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Copeland M, Landa S, Owoyemi A, Jonika MM, Alfieri J, Sylvester T, Hoover Z, Hjelmen CE, Spencer Johnston J, Kyre BR, Rieske LK, Blackmon H, Casola C. Genome assembly of the southern pine beetle ( Dendroctonus frontalis Zimmerman) reveals the origins of gene content reduction in Dendroctonus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.592785. [PMID: 38766115 PMCID: PMC11100688 DOI: 10.1101/2024.05.08.592785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Dendroctonus frontalis, also known as southern pine beetle (SPB), represents the most damaging forest pest in the southeastern United States. Strategies to predict, monitor and suppress SPB outbreaks have had limited success. Genomic data are critical to inform on pest biology and to identify molecular targets to develop improved management approaches. Here, we produced a chromosome-level genome assembly of SPB using long-read sequencing data. Synteny analyses confirmed the conservation of the core coleopteran Stevens elements and validated the bona fide SPB X chromosome. Transcriptomic data were used to obtain 39,588 transcripts corresponding to 13,354 putative protein-coding loci. Comparative analyses of gene content across 14 beetle and 3 other insects revealed several losses of conserved genes in the Dendroctonus clade and gene gains in SPB and Dendroctonus that were enriched for loci encoding membrane proteins and extracellular matrix proteins. While lineage-specific gene losses contributed to the gene content reduction observed in Dendroctonus, we also showed that widespread misannotation of transposable elements represents a major cause of the apparent gene expansion in several non-Dendroctonus species. Our findings uncovered distinctive features of the SPB gene complement and disentangled the role of biological and annotation-related factors contributing to gene content variation across beetles.
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Affiliation(s)
- Megan Copeland
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Shelby Landa
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Adekola Owoyemi
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | | | - Jamie Alfieri
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Terrence Sylvester
- Department of Biological Sciences, The University of Memphis, Memphis, TN, USA
| | - Zachary Hoover
- Department of Biochemistry, Texas A&M University, College Station, TX, USA
| | - Carl E. Hjelmen
- Department of Biology, Utah Valley University, Orem, UT, USA
| | | | - Bethany R. Kyre
- USDA Forest Service, Forest Health Protection, San Bernardino, CA, USA
| | - Lynne K. Rieske
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, USA
- Interdisciplinary Doctoral Degree Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, USA
- Interdisciplinary Doctoral Degree Program in Genetics and Genomics, Texas A&M University, College Station, USA
| | - Claudio Casola
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
- Interdisciplinary Doctoral Degree Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, USA
- Interdisciplinary Doctoral Degree Program in Genetics and Genomics, Texas A&M University, College Station, USA
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Perry A, Eddelbuettel D, Rosenthal G, Blackmon H. Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short-read data. Mol Ecol Resour 2024; 24:e13933. [PMID: 38299378 PMCID: PMC10994724 DOI: 10.1111/1755-0998.13933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
Highly polymorphic markers, such as microsatellites, are invaluable for the study of natural populations. However, contemporary methods for genotyping highly polymorphic variants have serious drawbacks that impede their efficiency. We created Polly, an R package with C++ source code that uses Illumina short-read data to genotype microsatellites, detect highly polymorphic variants and identify clusters of highly polymorphic SNPs, indels and microsatellites. We tested Polly on short-read data from Xiphophorus birchmanni (Teleostei: Poeciliidae) and Arabidopsis thaliana, finding it to be efficient and accurate both for microsatellite genotyping and polymorphic marker detection. This program can be applied to any diploid population for which there exists short-read data and at least one scaffolded reference genome.
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Affiliation(s)
- Annabel Perry
- Harvard University, Department of Human Evolutionary Biology
- Texas A&M University, Department of Biology
| | | | - Gil Rosenthal
- Texas A&M University, Department of Biology
- Università degli Studi di Padova, Dipartimento di Biologia
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Sylvester T, Adams R, Hunter WB, Li X, Rivera-Marchand B, Shen R, Shin NR, McKenna DD. The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes. J Hered 2024; 115:94-102. [PMID: 37878740 DOI: 10.1093/jhered/esad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/14/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
The Diaprepes root weevil (DRW), Diaprepes abbreviatus, is a broadly polyphagous invasive pest of agriculture in the southern United States and the Caribbean. Its genome was sequenced, assembled, and annotated to study genomic correlates of specialized plant-feeding and invasiveness and to facilitate the development of new methods for DRW control. The 1.69 Gb D. abbreviatus genome assembly was distributed across 653 contigs, with an N50 of 7.8 Mb and the largest contig of 62 Mb. Most of the genome was comprised of repetitive sequences, with 66.17% in transposable elements, 5.75% in macrosatellites, and 2.06% in microsatellites. Most expected orthologous genes were present and fully assembled, with 99.5% of BUSCO genes present and 1.5% duplicated. One hundred and nine contigs (27.19 Mb) were identified as putative fragments of the X and Y sex chromosomes, and homology assessment with other beetle X chromosomes indicated a possible sex chromosome turnover event. Genome annotation identified 18,412 genes, including 43 putative horizontally transferred (HT) loci. Notably, 258 genes were identified from gene families known to encode plant cell wall degrading enzymes and invertases, including carbohydrate esterases, polysaccharide lyases, and glycoside hydrolases (GH). GH genes were unusually numerous, with 239 putative genes representing 19 GH families. Interestingly, several other beetle species with large numbers of GH genes are (like D. abbreviatus) successful invasive pests of agriculture or forestry.
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Affiliation(s)
- Terrence Sylvester
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Richard Adams
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, United States
- Agricultural Statistics Laboratory, University of Arkansas, Fayetteville, AR, United States
| | - Wayne B Hunter
- USDA, ARS, U. S. Horticultural Research Laboratory, Fort Pierce, FL 34945, United States
| | - Xuankun Li
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Bert Rivera-Marchand
- Office of Academic Affairs, Polk State College, Lakeland Campus, Lakeland, FL, 33803, United States
| | - Rongrong Shen
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Na Ra Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, United States
- Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, United States
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Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution. Genes (Basel) 2020; 11:genes11080945. [PMID: 32824315 PMCID: PMC7464534 DOI: 10.3390/genes11080945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 01/02/2023] Open
Abstract
Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes.
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