Special Issue "Insect Genomics"

A special issue of Insects (ISSN 2075-4450). This special issue belongs to the section "Insect Molecular Biology and Genomics".

Deadline for manuscript submissions: closed (30 May 2021).

Special Issue Editors

Dr. Monica Poelchau
E-Mail Website
Chief Guest Editor
USDA-ARS National Agricultural Library, Beltsville, MD 20705, USA
Interests: genomics; arthropods; databases; data standards
Dr. Surya Saha
E-Mail Website
Guest Editor
Boyce Thompson Institute, Ithaca, NY 14853, USA; School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA
Interests: vector biology; comparative genomics; bioinformatics; genome assembly; annotation; proteomics; metagenomics; microbiome; transcriptomics and databases

Special Issue Information

Dear Colleagues,

Advances in genome sequencing have made scientific infrastructure previously reserved for model organisms available to the broader entomology community. Large-scale coordinated sequencing projects, such as the i5k pilot project, have increased the taxonomic breadth of insect draft genomes, and newer initiatives under the Earth BioGenome Project, such as Ag100Pest and Darwin Tree of Life, promise reference-quality genomes at an unprecedented scale. Rapid improvements in long-read sequencing technology, assembly methods and genome annotation in addition to new databases have improved accessibility. This special issue on insect genomics will highlight how whole genome assemblies and transcriptomes increase our understanding of the biology, physiology and behavior of this most diverse class of animals.

Dr. Monica Poelchau
Dr. Surya Saha
Guest Editors

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 papers will be 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. Insects 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 1600 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

  • genomics
  • genome sequencing
  • genome assembly
  • genome annotation
  • genome databases

Published Papers (4 papers)

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Research

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Article
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research
Insects 2021, 12(7), 626; https://doi.org/10.3390/insects12070626 - 09 Jul 2021
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Abstract
The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods [...] Read more.
The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale. Full article
(This article belongs to the Special Issue Insect Genomics)
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Communication
Aquatic Insects Are Dramatically Underrepresented in Genomic Research
Insects 2020, 11(9), 601; https://doi.org/10.3390/insects11090601 - 05 Sep 2020
Cited by 1 | Viewed by 1378
Abstract
Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. However, aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic [...] Read more.
Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. However, aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ~9 terrestrial insect genomes. Instead, ~24 terrestrial insect genomes have been sequenced for every aquatic insect genome. This discrepancy is even more dramatic if the quality of genomic resources is considered; for instance, while no aquatic insect genome has been assembled to the chromosome level, 29 terrestrial insect genomes spanning four orders have. We argue that a lack of aquatic insect genomes is not due to any underlying difficulty (e.g., small body sizes or unusually large genomes), yet it is severely hampering aquatic insect research at both fundamental and applied scales. By expanding the availability of aquatic insect genomes, we will gain key insight into insect diversification and empower future research for a globally important taxonomic group. Full article
(This article belongs to the Special Issue Insect Genomics)
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Review

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Review
Annotating the Insect Regulatory Genome
Insects 2021, 12(7), 591; https://doi.org/10.3390/insects12070591 - 29 Jun 2021
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Abstract
An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical [...] Read more.
An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify cis-regulatory modules (CRMs), sequences such as enhancers that play a major role in regulating transcription. Nevertheless, providing a timely and comprehensive regulatory annotation of newly sequenced insect genomes is an ongoing challenge. We review here the methods being used to identify CRMs in both model and non-model insect species, and focus on two tools that we have developed, REDfly and SCRMshaw. These resources can be paired together in a powerful combination to facilitate insect regulatory annotation over a broad range of species, with an accuracy equal to or better than that of other state-of-the-art methods. Full article
(This article belongs to the Special Issue Insect Genomics)
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Other

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Brief Report
Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees
Insects 2021, 12(7), 652; https://doi.org/10.3390/insects12070652 - 16 Jul 2021
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Abstract
In Pakistan, Apis cerana, the Asian honeybee, has been used for honey production and pollination services. However, its genomic makeup and phylogenetic relationship with those in other countries are still unknown. We collected A. cerana samples from the main cerana-keeping region in Pakistan [...] Read more.
In Pakistan, Apis cerana, the Asian honeybee, has been used for honey production and pollination services. However, its genomic makeup and phylogenetic relationship with those in other countries are still unknown. We collected A. cerana samples from the main cerana-keeping region in Pakistan and performed whole genome sequencing. A total of 28 Gb of Illumina shotgun reads were generated, which were used to assemble the genome. The obtained genome assembly had a total length of 214 Mb, with a GC content of 32.77%. The assembly had a scaffold N50 of 2.85 Mb and a BUSCO completeness score of 99%, suggesting a remarkably complete genome sequence for A. cerana in Pakistan. A MAKER pipeline was employed to annotate the genome sequence, and a total of 11,864 protein-coding genes were identified. Of them, 6750 genes were assigned at least one GO term, and 8813 genes were annotated with at least one protein domain. Genome-scale phylogeny analysis indicated an unexpectedly close relationship between A. cerana in Pakistan and those in China, suggesting a potential human introduction of the species between the two countries. Our results will facilitate the genetic improvement and conservation of A. cerana in Pakistan. Full article
(This article belongs to the Special Issue Insect Genomics)
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