The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free‐living and major plant‐parasitic nematodes

Aphelenchoides besseyi is a plant‐parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides specie...

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Veröffentlicht in:Molecular ecology resources 2023-05, Vol.23 (4), p.905-919
Hauptverfasser: Lai, Cheng‐Kuo, Lee, Yi‐Chien, Ke, Huei‐Mien, Lu, Min R., Liu, Wei‐An, Lee, Hsin‐Han, Liu, Yu‐Ching, Yoshiga, Toyoshi, Kikuchi, Taisei, Chen, Peichen J., Tsai, Isheng Jason
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container_issue 4
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container_title Molecular ecology resources
container_volume 23
creator Lai, Cheng‐Kuo
Lee, Yi‐Chien
Ke, Huei‐Mien
Lu, Min R.
Liu, Wei‐An
Lee, Hsin‐Han
Liu, Yu‐Ching
Yoshiga, Toyoshi
Kikuchi, Taisei
Chen, Peichen J.
Tsai, Isheng Jason
description Aphelenchoides besseyi is a plant‐parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7–47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.
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subjects Animals
Annotations
Aphelenchoides
Chromosomes
comparative genomics
Gene transfer
Gene Transfer, Horizontal
Genes
genome reduction
Genomes
horizontal gene transfer
Horizontal transfer
Nematoda - genetics
Nematodes
Pathogenicity
Pathogens
Phylogeny
plant parasitism
Plant species
Plants - genetics
Plants - parasitology
Species
Strains (organisms)
Synteny
title The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free‐living and major plant‐parasitic nematodes
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