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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) | Viewed by 36460

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Special Issue Editors

Dr. Monica Poelchau

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Chief Guest Editor

USDA-ARS National Agricultural Library, Beltsville, MD 20705, USA
Interests: genomics; arthropods; databases; data standards

Dr. Surya Saha

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Guest Editor

1. Boyce Thompson Institute, Ithaca, NY 14853, USA
2. 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

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Keywords

genomics
genome sequencing
genome assembly
genome annotation
genome databases

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Published Papers (10 papers)

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Research

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11 pages, 1966 KiB

Open AccessArticle

Genus-Wide Characterization of Nuclear Mitochondrial DNAs in Bumblebee (Hymenoptera: Apidae) Genomes

by Lele Ding, Huiling Sang and Cheng Sun

Insects 2021, 12(11), 963; https://doi.org/10.3390/insects12110963 - 23 Oct 2021

Cited by 5 | Viewed by 2183

Abstract

In eukaryotes, DNA of mitochondria is transferred into the nucleus and forms nuclear mitochondrial DNAs (NUMTs). Taking advantage of the abundant genomic resources for bumblebees, in this study, we de novo generated mitochondrial genomes (mitogenomes) for 11 bumblebee species. Then, we identified and characterized NUMTs in genus-wide bumblebee species. The number of identified NUMTs varies across those species, with numbers ranging from 32 to 72, and nuclear genome size is not positively related to NUMT number. The insertion sites of NUMTs in the nuclear genome are not random, with AT-rich regions harboring more NUMTs. In addition, our results suggest that NUMTs derived from the mitochondrial COX1 gene are most abundant in the bumblebee nuclear genome. Although the majority of NUMTs are found within intergenic regions, some NUMTs do reside within genic regions. Transcripts that contain both the NUMT sequence and its flanking non-NUMT sequences could be found in the bumblebee transcriptome, suggesting a potential domestication of NUMTs in the bumblebee. Taken together, our results shed light on the molecular features of NUMTs in the bumblebee and uncover their contribution to genome innovation. Full article

(This article belongs to the Special Issue Insect Genomics)

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13 pages, 2595 KiB

Open AccessArticle

The Identification of Boll Weevil, Anthonomus grandis grandis (Coleoptera: Curculionidae), Genes Involved in Pheromone Production and Pheromone Biosynthesis

by Lindsey C. Perkin, Jose L. Perez and Charles P.-C. Suh

Insects 2021, 12(10), 893; https://doi.org/10.3390/insects12100893 - 1 Oct 2021

Cited by 5 | Viewed by 2820

Abstract

Eradication programs for the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), rely almost exclusively on pheromone traps to indicate the need for insecticide applications. However, the effectiveness of traps in detecting weevil populations is reduced during certain times of the year, particularly when cotton is actively fruiting. Consequently, this could result in fields becoming heavily infested with weevils. It is widely speculated that the lack of weevil captures in traps during this period is largely due to the overwhelming amount of pheromone released by weevils in the field, which outcompete the pheromone released from traps. Thus, this work sought to identify genes involved in pheromone production so that new control methods that target these genes can be explored. We conducted an RNA-seq experiment that revealed 2479 differentially expressed genes between pheromone-producing and non-pheromone-producing boll weevils. Of those genes, 1234 were up-regulated, and 1515 were down-regulated, and most had gene annotations associated with pheromone production, development, or immunity. This work advances our understanding of boll weevil pheromone production and brings us one step closer to developing gene-level control strategies for this cotton pest. Full article

(This article belongs to the Special Issue Insect Genomics)

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16 pages, 4800 KiB

Open AccessArticle

De Novo Genome Assembly of Chinese Plateau Honeybee Unravels Intraspecies Genetic Diversity in the Eastern Honeybee, Apis cerana

by Lan Lan, Peng Shi, Huali Song, Xiangyou Tang, Jianyang Zhou, Jiandong Yang, Mingxian Yang and Jinshan Xu

Insects 2021, 12(10), 891; https://doi.org/10.3390/insects12100891 - 1 Oct 2021

Cited by 6 | Viewed by 2404

Abstract

Apis cerana abansis, widely distributed in the southeastern margin of the Qinghai-Tibet Plateau, is considered an excellent model to study the phenotype and genetic variation for highland adaptation of Asian honeybee. Herein, we assembled and annotated the chromosome-scale assembly genome of A. cerana abansis with the help of PacBio, Illumina and Hi-C sequencing technologies in order to identify the genome differences between the A. cerana abansis and the published genomes of different A. cerana strains. The sequencing methods, assembly and annotation strategies of A. cerana abansis were more comprehensive than previously published A. cerana genomes. Then, the intraspecific genetic diversity of A. cerana was revealed at the genomic level. We re-identified the repeat content in the genome of A. cerana abansis, as well as the other three A. cerana strains. The chemosensory and immune-related proteins in different A. cerana strains were carefully re-identified, so that 132 odorant receptor subfamilies, 12 gustatory receptor subfamilies and 22 immune-related pathways were found. We also discovered that, compared with other published genomes, the A. ceranaabansis lost the largest number of chemoreceptors compared to other strains, and hypothesized that gene loss/gain might help different A. cerana strains to adapt to their respective environments. Our work contains more complete and precise assembly and annotation results for the A. cerana genome, thus providing a resource for subsequent in-depth related studies. Full article

(This article belongs to the Special Issue Insect Genomics)

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16 pages, 2793 KiB

Open AccessArticle

Transcriptomic Characterization of Odorant Binding Proteins in Cacia cretifera thibetana and Their Association with Different Host Emitted Volatiles

by Ning Zhao, Xiangzhong Mao, Naiyong Liu, Ling Liu, Zhixiao Zhang, Sangzi Ze and Bin Yang

Insects 2021, 12(9), 787; https://doi.org/10.3390/insects12090787 - 3 Sep 2021

Cited by 1 | Viewed by 2082

Abstract

This study characterized the transcriptome of Cacia cretifera thibetana and explored odorant binding proteins (OBPs) and their interaction with host-specific compounds. A total of 36 samples from six different organs including antennae, head, thorax, abdomen, wings, and legs (12 groups with 3 replicates per group) from both male and female insects were collected for RNA extraction. Transcriptomic analysis revealed a total of 89,897 transcripts as unigenes, with an average length of 1036 bp. Between male and female groups, 31,095 transcripts were identified as differentially expressed genes (DEGs). The KEGG pathway analysis revealed 26 DEGs associated with cutin, suberine, and wax biosynthesis and 70, 48, and 62 were linked to glycerophospholipid metabolism, choline metabolism in cancer, and chemokine signaling pathways, respectively. A total of 31 OBP genes were identified. Among them, the relative expression of 11 OBP genes (OBP6, 10, 12, 14, 17, 20, 22, 26, 28, 30, and 31) was confirmed by quantitative RT-PCR in different tissues. Seven OBP genes including CcreOBP6 and CcreOBP10 revealed antennae-specific expression. Further, we selected two OBPs (CcreOBP6 and CcreOBP10) for functional analysis to evaluate their binding affinity with 20 host odorant compounds. The CcreOBP6 and CcreOBP10 exhibited strong binding affinities with terpineol and trans-2-hexenal revealing their potential as an attractant or repellent for controlling C. cretifera thibetana. Full article

(This article belongs to the Special Issue Insect Genomics)

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15 pages, 1763 KiB

Open AccessArticle

Age and Behavior-Dependent Differential miRNAs Expression in the Hypopharyngeal Glands of Honeybees (Apis mellifera L.)

by Tengfei Shi, Yujie Zhu, Peng Liu, Liang Ye, Xingchuan Jiang, Haiqun Cao and Linsheng Yu

Insects 2021, 12(9), 764; https://doi.org/10.3390/insects12090764 - 26 Aug 2021

Cited by 8 | Viewed by 3052

Abstract

This study aims to investigate the expression differences of miRNAs in the hypopharyngeal glands (HPGs) of honeybees at three developmental stages and to explore their regulation functions in the HPGs development. Small RNA sequencing was employed to analyze the miRNA profiles of HPGs in newly-emerged bees (NEB), nurse bees (NB), and forager bees (FB). Results showed that a total of 153 known miRNAs were found in the three stages, and ame-miR-276-3p, ame-miR-375-3p, ame-miR-14-3p, ame-miR-275-3p, and ame-miR-3477-5p were the top five most abundant ones. Furthermore, the expression of 11 miRNAs, 17 miRNAs, and 18 miRNAs were significantly different in NB vs. FB comparison, NB vs. NEB comparison, and in FB vs. NEB comparison, respectively, of which ame-miR-184-3p and ame-miR-252a-5p were downregulated in NB compared with that in both the FB and NEB, while ame-miR-11-3p, ame-miR-281-3p, and ame-miR-31a-5p had lower expression levels in FB compared with that in both the NB and NEB. Bioinformatic analysis showed that the potential target genes of the differentially expressed miRNAs (DEMs) were mainly enriched in several key signaling pathways, including mTOR signaling pathway, MAPK signaling pathway-fly, FoxO signaling pathway, Hippo signaling pathway-fly. Overall, our study characterized the miRNA profiles in the HPGs of honeybees at three different developmental stages and provided a basis for further study of the roles of miRNAs in HPGs development. Full article

(This article belongs to the Special Issue Insect Genomics)

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17 pages, 590 KiB

Open AccessArticle

Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes

by Surya Saha, Amanda M. Cooksey, Anna K. Childers, Monica F. Poelchau and Fiona M. McCarthy

Insects 2021, 12(8), 748; https://doi.org/10.3390/insects12080748 - 19 Aug 2021

Cited by 7 | Viewed by 3886

Abstract

Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide the foundational information required to apply ‘omics technologies to a more diverse set of species. However, biologists require genome annotation to use these genomes and derive a better understanding of complex biological systems. Genome annotation incorporates two related, but distinct, processes: Demarcating genes and other elements present in genome sequences (structural annotation); and associating a function with genetic elements (functional annotation). While there are well-established and freely available workflows for structural annotation of gene identification in newly assembled genomes, workflows for providing the functional annotation required to support functional genomics studies are less well understood. Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.). A first-pass genome-wide functional annotation effort can rapidly identify under-represented gene sets for focused community annotation efforts. We present an open-source, open access, and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to various arthropod species. We show that the performance of the predictions is consistent across a set of arthropod genomes with varying assembly and annotation quality. Full article

(This article belongs to the Special Issue Insect Genomics)

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14 pages, 1063 KiB

Open AccessArticle

The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

by Anna K. Childers, Scott M. Geib, Sheina B. Sim, Monica F. Poelchau, Brad S. Coates, Tyler J. Simmonds, Erin D. Scully, Timothy P. L. Smith, Christopher P. Childers, Renee L. Corpuz, Kevin Hackett and Brian Scheffler

Insects 2021, 12(7), 626; https://doi.org/10.3390/insects12070626 - 9 Jul 2021

Cited by 30 | Viewed by 5693

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 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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7 pages, 1145 KiB

Open AccessCommunication

Aquatic Insects Are Dramatically Underrepresented in Genomic Research

by Scott Hotaling, Joanna L. Kelley and Paul B. Frandsen

Insects 2020, 11(9), 601; https://doi.org/10.3390/insects11090601 - 5 Sep 2020

Cited by 30 | Viewed by 4643

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 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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18 pages, 1295 KiB

Open AccessReview

Annotating the Insect Regulatory Genome

by Hasiba Asma and Marc S. Halfon

Insects 2021, 12(7), 591; https://doi.org/10.3390/insects12070591 - 29 Jun 2021

Cited by 5 | Viewed by 3921

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 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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7 pages, 453 KiB

Open AccessBrief Report

Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees

by Hongwei Tan, Muhammad Naeem, Hussain Ali, Muhammad Shakeel, Haiou Kuang, Ze Zhang and Cheng Sun

Insects 2021, 12(7), 652; https://doi.org/10.3390/insects12070652 - 16 Jul 2021

Cited by 2 | Viewed by 2901

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 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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