Genomic divergence between two sister <i>Ostrya</i> species through linked selection and recombination

Zhang, Jin; Zhang, Shangzhe; Zheng, Zeyu; Lu, Zhiqiang; Yang, Yongzhi

doi:10.1002/ece3.9611

Cited by 3 publications

(1 citation statement)

References 78 publications

(124 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…If the status of an SV remains uncertain, inferences of its impact on divergence and adaptation are difficult. Analysing the genomic differences between recently diverged species has revealed genome regions involved in reproductive isolation (Hejase et al, 2020), adaptive genes (Eshel et al, 2021), and the genome-wide landscape of diversification between and within chromosomes (Henderson & Brelsford, 2020;Piatkowski et al, 2023;Zhang et al, 2022). Here using two closely related Eucalyptus species, E. melliodora and E. sideroxylon (Ferguson et al, 2023;Thornhill et al, 2019), we genotype SVs within their respective populations and calculate their rates of population variability.…”

Section: Introductionmentioning

confidence: 99%

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

Ferguson,

Jones,

Murray

et al. 2023

Preprint

View full text Add to dashboard Cite

Structural variants (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely related Eucalyptus species to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences, or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals of E. melliodora and E. sideroxylon, along with recent high quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads, in E. melliodora and E. sideroxylon respectively. Focusing on inversions and translocations, symmetric SVs which are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.

show abstract

Section: Introductionmentioning

confidence: 99%

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

Ferguson,

Jones,

Murray

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus

Ferguson,

Jones,

Murray

et al. 2024

GigaScience

View full text Add to dashboard Cite

Structural variations (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely related Eucalyptus species to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals of Eucalyptus melliodora and Eucalyptus sideroxylon, along with recent high-quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads in E. melliodora and E. sideroxylon, respectively. Focusing on inversions and translocations, symmetric SVs that are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.

show abstract

Characterising the Genomic Landscape of Differentiation Between Annual and Perennial Rye

Waesch,

Pfeifer,

Dreissig

2024

Evolutionary Applications

View full text Add to dashboard Cite

Annuality and perenniality represent two different life‐history strategies in plants, and an analysis of genomic differentiation between closely related species of different life histories bears the potential to identify the underlying targets of selection. Additionally, understanding the interactions between patterns of recombination and signatures of natural selection is a central aim in evolutionary biology, because patterns of recombination shape the evolution of genomes by affecting the efficacy of selection. Here, our aim was to characterise the landscape of genomic differentiation between weedy annual rye (Secale cereale L.) and wild perennial rye (Secale strictum C. Presl), and explore the extent to which signatures of selection are influenced by recombination rate variation. We used population‐level sequence data of annual and perennial rye to analyse population structure and their demographic history. Based on our analyses, annual and perennial rye diverged approximately 26,500 years ago (ya) from an ancestral population size of ~85,000 individuals. We analysed patterns of genetic diversity and genetic differentiation, and found highly differentiated regions located in low‐recombination regions, indicative of linked selection. Although all highly differentiated regions, as revealed by FST‐outlier scans, were located in low‐recombining regions, not all chromosomes showed this tendency. We therefore performed a gene ontology enrichment analysis, which showed that highly differentiated regions comprise genes involved in photosynthesis. This enrichment was confirmed when FST outlier scans were performed separately in low‐ and intermediate‐recombining regions, but not in high‐recombining regions, suggesting that local recombination rate variation in rye affects outlier scans. Cultivated rye is an annual crop, but the introduction of perenniality may be advantageous in regions with poor soil quality or under low‐input farming. Although the resolution of our analysis is limited to a broad‐scale, knowledge about the evolutionary divergence between annual and perennial rye might support breeding efforts towards perennial rye cultivation.

show abstract

Genomic divergence between two sister Ostrya species through linked selection and recombination

Cited by 3 publications

References 78 publications

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus

Characterising the Genomic Landscape of Differentiation Between Annual and Perennial Rye

Contact Info

Product

Resources

About