ArticleMolecular biology and evolution2019
Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed, 125 citations in OpenAlex.
- New annotations for three pea aphid genome assemblies allow comparative analyses of duplication and gene family evolution.G3 (Bethesda, Md.) · 2026Article
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- A chromatin accessibility map of pea aphid brain and embryo identifies tissue-specific regulatory elements.bioRxiv : the preprint server for biology · 2026Article
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- Genomic insights into clonal diversity in UK populations of the potato aphid, Macrosiphum euphorbiae.BMC genomics · 2025Article
- The Genetics of Host Plant Acceptance in Pea Aphids.Molecular ecology · 2025Article
- Hemipteran insects experience recurrent and synergistic molecular evolution adapting to diet shift.BMC biology · 2025Article
- Analysis of salivary proteins in gall-inducing psylla and their potential influence on host plants.BMC genomics · 2025Article
- Exploring the Satellitome of the Pest Aphid Acyrthosiphon pisum (Hemiptera, Aphididae): Insights Into Genome Organization and Intraspecies Evolution.Genome biology and evolution · 2025Article
- ArtSymbioCyc, a metabolic network database collection dedicated to arthropod symbioses: a case study, the tripartite cooperation inmSystems · 2025Article
- A comparative genomic analysis at the chromosomal-level reveals evolutionary patterns of aphid chromosomes.Communications biology · 2025Article
- A chromosome-level genome assembly of the cabbage aphid Brevicoryne brassicae.Scientific data · 2025Article
- Functional analysis and interaction networks of Rboh in poplar under abiotic stress.Frontiers in plant science · 2025Article
- Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes.BMC genomics · 2024Article
- A pipeline contributes to efficient identification of salivary proteins in short-headed planthopper, Epeurysa nawaii.Scientific reports · 2024Article
- Transcriptomic basis of sex loss in the pea aphid.BMC genomics · 2024Article
- Genomic and Transcriptomic Insights into the Genetic Basis of Foam Secretion in Rice SpittlebugInternational journal of molecular sciences · 2024Article
- Chromosome-Level Genome Assembly and Annotation of a Periodical Cicada Species: Magicicada septendecula.Genome biology and evolution · 2024Article
- The nutritional dimension of facultative bacterial symbiosis in aphids: Current status and methodological considerations for future research.Current research in insect science · 2024Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome structural variations, including duplications, deletions, insertions, and inversions, are central in the evolution of eukaryotic genomes. However, structural variations present challenges for high-quality genome assembly, hampering efforts to understand the evolution of gene families and genome architecture. An example is the genome of the pea aphid (Acyrthosiphon pisum) for which the current assembly is composed of thousands of short scaffolds, many of which are known to be misassembled. Here, we present an improved version of the A. pisum genome based on the use of two long-range proximity ligation methods. The new assembly contains four long scaffolds (40-170 Mb), corresponding to the three autosomes and the X chromosome of A. pisum, and encompassing 86% of the new assembly. Assembly accuracy is supported by several quality assessments. Using this assembly, we identify the chromosomal locations and relative ages of duplication events, and the locations of horizontally acquired genes. The improved assembly illuminates the mode of gene family evolution by providing proximity information between paralogs. By estimating nucleotide polymorphism and coverage depth from resequencing data, we determined that many short scaffolds not assembling to chromosomes represent hemizygous regions, which are especially frequent on the highly repetitive X chromosome. Aligning the X-linked aphicarus region, responsible for male wing dimorphism, to the new assembly revealed a 50-kb deletion that cosegregates with the winged male phenotype in some clones. These results show that long-range scaffolding methods can substantially improve assemblies of repetitive genomes and facilitate study of gene family evolution and structural variation.
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