Genomic changes and stabilization following homoploid hybrid speciation of the Oxford ragwort Senecio squalidus

被引:0
作者
Nevado, Bruno [1 ,2 ,3 ,4 ]
Chapman, Mark A. [5 ]
Brennan, Adrian C. [6 ]
Clark, James W. [1 ,7 ]
Wong, Edgar L. Y. [1 ]
Batstone, Tom [7 ]
McCarthy, Shane A. [8 ]
Tracey, Alan [8 ]
Torrance, James [8 ]
Sims, Ying [8 ]
Abbott, Richard J. [9 ]
Filatov, Dmitry [1 ]
Hiscock, Simon J. [1 ,10 ]
机构
[1] Univ Oxford, Dept Biol, Oxford OX1 3RB, England
[2] Univ Lisbon, Fac Sci, Ctr Ecol Evolut & Environm Changes cE3c, P-1749016 Lisbon, Portugal
[3] Univ Lisbon, CHANGE Global Change & Sustainabil Inst, Fac Sci, P-1749016 Lisbon, Portugal
[4] Univ Lisbon, Fac Sci, Dept Anim Biol, P-1749016 Lisbon, Portugal
[5] Univ Southampton, Sch Biol Sci, Southampton SO17 1BJ, England
[6] Univ Durham, Biosci Dept, Durham DH1 3LE, England
[7] Univ Bath, Milner Ctr Evolut, Dept Life Sci, Bath BA2 7AY, England
[8] Wellcome Sanger Inst, Cambridge CB10 1SA, England
[9] Univ St Andrews, Sch Biol, St Andrews KY16 9ST, Scotland
[10] Univ Oxford, Bot Garden & Arboretum, Rose Lane, Oxford OX1 4AZ, England
基金
英国自然环境研究理事会; 英国惠康基金;
关键词
SPOROPHYTIC SELF-INCOMPATIBILITY; POPULATION-GENETICS; L; ASTERACEAE; MOUNT-ETNA; SEQUENCE ALIGNMENT; BRITISH-ISLES; HYBRIDIZATION; RECOMBINATION; ANNOTATION; DIVERGENCE;
D O I
10.1016/j.cub.2024.08.009
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Oxford ragwort ( Senecio squalidus) ) is one of only two homoploid hybrid species known to have originated very recently, so it is a unique model for determining genomic changes and stabilization following homoploid hybrid speciation. Here, we provide a chromosome-level genome assembly of S. squalidus with 95% of the assembly contained in the 10 longest scaffolds, corresponding to its haploid chromosome number. We annotated 30,249 protein-coding genes and estimated that '62% of the genome consists of repetitive elements. We then characterized genome-wide patterns of linkage disequilibrium, polymorphism, and divergence in S. squalidus and its two parental species, finding that (1) linkage disequilibrium is highly heterogeneous, with a region on chromosome 4 showing increased values across all three species but especially in S. squalidus; ; (2) regions harboring genetic incompatibilities between the two parental species tend to be large, show reduced recombination, and have lower polymorphism in S. squalidus; ; (3) the two parental species have an unequal contribution (70:30) to the genome of S. squalidus, , with long blocks of parent-specific ancestry supporting a very rapid stabilization of the hybrid lineage after hybrid formation; and (4) genomic regions with major parent ancestry exhibit an overrepresentation of loci with evidence for divergent selection occurring between the two parental species on Mount Etna. Our results show that both genetic incompatibilities and natural selection play a role in determining genome-wide reorganization following hybrid speciation and that patterns associated with homoploid hybrid speciation-typically seen in much older systems-can evolve very quickly following hybridization.
引用
收藏
页码:4412 / 4423.e5
页数:18
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