Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.

Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.

Arabidopsis thaliana has been used as a model species for research in a diverse collection of plant species. However, previous studies based on single reference genomes and short-read sequencing data are restricted to detecting variable genes and large structural variation (SV) underlying local adaptation. Here we de novo assemble high-quality chromosomal genomes of 38 A. thaliana ecotypes (with 6 relict ones) using PacBio-HiFi long-read sequencing. From these newly assembled genomes, we annotate several thousand new genes through pan-genomic analysis in comparison to the previous reference genome. The identified variable genes are mainly enriched in and associated with ecological adaptation and this species substantially expands its gene repertoire for local adaptation. We construct a graph-based pan-genome and identify 62,525 SVs which overlap with 14,243 genes. These genes are enriched in multiple ecological adaptation functions, including secondary metabolic processes, enzyme regulation, and biotic/abiotic stimulus. For example, a 566 bp insertion in the promoter of the light-adaptation KNAT3 gene was specific to the high-altitude relict Tibet-0 ecotype. This SV reduces the expression level of KNAT3 and promotes A. thaliana adaptation to habitats high in light radiation. In addition, compared with the SNPs, the SVs identified in this study captured the missing heritability and we detected novel SV associations with environmental variables in their native range, highlighting the value of SVs in environmental adaptation. The genome resources presented here will help pinpoint genetic changes that include both SVs and the ecotype-specific genes for local adaptation of A. thaliana and increase our understanding of the molecular mechanisms in this model species to respond to varied habitats.