Genetics, Phylogeny, and Evolution of Insects

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 15 July 2024 | Viewed by 13508

Special Issue Editor


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Guest Editor
School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
Interests: insect taxonomy; insect genomics and genetics, insect phylogeny and evolution

Special Issue Information

Dear Colleagues,

The rapid development of sequencing technologies has allowed researchers in the field of natural science to quickly obtain molecular data and investigate the phylogeny and evolution of different organisms. Extensive different types of molecular data, such as mitochondrial DNA and nuclear DNA, have been generated and widely used in today's research. This Special Issue of Genes will bring together works exploiting various types of molecular data in understanding the phylogenetic and evolutionary aspects of insects.

We are inviting original research papers and short communications of preliminary but significant experimental results. We also invite proposals for review papers in relevant areas. The topics include but are not limited to the following:

  • insect molecular genetics
  • insect genomics
  • mitochondrial DNA (mtDNA)
  • nuclear DNA (nDNA)
  • molecular phylogeny
  • molecular evolution
  • molecular identification
  • biogeography
  • evolutionary biology
  • systematics
  • other topics that are of interest to the community of phylogenetic and evolutionary entomologists.

Dr. Zhiteng Chen
Guest Editor

Manuscript Submission Information

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Keywords

  • insect molecular genetics
  • insect genomics
  • mitochondrial DNA (mtDNA)
  • nuclear DNA (nDNA)
  • molecular phylogeny
  • molecular evolution
  • molecular identification
  • biogeography
  • evolutionary biology
  • systematics

Published Papers (9 papers)

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Research

17 pages, 12764 KiB  
Article
Comparative Transcriptomic Assessment of Chemosensory Genes in Adult and Larval Olfactory Organs of Cnaphalocrocis medinalis
by Hai-Tao Du, Jia-Qi Lu, Kun Ji, Chu-Chu Wang, Zhi-Chao Yao, Fang Liu and Yao Li
Genes 2023, 14(12), 2165; https://doi.org/10.3390/genes14122165 - 30 Nov 2023
Viewed by 842
Abstract
The rice leaf folder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), is a notorious pest of rice in Asia. The larvae and adults of C. medinalis utilize specialized chemosensory systems to adapt to different environmental odors and physiological behaviors. However, the differences in chemosensory genes between [...] Read more.
The rice leaf folder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), is a notorious pest of rice in Asia. The larvae and adults of C. medinalis utilize specialized chemosensory systems to adapt to different environmental odors and physiological behaviors. However, the differences in chemosensory genes between the olfactory organs of these two different developmental stages remain unclear. Here, we conducted a transcriptome analysis of larvae heads, male antennae, and female antennae in C. medinalis and identified 131 putative chemosensory genes, including 32 OBPs (8 novel OBPs), 23 CSPs (2 novel CSPs), 55 ORs (17 novel ORs), 19 IRs (5 novel IRs) and 2 SNMPs. Comparisons between larvae and adults of C. medinalis by transcriptome and RT-qPCR analysis revealed that the number and expression of chemosensory genes in larval heads were less than that of adult antennae. Only 17 chemosensory genes (7 OBPs and 10 CSPs) were specifically or preferentially expressed in the larval heads, while a total of 101 chemosensory genes (21 OBPs, 9 CSPs, 51 ORs, 18 IRs, and 2 SNMPs) were specifically or preferentially expressed in adult antennae. Our study found differences in chemosensory gene expression between larvae and adults, suggesting their specialized functions at different developmental stages of C. medinalis. These results provide a theoretical basis for screening chemosensory genes as potential molecular targets and developing novel management strategies to control C. medinalis. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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13 pages, 19204 KiB  
Article
The Genetic Diversity of White-Backed Planthoppers (Sogatella furcifera) between Myanmar and Yunnan Province of China
by Yue Liu, Khin Nyein Chan, Xiangyong Li, Xueqing Zhao, Dong Chu, Yanqiong Yin, Ying Liu and Aidong Chen
Genes 2023, 14(12), 2164; https://doi.org/10.3390/genes14122164 - 30 Nov 2023
Viewed by 974
Abstract
In order to clarify the migration route and the source of white-backed planthopper (WBPH) (Sogatella furcifera) between Myanmar and Yunnan Province, China, we collected six populations throughout Myanmar and five populations around the border areas in Yunnan Province, China. A total [...] Read more.
In order to clarify the migration route and the source of white-backed planthopper (WBPH) (Sogatella furcifera) between Myanmar and Yunnan Province, China, we collected six populations throughout Myanmar and five populations around the border areas in Yunnan Province, China. A total of 790 base pairs in the mtDNA COI genes from 416 individuals were obtained. A total of 43 haplotypes were identified, among which 37 were unique haplotypes, and the remaining 6 were shared among different populations. Two common shared haplotypes (H_1 and H_2) had a widespread distribution in all populations and accounted for 88.8% of the total haplotype frequency, suggesting a high-level gene flow among the Myanmar and Yunnan populations. Bayesian skyline plot (BSP) analysis results indicated that the effective population size of WBPH expanded between about 10,000 and 7000 years ago, and S. furcifera might follow the post-LGM (Last Glacial Maximum) expansion pattern. Based on the total migrant (Nem) value, it can be deduced that north and northeast Myanmar were the primary migration sources for WBPH populations in the southwest and south Yunnan regions. This study aims to contribute to the sustainable regional management of this important rice pest and provide new insights into the genetic diversity of WBPH in Southeast Asia. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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21 pages, 12012 KiB  
Article
Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences
by Su-Hao Wang, Shi-Yun Hu, Min Li, Min Liu, Hao Sun, Jia-Rui Zhao, Wen-Ting Chen and Ming-Long Yuan
Genes 2023, 14(9), 1738; https://doi.org/10.3390/genes14091738 - 30 Aug 2023
Cited by 1 | Viewed by 1145
Abstract
Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the [...] Read more.
Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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23 pages, 1230 KiB  
Article
The Transmission Patterns of the Endosymbiont Wolbachia within the Hawaiian Drosophilidae Adaptive Radiation
by Renée L. Corpuz, M. Renee Bellinger, Anne Veillet, Karl N. Magnacca and Donald K. Price
Genes 2023, 14(8), 1545; https://doi.org/10.3390/genes14081545 - 27 Jul 2023
Viewed by 1215
Abstract
The evolution of endosymbionts and their hosts can lead to highly dynamic interactions with varying fitness effects for both the endosymbiont and host species. Wolbachia, a ubiquitous endosymbiont of arthropods and nematodes, can have both beneficial and detrimental effects on host fitness. [...] Read more.
The evolution of endosymbionts and their hosts can lead to highly dynamic interactions with varying fitness effects for both the endosymbiont and host species. Wolbachia, a ubiquitous endosymbiont of arthropods and nematodes, can have both beneficial and detrimental effects on host fitness. We documented the occurrence and patterns of transmission of Wolbachia within the Hawaiian Drosophilidae and examined the potential contributions of Wolbachia to the rapid diversification of their hosts. Screens for Wolbachia infections across a minimum of 140 species of Hawaiian Drosophila and Scaptomyza revealed species-level infections of 20.0%, and across all 399 samples, a general infection rate of 10.3%. Among the 44 Wolbachia strains we identified using a modified Wolbachia multi-locus strain typing scheme, 30 (68.18%) belonged to supergroup B, five (11.36%) belonged to supergroup A, and nine (20.45%) had alleles with conflicting supergroup assignments. Co-phylogenetic reconciliation analysis indicated that Wolbachia strain diversity within their endemic Hawaiian Drosophilidae hosts can be explained by vertical (e.g., co-speciation) and horizontal (e.g., host switch) modes of transmission. Results from stochastic character trait mapping suggest that horizontal transmission is associated with the preferred oviposition substrate of the host, but not the host’s plant family or island of occurrence. For Hawaiian Drosophilid species of conservation concern, with 13 species listed as endangered and 1 listed as threatened, knowledge of Wolbachia strain types, infection status, and potential for superinfection could assist with conservation breeding programs designed to bolster population sizes, especially when wild populations are supplemented with laboratory-reared, translocated individuals. Future research aimed at improving the understanding of the mechanisms of Wolbachia transmission in nature, their impact on the host, and their role in host species formation may shed light on the influence of Wolbachia as an evolutionary driver, especially in Hawaiian ecosystems. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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16 pages, 5144 KiB  
Article
Complete Mitochondrial Genome of Piophila casei (Diptera: Piophilidae): Genome Description and Phylogenetic Implications
by Shenghui Bi, Yanfei Song, Linggao Liu, Jing Wan, Ying Zhou, Qiujin Zhu and Jianfeng Liu
Genes 2023, 14(4), 883; https://doi.org/10.3390/genes14040883 - 8 Apr 2023
Cited by 4 | Viewed by 1707
Abstract
Piophila casei is a flesh-feeding Diptera insect that adversely affects foodstuffs, such as dry-cured ham and cheese, and decaying human and animal carcasses. However, the unknown mitochondrial genome of P. casei can provide information on its genetic structure and phylogenetic position, which is [...] Read more.
Piophila casei is a flesh-feeding Diptera insect that adversely affects foodstuffs, such as dry-cured ham and cheese, and decaying human and animal carcasses. However, the unknown mitochondrial genome of P. casei can provide information on its genetic structure and phylogenetic position, which is of great significance to the research on its prevention and control. Therefore, we sequenced, annotated, and analyzed the previously unknown complete mitochondrial genome of P. casei. The complete mt genome of P. casei is a typical circular DNA, 15,785 bp in length, with a high A + T content of 76.6%. It contains 13 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 control region. Phylogenetic analysis of 25 Diptera species was conducted using Bayesian and maximum likelihood methods, and their divergence times were inferred. The comparison of the mt genomes from two morphologically similar insects P. casei and Piophila megastigmata indicates a divergence time of 7.28 MYA between these species. The study provides a reference for understanding the forensic medicine, taxonomy, and genetics of P. casei. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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14 pages, 6487 KiB  
Article
Characterization of the Complete Mitochondrial Genome of a Flea Beetle Luperomorpha xanthodera (Coleoptera: Chrysomelidae: Galerucinae) and Phylogenetic Analysis
by Jingjing Li, Bin Yan, Hongli He, Xiaoli Xu, Yongying Ruan and Maofa Yang
Genes 2023, 14(2), 414; https://doi.org/10.3390/genes14020414 - 4 Feb 2023
Cited by 1 | Viewed by 1866
Abstract
In this study, the mitochondrial genome of Luperomorpha xanthodera was assembled and annotated, which is a circular DNA molecule including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), and 1388 bp non-coding regions [...] Read more.
In this study, the mitochondrial genome of Luperomorpha xanthodera was assembled and annotated, which is a circular DNA molecule including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), and 1388 bp non-coding regions (A + T rich region), measuring 16,021 bp in length. The nucleotide composition of the mitochondrial genome is 41.3% adenine (A), 38.7% thymine (T), 8.4% guanine (G), and 11.6% cytosine (C). Most of the protein-coding genes presented a typical ATN start codon (ATA, ATT, ATC, ATG), except for ND1, which showed the start codon TTG. Three-quarters of the protein-coding genes showed the complete stop codon TAR (TAA, TAG), except the genes COI, COII, ND4, and ND5, which showed incomplete stop codons (T- or TA-). All the tRNA genes have the typical clover-leaf structure, except tRNASer1 (AGN), which has a missing dihydrouridine arm (DHU). The phylogenetic results determined by both maximum likelihood and Bayesian inference methods consistently supported the monophyly of the subfamily Galerucinae and revealed that the subtribe Luperina and genus Monolepta are polyphyletic groups. Meanwhile, the classification status of the genus Luperomorpha is controversial. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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21 pages, 8970 KiB  
Article
Characterizing the Complete Mitochondrial Genomes of Three Bugs (Hemiptera: Heteroptera) Harming Bamboo
by Wenli Zhu, Lin Yang, Jiankun Long, Zhimin Chang, Nian Gong, Yinlin Mu, Shasha Lv and Xiangsheng Chen
Genes 2023, 14(2), 342; https://doi.org/10.3390/genes14020342 - 28 Jan 2023
Cited by 4 | Viewed by 1794
Abstract
Herein, we report the mitochondrial genomic characteristics of three insect pests, Notobitus meleagris, Macropes harringtonae, and Homoeocerus bipunctatus, collected from bamboo plants in Guizhou Province, China. For the first time, the damaged conditions and life histories of M. harringtonae and H. [...] Read more.
Herein, we report the mitochondrial genomic characteristics of three insect pests, Notobitus meleagris, Macropes harringtonae, and Homoeocerus bipunctatus, collected from bamboo plants in Guizhou Province, China. For the first time, the damaged conditions and life histories of M. harringtonae and H. bipunctatus are described in detail and digital photographs of all their life stages are provided. Simultaneously, the mitochondrial genome sequences of three bamboo pests were sequenced and analyzed. Idiocerus laurifoliae and Nilaparvata lugens were used as outgroups, and the phylogenetic trees were constructed. The mitochondrial genomes of the three bamboo pests contained 37 classical genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNAs (tRNAs), and a control region, with a total length of 16,199 bp, 15,314 bp, and 16,706 bp, respectively. The A+T values of the three bamboo pests were similar, and trnS1 was a cloverleaf structure with missing arms. The phylogenetic analyses, using the Bayesian inference (BI) and Maximum likelihood (ML), supported that N. meleagris and H. bipunctatus belonged to the Coreoidea family, whereas M. harringtonae belonged to the Lygaeoidea family with high support values. This study involves the first complete sequencing of the mitochondrial genomes of two bamboo pests. By adding these newly sequenced mitochondrial genome data and detailed descriptions of life histories, the database of bamboo pests is improved. These data also provide information for the development of bamboo pest control methods by quick identification techniques and the use of detailed photographs. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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17 pages, 4116 KiB  
Article
The Adaptive Evolution in the Fall Armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) Revealed by the Diversity of Larval Gut Bacteria
by Yan-Ping Wang, Xu Liu, Chun-Yan Yi, Xing-Yu Chen, Chang-Hua Liu, Cui-Cui Zhang, Qing-Dong Chen, Song Chen, Hong-Ling Liu and De-Qiang Pu
Genes 2023, 14(2), 321; https://doi.org/10.3390/genes14020321 - 26 Jan 2023
Cited by 5 | Viewed by 1611
Abstract
Insect gut microbes have important roles in host feeding, digestion, immunity, development, and coevolution with pests. The fall armyworm, Spodoptera frugiperda (Smith, 1797), is a major migratory agricultural pest worldwide. The effects of host plant on the pest’s gut bacteria remain to be [...] Read more.
Insect gut microbes have important roles in host feeding, digestion, immunity, development, and coevolution with pests. The fall armyworm, Spodoptera frugiperda (Smith, 1797), is a major migratory agricultural pest worldwide. The effects of host plant on the pest’s gut bacteria remain to be investigated to better understand their coevolution. In this study, differences in the gut bacterial communities were examined for the fifth and sixth instar larvae of S. frugiperda fed on leaves of different host plants (corn, sorghum, highland barley, and citrus). The 16S rDNA full-length amplification and sequencing method was used to determine the abundance and diversity of gut bacteria in larval intestines. The highest richness and diversity of gut bacteria were in corn-fed fifth instar larvae, whereas in sixth instar larvae, the richness and diversity were higher when larvae were fed by other crops. Firmicutes and Proteobacteria were dominant phyla in gut bacterial communities of fifth and sixth instar larvae. According to the LDA Effect Size (LEfSe) analysis, the host plants had important effects on the structure of gut bacterial communities in S. frugiperda. In the PICRUSt2 analysis, most predicted functional categories were associated with metabolism. Thus, the host plant species attacked by S. frugiperda larvae can affect their gut bacterial communities, and such changes are likely important in the adaptive evolution of S. frugiperda to host plants. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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12 pages, 2231 KiB  
Article
Complete Mitochondrial Genome of Scolytoplatypodini Species (Coleoptera: Curculionidae: Scolytinae) and Phylogenetic Implications
by Guangyu Yu, Shengchang Lai, Song Liao, Yufeng Cao, Weijun Li, Chengpeng Long, Hagus Tarno and Jianguo Wang
Genes 2023, 14(1), 162; https://doi.org/10.3390/genes14010162 - 6 Jan 2023
Cited by 2 | Viewed by 1416
Abstract
The complete mitochondrial genomes (mitogenomes) of beetles in the tribe Scolytoplatypodini (genus Scolytoplatypus) were sequenced and annotated. These included Scolytoplatypus raja (15,324 bp), Scolytoplatypus sinensis (15,394 bp), Scolytoplatypus skyliuae (15,167 bp), and Scolytoplatypus wugongshanensis (15,267 bp). The four mitogenomes contained 37 typical [...] Read more.
The complete mitochondrial genomes (mitogenomes) of beetles in the tribe Scolytoplatypodini (genus Scolytoplatypus) were sequenced and annotated. These included Scolytoplatypus raja (15,324 bp), Scolytoplatypus sinensis (15,394 bp), Scolytoplatypus skyliuae (15,167 bp), and Scolytoplatypus wugongshanensis (15,267 bp). The four mitogenomes contained 37 typical genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The gene orientation and arrangement of the four mitogenomes were similar to other Coleoptera mitogenomes. PCGs mostly started with ATN and terminated with TAA. The Ka/Ks ratio of 13 PCGs in the four species revealed that cox1 had the slowest evolutionary rate and atp8 and nad6 had a higher evolutionary rate. All tRNAs had typical cloverleaf secondary structures, but trnS1 lacked dihydrouridine arm. Partial tRNAs lost the discriminator nucleotide. The trnY did not possess the discriminator nucleotide and also lost three bases, showing a special amino-acyl arm. Bayesian inference (BI) and maximum likelihood (ML) methods were conducted for phylogenetic analyses using 13 PCGs. Scolytoplatypodini was clustered with Hylurgini and Hylastini, and the monophyly of Scolytoplatypodini was supported. The four newly sequenced mitogenomes increase understanding of the evolutionary relationships of Scolytoplatypodini and other Scolytinae species. Full article
(This article belongs to the Special Issue Genetics, Phylogeny, and Evolution of Insects)
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