Research Article |
Corresponding author: Yan-Hui Wang ( wangyanh3@mail.sysu.edu.cn ) Academic editor: Christiane Weirauch
© 2024 Bao-Jun Xie, Ping-Ping Chen, Jakob Damgaard, Jie-Yi Xie, Qiang Xie, Yan-Hui Wang.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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The genus Micronecta Kirkaldy, 1897 is the most species-rich genus in the family Micronectidae, containing more than 160 species. Micronecta is currently divided into 11 subgenera, five of which are monotypic. Moreover, the subgenus Micronecta is an empirical mixture group. The definitions of some subgenera were based on only a few aberrant morphological features, which are specializations with few phylogenetic significances. The relationship between these subgenera remains unclear. In this study, we newly sequenced mitochondrial genomes (mitogenomes) and nuclear rDNAs (nrDNAs) for 13 Micronecta species, representing seven subgenera, and those for ten other water bugs. Our phylogenetic analyses showed that the subgenus Lundbladella represents the sister group to all other studied subgenera of Micronecta. The subgenus Unguinecta was the sister group to the clade that contains Dichaetonecta and Sigmonecta. More importantly, the subgenus Micronecta represents a paraphyletic group, which further forms a monophyletic group together with the subgenera Basileonecta and Ctenonecta. This is for the first time that the phylogeny of the genus Micronecta was investigated based on molecular data and the paraphyly of the subgenus Micronecta was revealed. Such evidence suggested the necessity of the revision of the taxonomic system of the genus in the future, and may also serve as a reference for the delimitation of subgeneric characters.
Aquatic insects, Corixoidea, Nepomorpha, water boatmen, phylogeny, subgenus
Micronectidae, commonly known as pygmy water boatmen due to their minute size (0.8−5 mm), is a family of aquatic bugs (Nepomorpha) and with representatives in all temperate, subtropical and tropical biogeographical regions (
Two subfamilies are currently recognized: Synaptogobiinae with two species of Synaptogobia
Currently, the genus Micronecta is divided into 11 subgenera: Basileonecta Hutchinson, 1940, Ctenonecta Wróblewski, 1962, Dichaetonecta Hutchinson, 1940, Indonectella Hutchinson, 1940, Lundbladella Wróblewski, 1967, Mesonecta Poisson, 1938, Micronecta Kirkaldy, 1897, Micronectella Lundblad, 1933, Pardanecta Horváth, 1904, Sigmonecta Wróblewski, 1962, and Unguinecta Nieser, Chen et Yang, 2005 (
Mitochondrial genomes (mitogenomes) have been widely used in molecular systematics and molecular evolutionary studies (
In this study, we sequenced the mitogenomes of 13 Micronecta species covering all 37 genes, and comprehensively analyzed the characteristic of these mitogenomes. Meanwhile, ten complete mitogenomes were also sequenced for other water boatmen representing Corixidae (Corixoidea) and Diaprepocoridae (Corixoidea). We also newly provided the corresponding nrDNAs of those 23 species. The nrDNAs for Lethocerus sp. (Belostomatidae), Laccotrephes sp. (Nepidae), Enithares sp. and Notonecta sp. (both Notonectidae) were provided for the first time as well. The phylogeny of the genus Micronecta was reconstructed based on the whole mitogenomes and nrDNAs.
Our taxon sampling included 31 species, of which 13 species of Micronecta were in-groups and 10 species of other water boatmen and 8 species of the remaining true water bugs were out-groups (Table
Family | Genus | Subgenus | Species | GenBank Accession | ||
Mitogenome | 18S nrDNA | 28S nrDNA | ||||
Micronectidae | Micronecta | Basileonecta | Micronecta orientalis * | OQ606211 | OQ598531 | OQ598681 |
Ctenonecta | Micronecta jaczewskii * | OQ606210 | OQ598532 | OQ598676 | ||
Dichaetonecta | Micronecta sahlbergii * | OQ606212 | OQ598530 | OQ598687 | ||
Lundbladella | Micronecta guttatostriata * | OQ606215 | OQ598533 | OQ598675 | ||
Micronecta | Micronecta wui wui * | OQ581713 | OQ598526 | OQ598678 | ||
Micronecta | Micronecta anatolica * | OQ606213 | OQ598529 | OQ598679 | ||
Micronecta | Micronecta vietnamica* | OQ606216 | OQ598534 | OQ598684 | ||
Micronecta | Micronecta drepani * | OQ606217 | OQ598535 | OQ598685 | ||
Micronecta | Micronecta erythra * | OQ606218 | OQ598536 | OQ598683 | ||
Micronecta | Micronecta tuberculata * | OQ606219 | OQ598537 | OQ598682 | ||
Micronecta | Micronecta ornitheia * | OQ606220 | OQ598538 | OQ598680 | ||
Micronecta | Micronecta griseola | OP850016(COI) OP850221(16S) | / | OP849810 | ||
Micronecta | Micronecta minutissima | OP849995(COI) OP850197(16S) | / | OP849786 | ||
Micronecta | Micronecta poweri | OP849996(COI) OP850198(16S) | / | OP849787 | ||
Sigmonecta | Micronecta quadristrigata * | OQ587936 | OQ598527 | OQ598686 | ||
Unguinecta | Micronecta melanochroa * | OQ606214 | OQ598528 | OQ598677 | ||
Unguinecta | Micronecta khasiensis | OP849907(COI) OP850107(16S) | / | OP849696 | ||
Tenagobia | Incertagobia | Tenagobia incerta * | OR545228 | OR544013 | OR552402 | |
Corixidae | Sigara | Sigara striata * | OQ606224 | OQ598548 | OQ598671 | |
Paracorixa | Paracorixa concinna * | OQ606223 | OQ598547 | OQ598672 | ||
Cymatia | Cymatia coleopterata * | OQ606225 | OQ598542 | OQ598668 | ||
Callicorixa | Callicorixa praeusta * | OQ606221 | OQ598543 | OQ598673 | ||
Corixa | Corixa punctata * | OQ606226 | OQ598544 | OQ598670 | ||
Glaenocorisa | Glaenocorisa propinqua * | OQ606222 | OQ598545 | OQ598674 | ||
Hesperocorixa | Hesperocorixa linnaei * | OQ606227 | OQ598546 | OQ598669 | ||
Diaprepocoridae | Diaprepocoris | Diaprepocoris barycephalus * | OQ612738 | OQ598549 | OQ598666 | |
Diaprepocoris zealandiae * | OQ612739 | OQ598550 | OQ598667 | |||
Belostomatidae | Diplonychus | Diplonychus rusticus | FJ456940 | KJ461265 | KJ461227 | |
Lethocerus | Lethocerus indicus | KM588201 | OQ598541* | OQ598663* | ||
Nepidae | Laccotrephes | Laccotrephes sp. | FJ456948 | OQ598540* | OQ598662* | |
Gelastocoridae | Nerthra | Nerthra indica | NC012838 | KJ461313 | KJ461276 | |
Ochteridae | Ochterus | Ochterus marginatus | FJ456950 | KJ461251 | KJ461315 | |
Notonectidae | Enithares | Enithares sp. | FJ456949 | OQ598539* | OQ598664* | |
Notonecta | Notonecta sp. | KX034086 | FJ372662 | OQ598665* | ||
Aphelocheiridae | Aphelocheirus | Aphelocheirus ellipsoideus | FJ456939 | KJ461184 | KJ461297 | |
* Species with newly sequenced mitogenomes and nrDNAs, or newly sequenced nrDNAs in the present study. |
An independent DNA library was constructed for each species with an insert size of 250 base pairs (bp), and then sequenced with a 150 bp paired end (PE) using the Illumina HiSeq 4000 Platform at Biomarker Technologies (Qingdao, China). The purified reads were filtered from raw data by removing adaptor contamination and low-quality sequences. To better distinguish the repeat fragment brought by the assemble process, two approaches were employed to assemble the complete mitogenome for each species. For the first method, SOAPDENOVO2 (
The online webserver of MITOS (
Base composition and relative synonymous codon usage (RSCU) were calculated using MEGA 11 (
Phylogenetic relationships of Micronecta were reconstructed based on 37 genes from mitochondrion and 18S and 28S nrDNAs. Individual genes were aligned using MUSCLE integrated in MEGA. The ambiguously aligned sites from both protein and nucleotide alignments were removed using GBlocks (
Phylogenetic analyses were conducted using MRBAYES 3.2.6 (
In this study, lengths of the 13 newly obtained mitogenomes of Micronecta species range from 14,825 bp to 15,405 bp (Table
Length of Micronecta mitochondrial genomes, AT-skew and GC-skew were measured for the 37 genes except the control regions.
Species | PCGs (bp) | tRNAs (bp) | 12S rRNA (bp) | 16S rRNA (bp) | CR (bp) | Total (bp) | AT-skew | GC-skew |
Micronecta (Basileonecta) orientalis | 11029 | 1425 | 730 | 1127 | 681 | 15163 | 0.16 | –0.14 |
Micronecta (Ctenonecta) jaczewskii | 11044 | 1425 | 761 | 1226 | 590 | 14998 | 0.16 | –0.13 |
Micronecta (Dichaetonecta) sahlbergii | 11017 | 1425 | 759 | 1241 | 664 | 15074 | 0.22 | –0.22 |
Micronecta (Lundbladella) guttatostriata | 10996 | 1430 | 768 | 1242 | 944 | 15311 | 0.22 | –0.27 |
Micronecta (Micronecta) wui wui | 11033 | 1425 | 761 | 1224 | 589 | 14992 | 0.15 | –0.12 |
Micronecta (Micronecta) anatolica | 10981 | 1423 | 761 | 1226 | 589 | 14990 | 0.15 | –0.11 |
Micronecta (Micronecta) vietnamica | 11024 | 1425 | 762 | 1223 | 666 | 15072 | 0.16 | –0.14 |
Micronecta (Micronecta) drepani | 11018 | 1428 | 759 | 1271 | 939 | 15405 | 0.21 | –0.14 |
Micronecta (Micronecta) erythra | 11023 | 1427 | 761 | 1224 | 777 | 15195 | 0.23 | –0.16 |
Micronecta (Micronecta) tuberculata | 11023 | 1425 | 761 | 1225 | 414 | 14825 | 0.14 | –0.12 |
Micronecta (Micronecta) ornitheia | 11028 | 1424 | 760 | 1262 | 592 | 15032 | 0.16 | –0.14 |
Micronecta (Sigmonecta) quadristrigata | 11014 | 1431 | 761 | 1248 | 578 | 15000 | 0.16 | –0.25 |
Micronecta (Unguinecta) melanochroa | 11187 | 1428 | 763 | 1244 | 519 | 14948 | 0.19 | –0.23 |
The nucleotide composition of Micronecta mitogenomes biased toward A/T, with A+T contents ranging from 69.65% to 74.0% (Fig. S2). The mitogenomes of M. (Dichaetonecta) sahlbergii and M. vietnamica exhibit the lowest and highest A+T contents, respectively. The AT skew and GC skew present similar patterns in all Micronecta mitogenomes, with positive AT skews (from 0.14 to 0.23) and negative GC skews (from –0.27 to –0.11) (Table
The total length of all 13 PCGs ranges from 10,981 bp in M. anatolica to 11,187 bp in M. melanochroa (Table
The Ka/Ks ratio is used to evaluate the evolutionary rate of 13 PCGs of the Micronecta species (Fig. S4). The results showed that the average Ka/Ks ratios are lower than 1, indicating that these PCGs evolved likely under the purifying selection (
There are 22 tRNA genes in the Micronecta mitogenomes, as observed in other heteropteran mitogenomes. All tRNAs display the classic clover-leaf secondary structure except tRNA-Ser (GCU), with the dihydrouridine (DHU) stem simply forms a loop (Fig. S5). The A+T content of tRNAs ranges from 72.54% (M. (Unguinecta) quadristrigata) to 76.0% (M. vietnamica).
The 12S and 16S rRNA genes in Micronecta species are encoded on the J-strand and located at conserved positions between trnL1 and trnV and between trnV and control region, respectively. The length of 12S rRNA varies from 730 bp in M. (Basileonecta) orientalis to 768 bp in M. (Lundbladella) guttatostriata, with A+T content from 71.22% in M. guttatostriata to 76.61% in M. (Micronecta) tuberculata. The length of 16S rRNA ranges from 1,127 bp in M. orientalis to 1,271 bp in M. (Micronecta) drepani, with A + T content from 73.67% in M. guttatostriata to 78.09% in M. vietnamica. Hence, there is no substantial size variation in 12S and 16S rRNA among the mitogenomes of the thirteen Micronecta species (Table
Heterogeneous composition of amino-acid or nucleotide sequences may bias results of likelihood based tree reconstructions. The AliGROOVE analyses showed a low heterogeneity in both nucleotide sequences and amino-acid sequences of PCGs (Fig.
The compositional heterogeneity of mitochondrial sequences used in phylogenetic analyses. The mean similarity score between sequences is represented by a colored square, based on the AliGROOVE scores from -1, indicating great differences in rates from the remainder of the datasets (red), to +1, indicating rates match all other comparisons (blue).
Phylogenetic analyses using both BI and ML approaches based on different datasets produced a congruent and well-resolved tree (Fig.
Phylogenomic relationships of Micronecta. The tree was constructed using the PCGNT12RNA dataset with Bayesian analysis. The bootstrap values of maximum-likelihood analyses and posterior probabilities of Bayesian analyses are summarized and labelled around each node. Higher taxa are indicated as taxon labels on the right of the tree.
Within Micronectidae, the genus Micronecta was strongly supported as a monophyletic group and split into three well-supported clades. subgenus Lundbladella was recovered as the sister group to all other Micronecta by all analyses. Subgenus Unguinecta were supported as the sister group to subgenera Dichaetonecta and Sigmonecta. Subgenus Micronecta together with subgenera Ctenonecta and Basileonecta formed a monophyletic clade. Subgenus Micronecta were recovered as paraphyly based on both BI and ML analyses. For this clade, the relationship among the three groups, i.e., (M. vietnamica + M. drepani + M. (Micronecta) erythra), (M. orientalis + M. tuberculata), and (M. ornitheia, M. wui wui, M. anatolica, M. (Ctenonecta) jaczewskii, M. poweri, M. griseola, M. minutissima) are controversial among different analyses (Fig. S6–S11). The results of all BI analyses support the sister relationship between (M. orientalis + M. tuberculata) and (M. ornitheia, M. wui wui, M. anatolica, M. jaczewskii, M. poweri, M. griseola, M. minutissima), while the ML analyses exhibit different topologies.
Our study presents 13 newly sequenced mitogenomes of the genus Micronecta, 1 that of the genus Tenagobia (Micronectidae) and ten those of the remaining water boatmen (Corixidae, Diaprepocoridae). All mitogenomes exhibited the similar putative pattern as in other heteropteran insects (Cameron et al. 2014;
Phylogenetic trees based on mitogenomes and nrDNAs are largely congruent among different analyses, which laid a foundation for further phylogenetic analyses and taxonomic studies. Before this study, only two works involved the phylogenetic relationships between micronectid genera of continental Australia based on morphological characters (i.e., Tinerella, 2008, 2013), in which the subgenera Dichaetonecta and Sigmonecta were also recovered as sister groups. They share the same shape of the left paramere shaft, which is long, straight and narrow.
Among the 11 nominated subgenera, male individuals of three subgenera, i.e., Lundbladella, Indonectella, Micronectella, lack the strigil structure on abdominal tergite VI (
According to the identification key provided by
The genus Micronecta is the most diverse and speciose group of Micronectidae, which is the same condition with the subgenus Micronecta. Although 11 subgenera have been proposed to accompany the extant species of the genus Micronecta, there are still some species which do not fit any known subgenus. As a result, they were just placed tentatively into the subgenus Micronecta (see
As a result, the current taxonomy of Micronecta does not yet satisfactorily reflect natural relationships among subgeneric taxa. As more and more species are being describ, it is necessary to redefine the subgenus Micronecta or split it into more subgenera. The taxon sampling might not be that complete, although the paraphyly of the subgenus Micronecta can be revealed convincingly.
In this study, we investigated the phylogenetic relationships concerning the genus Micronecta based on the species sampled in China. This is the first time that the subgeneric relationships among Micronecta were investigated based on molecular evidence. Our main findings are the paraphyly of the subgenus Micronecta, the status of the subgenus Lundbladella as sister group to all other studied Micronecta, and the sister relationship between the subgenera Dichaetonecta and Sigmonecta. This study provided a chance to redefine the subgenera level classification of the genus Micronecta and laid a foundation for further molecular studies with complete taxon sampling to fully resolve the phylogeny of Micronecta via a broad range of international collaborations.
Conceptualization, Y.W., Q.X.; funding acquisition, Y.W.; formal analysis, B.X., Y.W. and J.X.; writing—original draft preparation, B.X., Y.W., Q.X.; writing—review and editing, J.D., P.C. and Q.X. All authors have read and agreed to the published version of the manuscript.
We are grateful to Dr. Jiu-Yang Luo (Yancheng Teachers University, China) and Dr. Yu Men (Zhaoqing University, China) for collecting specimens and providing helpful assistance during phylogenetic analyses. We appreciate Dr. Michael Raupach (Zoologische Staatssammlung München) and Dr. Anh Duc Tran (Vietnam National University) for valuable suggestions to improve the quality of our manuscript. This work was supported by the National Natural Science Foundation of China (grant number: 32370468). The authors have declared that no competing interests exist.
Figures S1–S11
Data type: .docx
Explanation notes: Figure S1. Circular diagram of the mitochondrial genomes of Micronecta spp. and Tenagobia incerta. — Figure S2. The A+T content of Micronecta spp. mitochondrial genomes. — Figure S3. Relative synonymous codon usage (RSCU) of mitochondrial genomes of Micronecta spp. — Figure S4. Average evolutionary rate of Micronecta mitochondrial PCGs. — Figure S5. Universal models of Micronecta mitochondrial tRNAs. — Figure S6. Phylogenetic tree inferred from PCGNTRNA matrix using ML analysis. Numbers at the nodes are bootstrap values. — Figure S7. Phylogenetic tree inferred from PCGNTRNA matrix using BI analysis. Numbers at the nodes are Bayesian posterior probabilities. — Figure S8. Phylogenetic tree inferred from PCGNT12RNA matrix using ML analysis. Numbers at the nodes are bootstrap values. — Figure S9. Phylogenetic tree inferred from PCGNT12RNA matrix using BI analysis. Numbers at the nodes are Bayesian posterior probabilities. — Figure S10. Phylogenetic tree inferred from PCGAARNA matrix using ML analysis. Numbers at the nodes are bootstrap values. — Figure S11. Phylogenetic tree inferred from PCGAARNA matrix using BI analysis. Numbers at the nodes are Bayesian posterior probabilities.
Tables S1, S2
Data type: .docx
Explanation notes: Table S1. Mitochondrial genome statistics for the other water boatmen. AT-skew and GC-skew were measured for the 37 genes except the control regions. Only partial mitogenome of Diaprepocoris zealandiae was available, so it was not included in this table. — Table S2. Locality data for each Micronecta species used in this study.
Files S1–S3
Data type: .zip
Explanation notes: File S1. PCGNTRNA matrix. — File S2. PCGNT12RNA matrix. — File S3. PCGAARNA matrix.