Aquatic insects are dramatically underrepresented in genomic research

Hotaling, Scott; Kelley, Joanna L.; Frandsen, Paul B.

doi:10.1101/2020.08.20.259754

Cited by 8 publications

(7 citation statements)

References 28 publications

(20 reference statements)

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“…In this study, we report new genomic resources for the order Trichoptera. This is important since aquatic insects have been underrepresented in genomics research (Hotaling et al, 2020, 2021a, 2021b). For the first time, we provide long high-fidelity sequences of a fixed retreat-making caddisfly species.…”

Section: Discussionmentioning

confidence: 99%

Characterization of primary structure of the major silk gene,h-fibroin, across caddisfly suborders (Trichoptera)

Heckenhauer

Stewart

Ríos-Touma

et al. 2022

Preprint

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Similar to their sister order Lepidoptera (moths and butterflies), the primarily aquatic larvae of Trichoptera (caddisflies) produce silk, which is used to build a wide variety of underwater architectures, such as cocoons, fixed retreats, and tube-cases. This diverse silk usage allows them to exploit a wide range of aquatic environments. Studies of the long and highly repetitive major silk gene, heavy chain fibroin (h-fibroin), are rare due to difficulties in sequence assembly. Only recently, new long-read sequencing techniques have been used to assemble high-quality, full-length sequences of this gene. Here, we report seven new gene and protein sequences of h-fibroin covering the breadth of the order Trichoptera, including the three major life history strategies characterized by different silk usage (fixed retreat-, cocoon- and tube case-making). When comparing the primary structure of the h-fibroin, we find conserved patterns, but also substantial diversity across groups. The signatures of conservation, such as conservation of N- and C-termini and characteristic repeating structural modules, suggest a common mechanism of silk formation and similar material properties across all three groups. The diversity in the number and order of the repeating modules, as well as the increasing structural complexity of h-fibroin in fixed retreat and tube-case building compared to cocoon-builders, may reflect differences in mechanical properties related to the diversity of silken architectures. This study presents a basis for future research into the role of fibroins in caddisfly silk function as a gauge of the potential of underwater silk in material applications.

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Section: Discussionmentioning

confidence: 99%

Characterization of primary structure of the major silk gene,h-fibroin, across caddisfly suborders (Trichoptera)

Heckenhauer

Stewart

Ríos-Touma

et al. 2022

Preprint

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“…Following Hotaling et al (56), we used the assembly-descriptors function in the NCBI datasets command line tool to download metadata for all nuclear genomes available for insects on GenBank (accessed 2 November 2020; (57). We then culled our data set to include only one representative genome per taxon (species or subspecies) by selecting the assembly with the highest contig N50 (the mid-point of the contig distribution where 50% of the genome is assembled into contigs of a given length or longer).…”

Section: Methodsmentioning

confidence: 99%

600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges

Sproul

Hotaling

Heckenhauer

et al. 2022

Preprint

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Repetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes. Yet, RE dynamics remain understudied in many taxonomic groups, preventing holistic understanding of how genomes and species evolve. Here, we investigated REs across 601 insect species (20 orders) to better understand the RE landscape of insects and to evaluate automated RE annotation methods in the era of biodiversity genomics. We identified wide variation in the types and frequency of REs across insect groups. We quantified associations between REs and protein-coding genes and found an elevated frequency of associations in insects with abundant long interspersed nuclear elements (LINEs). Sequencing technology impacts RE detection; ~36% more REs could be identified in long-read versus short-read assemblies. Long terminal repeats (LTRs) showed markedly improved detection in long-read assemblies (162% more), while DNA transposons and LINEs showed less respective technology-related bias. We illustrate fundamental challenges to efficient study of REs in diverse groups, showing that in most insect lineages, 25-85% of repetitive sequences were unclassified compared to only ~13% of unclassified repeats in Drosophila species. Our findings suggest this RE-annotation bottleneck, driven largely by uneven taxonomic representation in RE reference databases, is worsening. Although the diversity of available insect genomes has rapidly expanded, the rate of community contributions to RE databases (essential for RE annotation) has not kept pace, preventing high resolution study of REs in most groups. We highlight the tremendous opportunity and need for the field of biodiversity genomics to embrace REs and suggest collective steps for making progress towards this goal.

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“…Through efforts such as the i5k 5000 arthropod genomes initiative [ 28 ] and others, the arthropod genomics community has worked to overcome challenges in genome sequencing, assembly, and annotation [ 29–31 ]. Despite encompassing only a tiny fraction of all arthropod diversity and showing taxonomic biases in sampling, assemblies are accumulating rapidly and are now publicly available for hundreds of species [ 32 , 33 ].…”

Section: Introductionmentioning

confidence: 99%

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Féron

Waterhouse

2022

GigaScience

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Background Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. To guide forthcoming genome generation efforts and promote efficient prioritization of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Findings Here we present an automated analysis workflow that surveys genome assemblies from the United States NCBI, assesses their completeness using the relevant BUSCO datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, examine how key assembly metrics relate to gene content completeness, and compare results from using different BUSCO lineage datasets. Conclusions These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritizations for ongoing and future sampling, sequencing, and genome generation initiatives.

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Aquatic insects are dramatically underrepresented in genomic research

Cited by 8 publications

References 28 publications

Characterization of primary structure of the major silk gene,h-fibroin, across caddisfly suborders (Trichoptera)

Characterization of primary structure of the major silk gene,h-fibroin, across caddisfly suborders (Trichoptera)

600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

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