AffiliationDepartment of Ecology and Evolutionary Biology, University of Arizona
de novo genome assembly
genome size evolution
MetadataShow full item record
PublisherOxford University Press
CitationHeckenhauer, J., Frandsen, P. B., Sproul, J. S., Li, Z., Paule, J., Larracuente, A. M., Maughan, P. J., Barker, M. S., Schneider, J. V., Stewart, R. J., & Pauls, S. U. (2022). Genome size evolution in the diverse insect order Trichoptera. GigaScience.
RightsCopyright © The Author(s) 2022. Published by Oxford University Press GigaScience. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at email@example.com.
AbstractBackground: Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. Results: We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). Conclusion: Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities. © 2022 The Author(s) 2022. Published by Oxford University Press GigaScience.
NoteOpen access journal
VersionFinal published version
Except where otherwise noted, this item's license is described as Copyright © The Author(s) 2022. Published by Oxford University Press GigaScience. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
- Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera).
- Authors: Olsen LK, Heckenhauer J, Sproul JS, Dikow RB, Gonzalez VL, Kweskin MP, Taylor AM, Wilson SB, Stewart RJ, Zhou X, Holzenthal R, Pauls SU, Frandsen PB
- Issue date: 2021 Mar 1
- The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera).
- Authors: Luo S, Tang M, Frandsen PB, Stewart RJ, Zhou X
- Issue date: 2018 Dec 1
- Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera).
- Authors: Heckenhauer J, Frandsen PB, Gupta DK, Paule J, Prost S, Schell T, Schneider JV, Stewart RJ, Pauls SU
- Issue date: 2019 Dec 1
- Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects.
- Authors: Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B
- Issue date: 2019 Jan 9
- Multiple large-scale gene and genome duplications during the evolution of hexapods.
- Authors: Li Z, Tiley GP, Galuska SR, Reardon CR, Kidder TI, Rundell RJ, Barker MS
- Issue date: 2018 May 1
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Genome assembly of the JD17 soybean provides a new reference genome for comparative genomicsYi, X.; Liu, J.; Chen, S.; Wu, H.; Liu, M.; Xu, Q.; Lei, L.; Lee, S.; Zhang, B.; Kudrna, D.; et al. (Oxford Academic, 2022)Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromosome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with 3 published soybeans (WM82, ZH13, and W05), which identified 5 large inversions and 2 large translocations specific to JD17, 20,984-46,912 presence-absence variations spanning 13.1-46.9 Mb in size. A total of 1,695,741-3,664,629 SNPs and 446,689-800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research. © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.
Changes in the Genome: Polyploidy, Hybridization, and Genome Size Evolution Explored Through Selaginella and Vascular PlantsBarker, Michael S.; Baniaga, Anthony Ernest-Fiorentino; Ferriere, Regis; Robichaux, Robert H.; Sanderson, Michael J.; Worobey, Michael (The University of Arizona., 2019)The evolutionary processes responsible for generating and maintaining the remarkable diversity of life on earth are mutation, selection, drift, recombination, and gene flow. The relative magnitude of these processes, and their tempo, can be inferred from studying genomes or samples of the genome from individuals or multiple individuals. My dissertation focuses on three types of change in vascular plant genomes, with a focus on lycophytes in the genus Selaginella (Selaginellaceae). In Appendix A I characterize the extremely small genome sizes of Selaginella, and compare their observed disparity in genome size to other vascular plant clades. In Appendix B I examine the temporal activity of long terminal repeat retrotransposons (LTR-RTs) in vascular plants. I illustrate that across vascular plants LTR-RT activity largely explains the observed diversity in genome size. In Appendix C and D I focus on abrupt changes in the genome via polyploidy and hybridization. In Appendix C I demonstrate the importance of climatic niche divergence in polyploid plant species. In Appendix D I investigate the evidence of hybrid speciation in hybrids formed between Selaginella arizonica and S. eremophila in the Sonoran Desert. Using transcriptome sequencing and complementary morphological and ploidal inference, I suggest that both homoploid hybrid and allopolyploid species were formed from the same parents S. arizonica and S. eremophila. This system is the first known example of two types of stabilized hybrid derivatives from the same parents in natural populations.
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structureZuccolo, Andrea; Bowers, John; Estill, James; Xiong, Zhiyong; Luo, Meizhong; Sebastian, Aswathy; Goicoechea, Jose; Collura, Kristi; Yu, Yeisoo; Jiao, Yuannian; et al. (BioMed Central, 2011)BACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.RESULTS:Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.CONCLUSIONS:When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.