References

Fast model-based estimation of ancestry in unrelated individuals

10.1101/gr.094052.109 · 2009 · External reference

Major impacts of widespread structural variation on gene expression and crop improvement in tomato

10.1016/j.cell.2020.05.021 · 2020 · External reference

A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes

10.1016/j.xplc.2026.101814 · 2026 · External reference

Tandem repeats finder: a program to analyze DNA sequences

10.1093/nar/27.2.573 · 1999 · External reference

The InterPro protein families and domains database: 20 years on

10.1093/nar/gkaa977 · 2021 · External reference

Scots pine—panmixia and the elusive signal of genetic adaptation

10.1111/nph.19563 · 2024 · External reference

eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale

10.1093/molbev/msab293 · 2021 · External reference

Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis

10.1038/s41477-023-01565-z · 2023 · External reference

Fastp: an ultra-fast all-in-one FASTQ preprocessor

10.1093/bioinformatics/bty560 · 2018 · External reference

Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis

10.1186/s13059-021-02392-1 · 2021 · External reference

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

10.4161/fly.19695 · 2012 · External reference

UpSetR: an R package for the visualization of intersecting sets and their properties

10.1093/bioinformatics/btx364 · 2017 · External reference

The variant call format and VCFtools

10.1093/bioinformatics/btr330 · 2011 · External reference

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

10.1101/gr.244939.118 · 2019 · External reference

NanoPack: visualizing and processing long-read sequencing data

10.1093/bioinformatics/bty149 · 2018 · External reference

SweepFinder2: increased sensitivity, robustness and flexibility

10.1093/bioinformatics/btw051 · 2016 · External reference

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

10.1111/mec.15565 · 2020 · External reference

A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline

10.1186/s13059-024-03239-1 · 2024 · External reference

Truvari: refined structural variant comparison preserves allelic diversity

10.1186/s13059-022-02840-6 · 2022 · External reference

Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau

10.1111/j.1365-294x.2012.05712.x · 2012 · External reference

Variation graph toolkit improves read mapping by representing genetic variation in the reference

10.1038/nbt.4227 · 2018 · External reference

Adaptation repeatedly uses complex structural genomic variation

10.1126/science.adp3745 · 2025 · External reference

A pangenome reference of wild and cultivated rice

10.1038/s41586-025-08883-6 · 2025 · External reference

Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau

10.1016/j.xplc.2023.100574 · 2023 · External reference

Divergent patterns between phenotypic and genetic variation in Scots pine

10.1016/j.xplc.2020.100139 · 2021 · External reference

Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree

10.1073/pnas.2102914118 · 2021 · External reference

Impact of whole-genome duplications on structural variant evolution in Cochlearia

10.1038/s41467-024-49679-y · 2024 · External reference

Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa

10.1038/s41588-025-02164-8 · 2025 · External reference

SVIM: structural variant identification using mapped long reads

10.1093/bioinformatics/btz041 · 2019 · External reference

Genotyping structural variants in pangenome graphs using the vg toolkit

10.1186/s13059-020-1941-7 · 2020 · External reference

Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora

10.1038/s41588-024-01944-y · 2024 · External reference

Long-read-based human genomic structural variation detection with cuteSV

10.1186/s13059-020-02107-y · 2020 · External reference

Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines

10.1073/pnas.2022302118 · 2021 · External reference

Mobile elements: drivers of genome evolution

10.1126/science.1089670 · 2004 · External reference

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

10.1093/bioinformatics/btr509 · 2011 · External reference

Minimap2: pairwise alignment for nucleotide sequences

10.1093/bioinformatics/bty191 · 2018 · External reference

Fast and accurate short read alignment with Burrows-Wheeler transform

10.1093/bioinformatics/btp324 · 2009 · External reference

Local PCA shows how the effect of population structure differs along the genome

10.1534/genetics.118.301747 · 2019 · External reference

Pan-genome analysis reveals the evolution and diversity of Malus

10.1038/s41588-025-02166-6 · 2025 · External reference

Ecophysiological transition mediated by hybridization in a hybrid pine species complex

10.1016/j.pld.2025.05.009 · 2025 · External reference

Pan-genome analysis reveals local adaptation to climate driven by introgression in oak species

10.1093/molbev/msaf088 · 2025 · External reference

Pan-genome of wild and cultivated soybeans

10.1016/j.cell.2020.05.023 · 2020 · External reference

Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data

10.1038/s41467-024-46614-z · 2024 · External reference

Grapevine pangenome facilitates trait genetics and genomic breeding

10.1038/s41588-024-01967-5 · 2024 · External reference

From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes

10.1038/s41586-025-09637-0 · 2025 · External reference

Dynamics of genome evolution in the era of pangenome analysis

10.1016/j.xgen.2025.101067 · 2026 · External reference

Complex genetic variation in nearly complete human genomes

10.1038/s41586-025-09140-6 · 2025 · External reference

Structural variant calling: the long and the short of it

10.1186/s13059-019-1828-7 · 2019 · External reference

Empirical assessment of the reproductive fitness components of the hybrid pine on the Tibetan Plateau

10.1007/s10682-008-9244-6 · 2009 · External reference

Distinct niche divergence characterizes the homoploid hybrid speciation of Pinus densata on the Tibetan Plateau

10.1086/658905 · 2011 · External reference

A roadmap for understanding the evolutionary significance of structural genomic variation

10.1016/j.tree.2020.03.002 · 2020 · External reference

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

10.1371/journal.pgen.1011086 · 2023 · External reference

A genome sequence for the threatened whitebark pine

10.1093/g3journal/jkae061 · 2024 · External reference

The Chinese pine genome and methylome unveil key features of conifer evolution

10.1016/j.cell.2021.12.006 · 2022 · External reference

The Norway spruce genome sequence and conifer genome evolution

10.1038/nature12211 · 2013 · External reference

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

10.1186/s13059-019-1905-y · 2019 · External reference

PLINK: a tool set for whole-genome association and population-based linkage analyses

10.1086/519795 · 2007 · External reference

BEDTools: a flexible suite of utilities for comparing genomic features

10.1093/bioinformatics/btq033 · 2010 · External reference

A super pan-genomic landscape of rice

10.1038/s41422-022-00685-z · 2022 · External reference

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

10.1016/j.molp.2024.03.009 · 2024 · External reference

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

10.1126/science.abg8871 · 2021 · External reference

Detection of mosaic and population-level structural variants with Sniffles2

10.1038/s41587-023-02024-y · 2024 · External reference

Cytoplasmic composition in Pinus densata and population establishment of the diploid hybrid pine

10.1046/j.1365-294x.2003.01962.x · 2003 · External reference

Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination

10.1093/nar/gku1394 · 2015 · External reference

Sequence of the sugar pine megagenome

10.1534/genetics.116.193227 · 2016 · External reference

A beginner's guide to structural variants in eco-evolutionary population genomics

10.1111/mec.70216 · 2026 · External reference

REVIGO summarizes and visualizes long lists of gene ontology terms

10.1371/journal.pone.0021800 · 2011 · External reference

Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration

10.1093/bib/bbs017 · 2013 · External reference

Massive haplotypes underlie ecotypic differentiation in sunflowers

10.1038/s41586-020-2467-6 · 2020 · External reference

Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata

10.1111/j.1365-294x.2011.05157.x · 2011 · External reference

Hybridization and chloroplast DNA variation in a Pinus species complex from Asia

10.1111/j.1558-5646.1994.tb05290.x · 1994 · External reference

Human structural variation: mechanisms of chromosome rearrangements

10.1016/j.tig.2015.05.010 · 2015 · External reference

Going beyond SNPs: the role of structural genomic variants in adaptive evolution and species diversification

10.1111/mec.15066 · 2019 · External reference

clusterProfiler 4.0: a universal enrichment tool for interpreting omics data

10.1016/j.xinn.2021.100141 · 2021 · External reference

UV-B-induced molecular mechanisms of stress physiology responses in the major northern Chinese conifer Pinus tabuliformis Carr

10.1093/treephys/tpaa180 · 2021 · External reference

A pangenome of maize provides genetic insights into drought resistance

10.1038/s41588-025-02378-w · 2025 · External reference

High-quality genome of a modern soybean cultivar and resequencing of 547 accessions provide insights into the role of structural variation

10.1038/s41588-024-01901-9 · 2024 · External reference

Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions

10.1038/s41588-024-01957-7 · 2024 · External reference

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

10.1038/s41588-018-0041-z · 2018 · External reference

Effects of landscapes and range expansion on population structure and local adaptation

10.1111/nph.16619 · 2020 · External reference

Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow

10.1111/nph.19694 · 2024 · External reference

Graph pangenome captures missing heritability and empowers tomato breeding

10.1038/s41586-022-04808-9 · 2022 · External reference