Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(2)

Published: Feb. 1, 2024

Advances in genomic studies have revealed that hybridization nature is pervasive and raised questions about the dynamics of different genetic evolutionary factors following initial event. While recent research has proposed outcomes might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated introgression between 2 divergent lineages 9-spined sticklebacks (Pungitius pungitius) Baltic Sea. We found intensity direction selection on introgressed variation varied across elements: while functionally important regions displayed reduced rates introgression, promoter showed enrichment. Despite general trend negative selection, identified specific were enriched for variants, within these regions, detected footprints indicating adaptive introgression. Geographically, against functional changes strongest vicinity secondary contact zone weaken as a function distance from contact. Altogether, results suggest stabilization genomes complex, multistage process involving both positive selection. In spite predominance also evidence variants likely associated with adaptation Sea environmental conditions.

Language: Английский

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The western redcedar genome reveals low genetic diversity in a self-compatible conifer

Genome Research, Journal Year: 2022, Volume and Issue: unknown

Published: Sept. 15, 2022

We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species Cupressaceae. The assembly, derived from a uniquely inbred tree produced through five generations self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one most assemblies for conifer. Population genomic analysis revealed WRC genetically depauperate wild plant species, with effective population size approximately 300 no significant genetic differentiation across its geographic range. Nucleotide diversity, π, is low continuous many loci showing zero ratio π at zero- fourfold degenerate sites relatively high (approximately 0.33), suggestive weak purifying selection. Using array lines up selfing, we explored relationship between diversity mating system. Although overall heterozygosity found decline faster than expected during persisted loci, nearly 100 were deviate expectations drift, associative overdominance. Nonreference alleles such often harbor deleterious mutations are rare in natural populations, implying that balanced polymorphisms maintained linkage dominant beneficial alleles. This may account how remains responsive artificial selection, despite diversity.

Language: Английский

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Genomic analyses reveal dead‐end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation

The Plant Journal, Journal Year: 2023, Volume and Issue: 115(6), P. 1528 - 1543

Published: June 1, 2023

SUMMARY Despite the importance of hybridization in evolution, evolutionary consequence homoploid hybridizations plants remains poorly understood. Specially, events have been rarely documented due to a lack genomic resources and methodological limitations. Actinidia zhejiangensis was suspected arisen from eriantha hemsleyana or rufa . However, this species very rare nature exhibited sympatric distribution with its potential parent species, which implied it might be spontaneous hybrid ongoing hybridization. Here, we illustrate dead‐end basis isolating barriers between A. through whole genome sequencing population analyses. Chromosome‐scale assemblies were generated. The chromosomes are confidently assigned two haplomes, one them originates other Whole resequencing data reveal that mainly F 1 hybrids gene flow initiated about 0.98 million years ago, implying both strong genetic these deeply divergent kiwifruit species. Five inversions containing genes involved pollen germination tube growth account for fertility breakdown distinct morphological traits long recurrent origination, does not initiate speciation. Collectively, our study provides new insights into functional studies kiwifruit.

Language: Английский

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The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon)

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 193, P. 108013 - 108013

Published: Jan. 7, 2024

Language: Английский

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Haplotype-resolved genome assembly of poplar line NL895 provides a valuable tree genomic resource

Forestry Research, Journal Year: 2024, Volume and Issue: 4(1), P. 0 - 0

Published: Jan. 1, 2024

Poplar line NL895 can potentially become a model plant for poplar study as it is widely cultivated elite line. However, the lack of genome resources hindered use major material in poplar. In this study, we provided high-quality assembly with PacBio single molecule real-time (SMRT) sequencing and High-throughput chromosome conformation capture (Hi-C) technology. The raw diploid included 606 contigs total size ~815 Mb, monoploid 246 ~412 Mb. haplotype-resolved chromosomes genomes were also generated. All monoploid, diploid, showed more than 97% completeness they largely improve mapping efficiency RNA-Seq analysis. By comprehensively comparing two haplotype found heterozygosity much higher other lines. We that harbors genomic variants gene diversity. haplotype-specific genes variable expression patterns. These characters would be attributed to high heterosis NL895. allele-specific (ASE) was investigated lots alleles biased expressions different tissues or environmental conditions. Taken together, sequence valuable tree resource greatly facilitate studies

Language: Английский

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The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil Camellia plants

Cell Reports, Journal Year: 2024, Volume and Issue: 43(11), P. 114902 - 114902

Published: Oct. 25, 2024

Language: Английский

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A New Pattern of Species Diversification Revealed by Populus on the Qinghai-Tibet Plateau

Evolutionary Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Language: Английский

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The population chloroplast genomes of Populus reveal the phylogenetic relationship between three new taxa of sect. Leucoides and their parents

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 17, 2025

Poplars are important woody plants, which widely distributed in the forests from subtropics to north of Northern Hemisphere. have high ecological and economic value. However, there frequent interspecific intraspecific hybrids Populus, resulting a large number intermediate taxa, makes morphological identification Populus very challenging. Plastid genome is an tool study evolutionary relationship plants. Therefore, comparison phylogenetic analysis were carried out based on population chloroplast genomes 34 individuals 7 taxa. In this study, seven newly assembled annotated reported. They all had typical quadripartite structures with same GC content (37.6%), but differences within population, size ranged 155,736 bp 156,812 bp. species, 134 genes identified, including 88 protein coding (PCGs), 37 tRNA 8 rRNA genes. The gene sequences alignment different taxa showed that relatively conservative, was no rearrangement, only 3 highly variable regions (psbZ-trnG, ndhC-trnV trnN-trnR) can be used as molecular markers. Most PCGs codon usage bias positive selection (rps7, rps12 rpl16) been identified. genetic structure phylogeny supported monophyletic taxon, could divided into four sections (Abaso, Turanga, ATL (Aigeiros, Tacamahaca Leucoides)). Among them, P. dafengensis, butuoensis szechuanica closest relationship, gonggaensis cathayana it speculated Sect. may main female parent three new Leucoides. general, provides valuable insights for species identification, relationships, breeding resource development, diversity Populus.

Language: Английский

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Genomic Insights Into Introgression Between Quercus aquifolioides and Its Sympatric Relatives Across Elevational Gradients

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 4, 2025

Geographically widespread species tend to have more opportunities hybridise with different related species. However, the evolutionary consequences of such multi-species hybridisation are still poorly understood. In Hengduan Mountains southwest China, Quercus aquifolioides and its closely form two types elevational hybrid zone in geographical areas (i.e., Q. aquifolioides-Q. guyavaefolia-Q. longispica spinosa). Here, we investigated genome-wide patterns introgression between sympatric relatives assess hybridisation. A new assembled genome as a reference whole-genome resequencing data these focal oaks were used this study. Our results showed that bidirectional gene flow occurred relatives, candidate genomic regions derived from broadly distributed across oak genome. Local has fuelled intraspecific divergence compositions. We found signatures positive selection some introgressed regions. Putative adaptation signals detected genes diverse functions, including stress response organism development growth. addition, identified targets environment-associated aquifolioides, which located sum, study demonstrates local is non-negligible mechanism facilitating reveals putative adaptive relatives.

Language: Английский

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Genomic introgression underlies environmental adaptation in three species of Chinese wingnuts, Pterocarya

Plant Diversity, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

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