grouping was divided into 5
only 2 of them were from genus Nemurella and Lednia. For
families of the present superfamily Nemouroidea (Klapálek 1905,
those Nemourinae mitogenomes, only mitogenomes from genus
Zwick 1973). After revising most of the genera of Nemouridae,
Nemoura were used in previous phylogenetic studies because of an
Baumann (1975) divided this family into 2 subfamilies (Nemourinae
unannotated sequence of Nemurella pictetii (GenBank accession
and Amphinemurinae) and 17 genera. Recently, 4 more genera

© The Author(s) 2024. Published by Oxford University Press on behalf of Entomological Society of America. 1
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/
by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial
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2 Journal of Insect Science, 2024, Vol. 24, No. 2

Table 1. Species used for phylogenetic analyses in this study.

Subfamily Species Length Accession number

Nemourinae Nemoura avicularis 15,590 MT410776a

Nemoura cinerea 15,640 MT410849a
Nemoura flexura 15,780 MT584119a
Nemoura longicercia 15,728 OM287982
Nemoura meniscata 15,895 MN944386
Nemoura nankinensis 16,602 KY940360
Nemoura papilla 15,774 MK290826
Nemurella pictetii 15,934 OR601702
Lednia tumana 15,294 OR601701a
Ostrocerca truncata 15,971 OR398225
Amphinemurinae Amphinemura bulla 15,827 MW339348

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Amphinemura claviloba 15,707 MN720741
Amphinemura longispina 15,709 MH085446
Amphinemura sp. 15,176 KX091847a
Amphinemura yao 15,876 MH085447
Indonemoura auriformis 15,718 MN419915
Indonemoura jacobsoni 15,642 MH085448
Indonemoura nohirae 15,738 NC_044751
Malenka flexura 15,744 ON411527
Mesonemoura metafiligera 15,739 MH085450
Mesonemoura tritaenia 15,778 MH085451
Protonemura datongensis 15,756 MT276842
Protonemura kohnoae 15,707 MH085452
Protonemura meyeri 15,695 NC_050322
Protonemura orbiculata 15,758 MH085453
Sphaeronemoura acutispina 15,016 MH085455a
Sphaeronemoura elephas 15,846 MN944385
Sphaeronemoura grandicauda 15,661 MH085454
Sphaeronemoura hainana 15,260 MK111420a
Perlidae (outgroups) Caroperla siveci 15,353 MG677942a
Kamimuria klapaleki 16,077 MN400755

a
Nearly complete genome sequence.

no. OV121127) and an uncompleted sequence of Lednia tumana
(GenBank accession no. MH374046). Most of these studies
proposed a sister group of Nemoura and Amphinemura, leading a
paraphyletic Amphinemurinae (Chen and Du 2017a, 2017b, Cao et
al. 2019, 2021, Chen et al. 2020, Guo et al. 2022). Therefore, to
obtain a more precise phylogenetic relationship, it is necessary to
incorporate mitogenomic data, especially the data from other genera
of Nemourinae.
In this study, we sequenced the complete mitogenome of
Ostrocerca truncata and completed the missing rRNA sequences in
L. tumana mitogenome. In addition, we annotated the mitogenome
of N. pictetii for further analysis. We characterized and compared
the mitogenomes of these 3 Nemourinae species and revealed
mitogenomic characterizations of this subfamily in the present study
for the first time. Finally, phylogenetic analysis is provided to eval-
uate feasibility of mitogenome data to resolve relationships at the
genus level in Nemouridae.
Materials and Methods
Sample Collection and DNA Extraction
Specimens of O. truncata were collected from Hidden Valley,
Virginia. Specimens were soaked in 100% ethanol and stored at
−20 °C. Total genomic DNA was extracted from muscle tissue using
the DNeasy Extraction kit (Qiagen, Germany), according to the
manufacturer’s instructions.
Genome Sequencing, Assembly, and Annotation
Mitogenomes were sequenced and assembled as described in our
previous studies (Wang et al. 2018a, 2018b, 2019, Cao et al. 2019,
2021). Genomic DNA with qualified concentration was submitted
to Berry Genomics Co., Ltd. (Beijing, China) for library construction
and high-throughput sequencing. An Illumina TruSeq library with
an average insert size of 350 bp was generated and sequenced with
150 bp paired-end reads on the Illumina Hiseq 2500 platform. The
mitogenome was assembled using Trimmomatics v0.30 (Lohse et al.
2012) and IDBA-UD (Peng et al. 2012). MitoZ was used to annotate
the obtained mitogenome (Meng et al. 2019).
The transfer RNA (tRNA) genes of O. truncata were identified
by using the MITOS Web Server (Bernt et al. 2013). Protein-coding
genes (PCGs) and 2 ribosomal RNA (rRNA) genes were identified
by alignment with homologous genes from other published stonefly
mitogenomes. Base composition and codon usage were analyzed by
MEGA v.6.0 (Tamura et al. 2013). Composition skew analysis was
carried out with the formulas AT skew = [A − T]/[A + T] and GC
skew = [G − C]/[G + C], respectively (Perna and Kocher 1995).
Phylogenetic Analysis
Phylogenetic analysis was carried out based on the 30 complete or
nearly complete mitogenomes from the family Nemouridae. Two
species (Kamimuria klapaleki and Caroperla siveci) from Perlidae
were selected as outgroups (Table 1). Each PCG was individually
aligned using the MAFFT algorithm (Katoh and Standley 2013)
Journal of Insect Science, 2024, Vol. 24, No. 2 3

within the TranslatorX online platform (Abascal et al. 2010). Two
rRNA genes were independently aligned with the MAFFT online
service with G-INS-i strategy (Katoh and Standley 2013), and un-
reliably aligned regions were removed using Gblocks (Talavera and
Castresana 2007). One dataset was concatenated for phylogenetic
analyses: PCG12R matrix, including the first and second codon
positions of the 13 PCGs and 2 rRNAs (9,490 bp).
Bayesian inference (BI) and maximum likelihood (ML) analysis
were conducted using MrBayes 3.2.6 (Ronquist et al. 2012) and
IQ-TREE web server (Trifinopoulos et al. 2016), respectively. The best-
fit model of nucleotide sequences for ML and BI method was selected
by ModelFinder (Trifinopoulos et al. 2016), and the GTR + I + G
model was optimal for analysis with nucleotide alignments according
to the Akaike information criterion. For BI analyses, 2 simultaneous
runs of 10 million generations were performed for each dataset, and
trees were sampled every 1,000 generations, with a burn-in rate of
25%. For ML analyses, phylogenetic trees were conducted using an
ultrafast bootstrap approximation with 1,000 replicates.
Results and Discussion
Mitogenome Organization and Base Composition
The complete mitogenomes of O. truncata and N. pictetii are 15,971
and 15,934 bp in size, respectively (Fig. 1, Table 1). The partial

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Fig. 1. Mitochondrial genome maps of Ostrocerca truncata, Nemurella pictetii, and Lednia tumana. Genes shown on the inside of the map are transcribed in a
clockwise direction, whereas those on the outside of the map are transcribed counterclockwise. Different gene types are shown as filled boxes in different colors.
4 Journal of Insect Science, 2024, Vol. 24, No. 2

mitogenome of L. tumana is 15,294 bp in length (Fig. 1, Table 1).
The length of completely sequenced mitogenomes was medium sized
when compared with the mitogenomes of other nemourid species
(Table 1). Differences in gene length among 3 Nemourinae spe-
cies were primarily caused by insertions/deletions in the intergenic
spacers and control region (Supplementary Tables S1–S3). The
gene order of 3 Nemourinae mitogenomes is the same as all previ-
ously published stonefly mitogenomes 22–30 (Chen and Du 2017a,
2017b, Wang et al. 2017, 2021, Cao et al. 2019, 2021, Chen et al.
2020, Zhao et al. 2020, Guo et al. 2022), as well as the ancestral
gene order of Drosophila yakuba (Clary and Wolstenholme 1985).
There are 10, 11, and 10 intergenic spacers in the mitogenomes
of O. truncata, N. pictetii, and L. tumana, respectively, ranging in
size from 1 to 137 bp (Supplementary Tables S1–S3). The longest
has the highest A + T content value (82.4% and 85.8%), followed
by rRNAs (73.5% and 73.2%), tRNAs (71.6% and 71.5%), and
PCGs (70.7% and 68.7%). Similarly, the high A + T content value
among the 3 partitions also occurs in the partial mitogenome of L.
tumana (Table 2). As with published stoneflies (Chen and Du 2017a,
2017b, Wang et al. 2017, 2021, Cao et al. 2019, 2021, Chen et al.
2020, Zhao et al. 2020, Guo et al. 2022) and other insects (Wei et
al. 2010a), all 3 species showed a positive AT-skew and negative
GC-skew in the whole mitogenome (Table 2).
There are 22 traditional tRNAs, which ranged from 63 to 71 bp
in the 3 mitogenomes (Supplementary Tables S1–S3). All tRNAs can
be folded into the typical clover-leaf structure with the exception
of tRNASer(AGN) due to the lack of a stable dihydrouridine (DHU)
arm. Like other published stoneflies (Wang et al. 2017, 2021, Cao

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(137 bp) intergenic spacer was located between tRNASer(UCN) and
ND1 in N. pictetii (Supplementary Table S3). At the same region, the
lengths of the intergenic spacer are 36 and 20 bp in O. truncata and
L. tumana, respectively (Supplementary Tables S1 and S2). There are
12, 13, and 14 gene overlaps in the mitogenomes of O. truncata, N.
pictetii, and L. tumana, respectively, ranging from 1 to 8 bp in length
(Supplementary Tables S1–S3).
The nucleotide composition of 3 Nemourinae mitogenomes is sig-
nificantly biased toward A and T, ranging from 66.9% in L. tumana
to 71.8% in O. truncata (Table 2). Among the 4 partitions in 2 com-
plete mitogenomes of O. truncata and N. pictetii, the control region
et al. 2019, 2021, Chen et al. 2020, Guo et al. 2022), the anticodon
stem of tRNASer(AGN) in 3 mitogenomes has an extended nucleo-
tide (9 pairs of nucleotides) (Fig. 2). Five types of mismatched base
pairs (G-U, A-A, A-C, A-G, and C-U) are revealed in the tRNA sec-
ondary structures of 3 mitogenomes. These unmatched base pairs
might be corrected by RNA editing without leading to obstruction
in amino acid transportation (Bae et al. 2004). As in most other in-
sect mitogenomes, the large (lrRNA or 16S) and small (srRNA or
12S) ribosomal RNAs in 3 Nemourinae species are located between
tRNALeu(CUN) and tRNAVal, and tRNAVal and the control region, re-
spectively (Fig. 1).

Table 2. Nucleotide composition of the mitogenomes of Ostrocerca truncate, Lednia tumana, and Nemurella pictetii

O. truncate L. tumana N. pictetii

Full mitogenome Size 15,971 15,294 15,934

AT% 71.8 66.9 70.7
AT skew 0.03 0.07 0.04
GC skew −0.16 −0.21 −0.19
13PCGs Size 11,232 11,235 11,232
AT% 70.7 65.0 68.7
tRNAs Size 1,460 1,471 1,471
AT% 71.6 71.1 71.5
rRNAs Size 2,131 2,120 2,126
AT% 73.5 72.5 73.2
Control region Size 1,047 >462 969
AT% 82.4 — 85.5

Fig. 2. Inferred secondary structure of tRNASer (AGN) in 3 Nemourinae mitogenomes.

Journal of Insect Science, 2024, Vol. 24, No. 2
The mitochondrial control region is located between lrRNA and
tRNAIle and is suggested to act on the initiation and regulation of
insect replication and transcription (Sheffield et al. 2008, Wei et al.
2010b). The control region of O. truncata and N. pictetii is 1,047 and
969 bp, respectively (Supplementary Tables S1 and S3). However, the
control region of L. tumana has not been entirely sequenced, with a
measured length of 462 bp in this study (Supplementary Table S2).
Protein-Coding Genes
The total lengths of 13 PCGs are 11,232, 11,235, and 11,232 bp,
respectively (Table 2). Among 3 Nemourinae mitogenomes, most
PCGs initiate with ATN as the start codon. However, ND1 in 3 spe-
cies uses TTG as the start codon, and ND5 in O. truncata and N.
pictetii use GTG as the start codon (Supplementary Tables S1–S3).
These unconventional start codons are also used in some species to
minimize intergenic spacer and avoid overlap with adjacent genes
Fig. 3. Relative synonymous codon usage in 3 Nemourinae mitogenomes.
5
(Ojala et al. 1981, Yokobori and Pääbo 1995, Cha et al. 2007).
Most PCGs employ the complete termination codons TAA or TAG,
whereas COII and ND5 in 3 species have incomplete stop codon T
(Supplementary Tables S1–S3). The presence of an incomplete stop
codon is common in insect mitogenomes, and it has been presumed
that the complete stop codon TAA can be generated through post-
transcriptional polyadenylation (Zhang et al. 1995, Zhang and
Hewitt 1997).
The relative synonymous codon usage of the 3 Nemourinae
mitogenomes is summarized in Fig. 3. The codons ending with A or
U are preferred to both the 4- and 2-fold degenerate codons (Fig. 3).
The 4 most commonly used amino acid codons, UUA (Leu1), UUU
(Phe), AUU (Ile), and AUA (Met), are all exclusively composed of A
and/or U (Fig. 4).
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In 3 Nemourinae species, there is a high variation in nucleotide di-
versity among the 13 PCGs, with values ranging from 0.132 (ATP8)
to 0.286 (ND6). The gene ATP8 (Pi = 0.132) has the lowest value of
6 Journal of Insect Science, 2024, Vol. 24, No. 2
Fig. 4. Amino acid composition in 3 Nemourinae mitogenomes.
Fig. 5. Nucleotide diversity (Pi) and nonsynonymous (Ka) to synonymous (Ks) substitution rate ratios of 13 protein-coding genes of 3 Nemourinae species. The Pi
and Ka/Ks values of each PCGs shown under the gene name.
nucleotide diversity among all PCGs and is the most conserved gene.
In contrast, ND6 (Pi = 0.286) has the highest value of nucleotide di-
versity and is the most variable gene (Fig. 5).
To investigate evolutionary patterns of PCGs, the nonsynonymous
(Ka)/synonymous (Ks) substitution rate ratios for each PCG were cal-
culated (Fig. 5). The COI and ND6 exhibit the lowest (0.033) and
highest (0.290) evolutionary rates, respectively. However, the Ka/Ks
values for all PCGs are lower than 1, indicating that they are evolving
under the purifying selection and are suitable for investigating phy-
logenetic relationships within the Nemourinae.
Phylogenetic Analyses
In this study, the ML and BI analyses based on the PCG12R ma-
trix generated the phylogenic trees with same topologies and high
nodal supports (Fig. 6). In the 2 analyses, relationships of 5 genera
in Amphinemurinae were recovered as follows: (((Sphaeronemoura
+ Mesonemoura) + Indonemoura) + Protonemura) + Amphinemura.
In addition, the monophyly of Nemourinae and Amphinemurinae
was not recovered. Nemoura was recovered as the sister group of
Malenka, and they were grouped with other Amphinemurinae and
emerged from a paraphyletic Nemourinae. Relationships of the
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other 3 genera in Nemourinae were recovered as ((Nemurella + O
strocerca) + Lednia).
Baumann (1975) first studied the genus-level phylogenetic
relationships within Nemouridae using morphological data,
confirming the monophyly of 2 subfamilies. Subsequent research has
mainly focused on describing and identifying new species and genera,
without further investigation into the phylogenetic relationships
within Nemouridae. Currently, most molecular studies have failed
to support the monophyly of the subfamily Amphinemurinae (Terry
and Whiting 2003, Zhao et al. 2020, Cao et al. 2021, Wang et al.
2021, Guo et al. 2022). Previous morphological study supported
Amphinemura and Malenka as a sister group (Baumann 1975).
However, it was not supported by early molecular studies (Thomas
et al. 2000, Terry and Whiting 2003) and our previous mitochon-
drial study (Cao et al. 2022). Although our results still do not sup-
port the sister relationships between Amphinemura and Malenka,
the relationships among the remaining 4 genera are consistent with
the traditionally proposed relationships (Baumann 1975) and pre-
vious studies (Cao et al. 2019, 2021, Wang et al. 2021).
In our analyses, the sister group relationship between Nemurella
and Ostrocerca was supported, and then they were grouped with
Journal of Insect Science, 2024, Vol. 24, No. 2 7

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Fig. 6. Phylogenetic tree of the 31 sequenced stoneflies. BI and ML analyses inferred from PCG12R matrix supported the same topological structure. Values at
nodes are Bayesian posterior probabilities and ML bootstrap values. The tree was rooted with 3 outgroups.

Lednia. This result is consistent with that of morphological hypoth- Science & Technology Innovation Talents in Universities of Henan
esis (Baumann 1975). Although the monophyly of Nemourinae was Province (21HASTIT042), and the Key Scientific Research Project of
not recovered, the mitogenome from Ostrocerca allows us to have a Henan Province (22A210004).
more comprehensive understanding of its phylogenetic relationships
among Nemourinae for the first time. Apart from Amphinemura and
Nemoura, which are widely distributed in the Nearctic, Palearctic, Author Contributions
and Oriental regions, the majority of genera within Nemouridae are
Ying Wang (Conceptualization [Equal], Data curation [Lead],
endemic to either the Oriental and Palearctic regions or the Nearctic
Formal analysis [Equal], Funding acquisition [Equal], Investigation
region (Baumann 1975, DeWalt et al. 2023). It will also be extremely
[Equal], Writing—original draft [Equal], Writing—review & ed-
helpful to study and assign the species placed in incertae sedis to
iting [Equal]), Caiyue Guo (Formal analysis [Equal], Investigation
their proper places in the phylogenetic scheme (Baumann 1975).
[Equal], Writing—original draft [Equal]), Xiaoxiao Yue (Formal
These 3 genera belong to the subfamily Nemourinae, but all of them
analysis [Equal], Investigation [Equal]), Xing Fan (Formal analysis
are only distributed in North America. Maybe it can be explained by
[Equal], Investigation [Equal]), Yuying Fan (Investigation [Equal]),
animal geography. However, due to the limitations of mitochondrial
and Jinjun Cao (Conceptualization [Equal], Funding acquisition
genes, their relationship is still unclear, and more gene sequencing is
[Equal], Writing—review & editing [Equal])
necessary to explore this problem.

Acknowledgments Supplementary Material

This research was funded by the National Natural Science Supplementary material is available at Journal of Insect Science
Foundation of China (31801999; 32270492), the Program for online.
8 Journal of Insect Science, 2024, Vol. 24, No. 2

References Klapálek F. Conspectus Plecopterorum Bohemiae. Cas Cesk Spol Entomol.

1905:2:27–32.
Abascal F, Zardoya R, Telford MJ. TranslatorX: multiple alignment of nu-
Lin CP, Danforth BN. How do insect nuclear and mitochondrial gene substitu-
cleotide sequences guided by amino acid translations. Nucleic Acids Res.
tion patterns differ? Insights from Bayesian analyses of combined datasets.
2010:38(Web Server issue):W7–W13. https://doi.org/10.1093/nar/gkq291
Mol Phylogenet Evol. 2004:30(3):686–702. https://doi.org/10.1016/
Bae JS, Kim I, Sohn HD, Jin BR. The mitochondrial genome of the firefly,
S1055-7903(03)00241-0
Pyrocoelia rufa: complete DNA sequence, genome organization,
Lohse M, Bolger AM, Axel N, Fernie AR, Lunn JE, Mark S, Bjrn U. RobiNA: a
and phylogenetic analysis with other insects. Mol Phylogenet Evol.
user-friendly, integrated software solution for RNA-Seq based transcriptomics.
2004:32(3):978–985. https://doi.org/10.1016/j.ympev.2004.03.009
Nucleic Acids Res. 2012:40:W622–W627. https://doi.org/10.1093/nar/gks540
Baumann RW. Revision of the stonefly family Nemouridae (Plecoptera):
Meng G, Li YY, Yang C, Liu SL. MitoZ: a toolkit for animal mitochon-
a study of the world fauna at the generic level. Smithson Contr Zool.
drial genome assembly, annotation and visualization. Nucleic Acids Res.
1975:40(211):1–74. https://doi.org/10.5479/si.00810282.211
2019:47:e63. https://doi.org/10.1093/nar/gkz173
Baumann RW, Fiala GR. Nanonemoura, a new stonefly genus from the
Mo RR, Gamboa M, Watanabe K, Wang GQ, Murányi D. A remarkable
Columbia River Gorge, Oregon (Plecoptera: Nemouridae). West N Am
new genus and species of Nemourinae (Plecoptera, Nemouridae) from
Nat. 2001:61:403–408.
Sichuan, China, with systematic notes on the related genera. PLoS One.

Downloaded from https://academic.oup.com/jinsectscience/article/24/2/4/7619560 by guest on 07 March 2024

Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J,
2020:15:e0229120. https://doi.org/10.1371/journal.pone.0229120
Middendorf M, Stadler PF. MITOS: improved de novo metazoan mito-
Newman E. Proposed division of Neuroptera into two classes. Zoologist.
chondrial genome annotation. Mol Phylogenet Evol. 2013:69(2):313–319.
1853:11:82–204.
https://doi.org/10.1016/j.ympev.2012.08.023
Ojala D, Montoya J, Attardi G. tRNA punctuation model of RNA processing
Cameron SL. Insect mitochondrial genomics: implications for evolution and
in human mitochondria. Nature. 1981:290(5806):470–474. https://doi.
phylogeny. Annu Rev Entomol. 2014:59:95–117. https://doi.org/10.1146/
org/10.1038/290470a0
annurev-ento-011613-162007
Peng Y, Leung HCM, Yiu SM, Chin FYL. IBDA-UD: a de novo assembler
Cao JJ, Guo X, Guo CY, Wang X, Wang Y, Yan FM. Complete mitochondrial
for single-cell and metagenomic sequencing data with highly uneven
genome of Malenka flexura (Plecoptera: Nemouridae) and phylogenetic
depth. Bioinformatics. 2012:28(11):1420–1428. https://doi.org/10.1093/
analysis. Genes. 2022:13:911. https://doi.org/10.3390/genes13050911
bioinformatics/bts174
Cao JJ, Wang Y, Guo X, Wang GQ, Li WH, Murányi D. Two complete mi-
Perna NT, Kocher TD. Patterns of nucleotide composition at fourfold degen-
tochondrial genomes from Leuctridae (Plecoptera: Nemouroidea):
erate sites of animal mitochondrial genomes. J Mol Evol. 1995:41(3):353–
implications for the phylogenetic relationships among stoneflies. J Insect
358. https://doi.org/10.1007/BF00186547
Sci. 2021:21(1):16. https://doi.org/10.1093/jisesa/ieab009
Qian YH, Wu HY, Ji XY, Yu WW, Du YZ. Mitochondrial genome of thestonefly
Cao JJ, Wang Y, Li WH. Comparative mitogenomic analysis of species in the
Kamimuria wangi (Plecoptera: Perlidae) and phylogenetic position of
subfamily Amphinemurinae (Plecoptera: Nemouridae) reveal conserved
Plecoptera based on mitogenomes. PLoS One. 2014:9:e86328. https://doi.
mitochondrial genome organization. Int J Biol Macromol. 2019:138:292–
org/10.1371/journal.pone.0086328
301. https://doi.org/10.1016/j.ijbiomac.2019.07.087
Ronquist F, Teslenko M, Mark P. van der, Ayres DL, Darling A, Höhna S,
Cha SY, Yoon HJ, Lee EM, Yoon MH, Hwang JS, Jin BR, Han YS, Kim I. The
Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient
complete nucleotide sequence and gene organization of the mitochondrial
Bayesian phylogenetic inference and model choice across a large model
genome of the bumblebee, Bombus ignitus (Hymenoptera: Apidae). Gene.
space. Syst Biol. 2012:61:539–542. https://doi.org/10.1093/sysbio/sys029
2007:392(1–2):206–220. https://doi.org/10.1016/j.gene.2006.12.031
Salvato P, Simonato M, Battisti A, Negrisolo E. The complete mitochondrial genome
Chen SJ, Cao JJ, Li WH, Wang Y. Characterization of the complete mitochon-
of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae).
drial genome of Nemoura meniscata Li & Yang (Plecoptera: Nemouridae)
BMC Genomics. 2008:9:331–345. https://doi.org/10.1186/1471-2164-9-331
from China. Mitochondrial DNA Part B. 2020:5:1052–1053. https://doi.
Sheffield NC, Song H, Cameron SL, Whiting MF. A comparative analysis of
org/10.1080/23802359.2020.1721370
mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome
Chen ZT, Du YZ. Complete mitochondrial genome of Capnia zijinshana
descriptions of six new beetles. Mol Biol Evol. 2008:25(11):2499–2509.
(Plecoptera: Capniidae) and phylogenetic analysis among stoneflies. J Asia-Pac
https://doi.org/10.1093/molbev/msn198
Entomol. 2017a:20(2):305–312. https://doi.org/10.1016/j.aspen.2017.01.013
Shimizu T, Sivec I. Sphaeronemoura, a new genus of the Amphinemurinae
Chen ZT, Du YZ. First Mitochondrial genome from Nemouridae (Plecoptera)
(Nemouridae, Plecoptera) from Asia. New York (NY): Kluwer Academic/
reveals novel features of the elongated control region and phylogenetic
Plenum Publishers; 2001.
implications. Int J Mol Sci. 2017b:18(5):996. https://doi.org/10.3390/
Sivec I, Stark BP. Tominemoura, a new stonefly genus from Sabah, East
ijms18050996
Malaysia (Plecoptera: Nemouridae). Illiesia. 2009:5:199–203.
Clary DO, Wolstenholme DR. The ribosomal RNA genes of Drosophila mito-
South EJ, Skinner R, Dewalt E, Kondratieff B, Durfee R. Phylogenomics of the
chondrial DNA. Nucleic Acids Res. 1985:13(11):4029–4045. https://doi.
north American Plecoptera. Syst Entomol. 2021:46:287–305. https://doi.
org/10.1093/nar/13.11.4029
org/10.1111/syen.12462
DeWalt RE, Maehr MD, Hopkins H, Neu-Becker U, Stueber G. Plecoptera
Stewart KW, Stark BP. An Introduction to the Aquatic Insects of North America.
species file online. Version 5.0/5.0. 2023 [accessed 2023 Nov 11]. http://
4th ed. Dubuque (IA): Kendall–Hunt Publishing Company; 2008.
Plecoptera.SpeciesFile.org.
Talavera G, Castresana J. Improvement of phylogenies after removing divergent
Fochetti R, Figueroa JMT. Global diversity of stoneflies (Plecoptera, Insecta) in
and ambiguously aligned blocks from protein sequence alignments. Syst
freshwater. Hydrobiologia. 2008:595:365–377.
Biol. 2007:56(4):564–577. https://doi.org/10.1080/10635150701472164
Gamboa, MDM, Kanmori S, Watanabe K, Munderloh UG. Molecular phy-
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evo-
logeny and diversification timing of the Nemouridae family (Insecta,
lutionary genetics analysis version 6.0. Mol Biol Evol. 2013:30(12):2725–
Plecoptera) in the Japanese Archipelago. PLoS One. 2019:14:e0210269.
2729. https://doi.org/10.1093/molbev/mst197
https://doi.org/10.1101/440529
Terry MD, Whiting MF. Phylogeny of Plecoptera: molecular evidence and evo-
Gissi C, Iannelli F, Pesole G. Evolution of the mitochondrial genome of
lutionary trends. Entomol Abh. 2003:61:130–131.
metazoa as exemplified by comparison of congeneric species. Heredity.
Thomas MA, Walsh KA, Wolf MR, McPheron BA, Marden JH. Molecular
2008:101(4):301–320. https://doi.org/10.1038/hdy.2008.62
phylogenetic analysis of evolutionary trends in stonefly wing structure and
Guo X, Guo CY, Dong XJ, Zhang H, Li WH, Murányi D, Wang Y. Mitochondrial
locomotor behavior. Proc Natl Acad Sci USA. 2000:97(24):13178–13183.
genome of Strophopteryx fasciata (Plecoptera: Taeniopterygidae), with a
https://doi.org/10.1073/pnas.230296997
phylogenetic analysis of Nemouroidea. Genes. 2022:13:1116. https://doi.
Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ. W–IQ–TREE: a
org/10.3390/genes13071116
fast online phylogenetic tool for maximum likelihood analysis. Nucleic
Katoh K, Standley DM. MAFFT multiple sequence alignment software ver-
Acids Res. 2016:44(W1):W232–W235. https://doi.org/10.1093/nar/
sion 7: improvements in performance and usability. Mol Biol Evol.
gkw256
2013:30(4):772–780. https://doi.org/10.1093/molbev/mst010
Journal of Insect Science, 2024, Vol. 24, No. 2
Wang Y, Cao JJ, Li WH. The complete mitochondrial genome of the styloperlid
stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with
family-level phylogenetic analyses of the Pteronarcyoidea. Zootaxa.
2017:4243:125–138. https://doi.org/10.11646/zootaxa.4243.1.5
Wang Y, Cao JJ, Li WH. Complete Mitochondrial genome of Suwallia
teleckojensis (Plecoptera: Chloroperlidae) and implications for the higher
phylogeny of stoneflies. Int J Mol Sci . 2018a:19(3):680. https://doi.
org/10.3390/ijms19030680
Wang Y, Cao JJ, Li N, Ma GY, Li WH. The first mitochondrial genome from
Scopuridae (Insecta: Plecoptera) reveals structural features and phyloge-
netic implications. Int J Biol Macromol. 2019:122:893–902. https://doi.
org/10.1016/j.ijbiomac.2018.11.019
Wang Y, Cao JJ, Murányi D, Chen XL, Yan FM. The complete mitochondrial
genome of Amphinemura bulla Shimizu, 1997 (Plecoptera: Nemouridae)
from Japan. Mitochondrial DNA Part B. 2021:6:846–847. https://doi.org/
10.1080/23802359.2021.1884029.
Wang Y, Cao JJ, Murányi D, Li WH. Comparison of two complete mitochon-
drial genomes from Perlodidae (Plecoptera: Perloidea) and the family-
level phylogenetic implications of Perloidea. Gene. 2018b:675:254–264.
https://doi.org/10.1016/j.gene.2018.06.093
Wei SJ, Shi M, Chen XX, Sharkey MJ, Achterberg C. van, Ye GY, He JH. New
views on strand asymmetry in insect mitochondrial genomes. PLoS One.
2010a:5:e12708. https://doi.org/10.1371/journal.pone.0012708
Wei SJ, Tang P, Zheng LH, Shi M, Chen XX. The complete mitochondrial ge-
nome of Evania appendigaster (Hymenoptera: Evaniidae) has low a + T
9
content and a long intergenic spacer between atp8 and atp6. Mol Biol Rep.
2010b:37(4):1931–1942. https://doi.org/10.1007/s11033-009-9640-1
Wilson K, Valma C, Elizabeth B, John B. The complete sequence of the mito-
chondrial genome of the crustacean Penaeus mondon: are malacostracan
crustaceans more closely related to insects than to branchiopods? Mol Biol
Evol. 2000:17:863–874. https://doi.org/10.1093/oxfordjournals.molbev.
a026366
Yokobori S, Pääbo S. Transfer RNA editing in land snail mitochondria. Proc
Natl Acad Sci USA. 1995:92(22):10432–10435. https://doi.org/10.1073/
pnas.92.22.10432
Zhang DX, Hewitt GM. Insect mitochondrial control region: a review
of its structure, evolution and usefulness in evolutionary studies.
Biochem Syst Ecol. 1997:25(2):99–120. https://doi.org/10.1016/
s0305-1978(96)00042-7
Zhang DX, Szymura JM, Hewitt GM. Evolution and structural conser-
Downloaded from https://academic.oup.com/jinsectscience/article/24/2/4/7619560 by guest on 07 March 2024
vation of the control region of insect mitochondrial DNA. J Mol Evol.
1995:40(4):382–391. https://doi.org/10.1007/BF00164024
Zhao MY, Huo QB, Du YZ. Molecular phylogeny inferred from the mitochon-
drial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae).
Sci Rep. 2020:10(1):20955. https://doi.org/10.1038/s41598-020-78082-y
Zwick P. Insecta Plecoptera. Phylogenetisches system und katalog. Tierreich.
1973:94:XXXII–XX465.
Zwick P. Phylogenetic system and zoogeography of the Plecoptera. Annu
Rev Entomol. 2000:45:709–746. https://doi.org/10.1146/annurev.ento.
45.1.709