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Phylogeny and Genetic Diversity of Insects
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Phylogeny and Genetic Diversity 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: closed (25 May 2022) | Viewed by 6938

Special Issue Editor

Dr. Fan Song

E-Mail Website
Guest Editor
College of Plant Protection, China Agricultural University, Beijing, China
Interests: insects; phylogeny; mitochondrial genome; parasitic lice; genomics

Special Issue Information

Dear Colleagues,

Insects have shaped Earth’s biota and comprise over half of all described animal species. However, because of their unparalleled species diversity, many aspects of insect evolution are still poorly understood. The introduction of molecular phylogenetics has precipitated a revolution in our understanding of insect phylogeny. Thanks to the rapid development of high-throughput sequencing, we now have access to about 600 insect genomes, 440 transcriptomes, and 1500 mitochondrial genomes, which also show rich diversity in genome size, genome structure, etc. Although incongruence between morphological and molecular phylogenies as well as between competing molecular studies are arising, phylogenomic analyses have helped to resolve many contentious relationships within insects. As large-scale genomic data and species sampling become more routine, we move towards an integrated understanding of insect phylogeny.

In this Special Issue, we aim to highlight research on "Phylogeny and Genetic diversity of Insects". We invite submissions in the form of reviews or original research articles on any aspect of research using phylogenomic data to reveal diversity and relationships within insects. We invite studies that use genomic approaches to unravel basic questions of diversity and phylogeny in different insect groups. 

Dr. Fan Song
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • insects
  • phylogeny
  • genomics
  • evolution
  • systematics
  • diversity
  • genome
  • transcriptomes
  • mitochondrial genome

Published Papers (4 papers)

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Research

13 pages, 32644 KiB  
Article
The Complete Mitochondrial Genome of Spirobolus bungii (Diplopoda, Spirobolidae): The First Sequence for the Genus Spirobolus
by Hanmei Xu, Yu Fang, Guohua Cao, Caiqin Shen, Hongyi Liu and Honghua Ruan
Genes 2022, 13(9), 1587; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13091587 - 03 Sep 2022
Cited by 4 | Viewed by 1642
Abstract
Millipedes (Diplopoda) comprise one of the most important groups of large soil arthropods in terrestrial ecosystems; however, their phylogenetic relationships are poorly understood. Herein, the mitochondrial genome (mitogenome) of Spirobolus bungii was sequenced and annotated, which was 14,879 bp in size and included [...] Read more.
Millipedes (Diplopoda) comprise one of the most important groups of large soil arthropods in terrestrial ecosystems; however, their phylogenetic relationships are poorly understood. Herein, the mitochondrial genome (mitogenome) of Spirobolus bungii was sequenced and annotated, which was 14,879 bp in size and included 37 typical mitochondrial genes (13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs)). Most of the 13 PCGs had ATN (AT/A/T/G) as the start codon except for COX1, which used CGA, and most PCGs ended with the T end codon. By comparing the gene arrangements of the mitogenomes among Diplopoda species, rearrangement occurred between and within orders. In contrast to Narceus annularus, the mitogenome genes of S. bungii had consistent orders but were transcribed in completely opposite directions, which was a novel finding in Spirobolidae. Moreover, the phylogenetic relationships within Diplopoda, which were based on the sequences of 13 PCGs, showed that S. bungii was clustered with N. annularus, followed by Abacion magmun. This indicated that there might be a close relationship between Callipodida and Spirobolida. These results could contribute to further studies on the genetics and evolutionary processes of S. bungii and other Diplopoda species. Full article
(This article belongs to the Special Issue Phylogeny and Genetic Diversity of Insects)
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13 pages, 3039 KiB  
Article
Mitochondrial Genome of Strophopteryx fasciata (Plecoptera: Taeniopterygidae), with a Phylogenetic Analysis of Nemouroidea
by Xuan Guo, Caiyue Guo, Xiaojiao Dong, Heng Zhang, Dávid Murányi, Weihai Li and Ying Wang
Genes 2022, 13(7), 1116; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13071116 - 22 Jun 2022
Cited by 3 | Viewed by 1313
Abstract
Taeniopterygidae is a medium-sized family of stoneflies. The phylogeny of Taeniopterygidae was widely accepted based on the morphological analyses. However, there are different opinions based on molecular data. To date, only two taeniopterygid mitochondrial genomes (mitogenomes) were available, and more sampling is needed [...] Read more.
Taeniopterygidae is a medium-sized family of stoneflies. The phylogeny of Taeniopterygidae was widely accepted based on the morphological analyses. However, there are different opinions based on molecular data. To date, only two taeniopterygid mitochondrial genomes (mitogenomes) were available, and more sampling is needed to obtain precise phylogenetic relationships. In this research, the Strophopteryx fasciata mitogenome was sequenced and analyzed. The complete mitogenome of S. fasciata was 15,527 bp in length and contained 37 genes and a non-coding control region. Among taeniopterygid mitogenomes, the length variation was minimal in protein-coding genes (PCGs), transfer RNA genes (tRNAs) and ribosomal RNA genes (rRNAs), but very different in the control region. Similar to mitogenomes of other taeniopterygid species, the S. fasciata mitogenome was consistently AT biased and displayed positive AT- and negative GC-skews of the whole mitogenome. Most PCGs used ATN as the start codon and TAA/TAG as the stop codon. The stop codons were far less variable than the start codons in taeniopterygid mitogenomes. All Ka/Ks ratios were less than 1, indicating the presence of purifying selection in these genes. The secondary structures of transfer and ribosomal RNA genes of S. fasciata mitogenome are highly conserved with other taeniopterygid species. In the control region of the S. fasciata mitogenome, some essential elements (tandem repeats, stem–loop structures, and poly−N stretch, etc.) were observed. Two phylogenetic trees were inferred from Bayesian inference (BI) and Maximum Likelihood (ML) methods generated the identical topology across the PCGR dataset. The relationships of five families in Nemouroidea were recovered as Leuctridae + ((Capniidae + Taeniopterygidae) + (Nemouridae + Notonemouridae)). These results will help us understand the mitogenome structure of taeniopterygid species and the evolutionary relationship within Plecoptera. Full article
(This article belongs to the Special Issue Phylogeny and Genetic Diversity of Insects)
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11 pages, 1380 KiB  
Article
Complete Mitochondrial Genome of Malenka flexura (Plecoptera: Nemouridae) and Phylogenetic Analysis
by Jinjun Cao, Xuan Guo, Caiyue Guo, Xuan Wang, Ying Wang and Fengming Yan
Genes 2022, 13(5), 911; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13050911 - 19 May 2022
Cited by 5 | Viewed by 1519
Abstract
The genus-level relationships within the subfamily Amphinemurinae have been controversial, although attempts have been made based on morphology and limited molecular data. With the establishment of two new genera, the phylogenetic relationships within Amphinemurinae should be re-examined. In this study, the complete mitochondrial [...] Read more.
The genus-level relationships within the subfamily Amphinemurinae have been controversial, although attempts have been made based on morphology and limited molecular data. With the establishment of two new genera, the phylogenetic relationships within Amphinemurinae should be re-examined. In this study, the complete mitochondrial genome (mitogenome) of Malenka flexura of the genus Malenka was firstly sequenced and analyzed. The phylogeny of Amphinemurinae was also reconstructed using 13 proteincoding genes (PCGs) from previously published stoneflies. This mitogenome was 15,744 bp long and encoded the typical 37 genes, as well as a putative control region. The gene arrangement of M. flexura mitogenome is identical with the putative ancestral mitogenome in Drosophila yakuba. Most PCGs used standard ATN as start codons and TAA/TAG as termination codons. All tRNA genes exhibited the typical cloverleaf secondary structure, except for tRNASer(AGN), whose dihydrouridine (DHU) arm was lacking. Some structural elements in the control region were founded, such as tandem repeat regions, stemloop structures, polyN stretch and microsatellite structure, etc. Phylogenetic analyses of sequenced Amphinemurinae mitogenomes unsupported the sister relationship of Amphinemura and Malenka. Finally, the phylogenetic analyses inferred a relationship within Amphinemurinae: Amphinemura + (Malenka + (Protonemura + (Indonemoura + (Sphaeronemoura + Mesonemoura)))). Full article
(This article belongs to the Special Issue Phylogeny and Genetic Diversity of Insects)
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10 pages, 12519 KiB  
Article
The Complete Mitochondrial Genome of the Chicken Body Louse, Menacanthus cornutus, and Evolutionary Patterns of Extensive Gene Rearrangements in the Mitochondrial Genomes of Amblycera (Psocodea: Phthiraptera)
by Siyu Gong, Ye Xu, Shiwen Xu, Yanxin Liang, Li Tian, Wanzhi Cai, Hu Li and Fan Song
Genes 2022, 13(3), 522; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030522 - 16 Mar 2022
Cited by 2 | Viewed by 2011
Abstract
Animal mitochondrial (mt) genomes are typically double-strand circular DNA molecules, but diverse structural variations have been widely found in multiple groups. In parasitic lice (Phthiraptera), the structure of mt genomes varies remarkably across all five suborders. In this study, we reported the complete [...] Read more.
Animal mitochondrial (mt) genomes are typically double-strand circular DNA molecules, but diverse structural variations have been widely found in multiple groups. In parasitic lice (Phthiraptera), the structure of mt genomes varies remarkably across all five suborders. In this study, we reported the complete mt genome of a chicken body louse, Menacanthus cornutus, which has a typical single circular mt chromosome and drastic mt gene rearrangements. This mt genome is 15,693 bp in length, consisting of 13 protein-coding genes, 23 tRNA genes, 2 rRNA genes, and a control region. A comparison with a typical insect mt genome suggested that two highly similar trnM are present in the mt genome of M. cornutus. Moreover, almost every single gene was rearranged, and over half of mt genes were inverted. Phylogenetic analyses inferred from the mt genome sequences supported the monophyly and position of Amblycera. Mapped over the phylogenetic relationships of Amblycera, we identified two inversion events for the conserved gene blocks in Boopidae and Menoponidae. The inverted ND4L-ND4 was likely a synapomorphic rearrangement in Menoponidae. Our study demonstrated the importance of sequencing mt genomes for additional taxa to uncover the mechanism underlying the structural evolution of the mt genome in parasitic lice. Full article
(This article belongs to the Special Issue Phylogeny and Genetic Diversity of Insects)
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