A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China

Abstract

Tamarix austromongolica is endemic to the Yellow River Basin and has adapted to diverse ecological settings in the region, including the arid areas of northwestern China and the saline soil regions of the Yellow River Delta. However, the genetic basis of its local adaptation remains unclear. We report a chromosome-level assembly of the T. austromongolica genome based on PacBio high-fidelity sequencing and Hi-C technology. The 12 pseudochromosomes cover 98.44% of the 1.32 Gb assembly, with a contig N50 of 52.57 Mb and a BUSCO score of 98.2%. The genome comprises 913.6 Mb (68.83%) of repetitive sequences and 22,374 protein-coding genes. Genome evolution analyses suggest that genes under positive selection and significantly expanded gene families have facilitated T. austromongolica's adaptability to diverse environmental factors and high resistance to diseases. Using genotyping-by-sequencing, we conducted population structure and selection analyses of 114 samples from 15 sites. Two genetic groups were identified, and 114 and 289 candidate genes were assigned to the populations of the northwestern and eastern parts of the Yellow River, respectively. Furthermore, we discovered numerous candidate genes associated with high-altitude adaptability and salt tolerance. This research provides valuable genomic resources for the evolutionary study and genetic breeding of tamarisk.

Keywords: Tamarix austromongolica; chromosome-level genome assembly; local adaptation; population genetics.

Figure 1.

(A) Photograph of T. austromongolica; (B) leaf; (C) flower; and (D) fruit.

Figure 2.

(A) Landscape of the T. austromongolica genome. The tracks from the outer to the inner circles indicate the following: a, length of the genome for each chromosome; b, gene density; c, GC content; d, density of transposable elements; e, density of Copia elements; and f, density of Gypsy elements. (B) Heatmap showing Hi–C interactions at a resolution of 500 kb.

Figure 3.

(A) Chromosomal synteny blocks among V. vinifera, H. ammodendron, and T. austromongolica. Lines indicate the one versus one syntenic depth ratio between V. vinifera and H. ammodendron, and the two copies of T. austromongolica syntenic blocks per H. ammodendron. (B) The synonymous substitution rate (K_s) distribution of paralogous gene pairs in V. vinifera, H. ammodendron, and T. austromongolica. (C) Time-calibrated phylogenetic tree of T. austromongolica and 11 other species based on 539 single-copy orthogroup genes. The pie chart represents the number of gene family expansions and contractions. The node labels represent the inferred divergence times with 95% confidence intervals.

Figure 4.

(A) Map showing the sampling locations of T. austromongolica. (B) Phylogenetic tree of wild T. austromongolica constructed based on SNPs. (C) PCA plots of the first 2 principal components of the 114 accessions in the phylogenetic tree. (D) Population structure of wild T. austromongolica individuals based on ADMIXTURE analysis with K values of 2 and 3.

Figure 5.

Distribution of log₂π ratios and F_ST values between the northwestern Yellow River and eastern Yellow River populations. The dashed line indicates the threshold value (the top 5%) for the identification of selection signatures.