Chromosome-level genome assembly,annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

Asparagus setaceus is a popular ornamental plant cultivated in tropical and subtropical regions globally.Here,we constructed a chromosome-scale reference genome of A.setaceus to facilitate the investigation of its genome characteristics and evolution.Using a combination of Nanopore long reads,Illumina short reads,10×Genomics linked reads,and Hi-C data,we generated a high-quality genome assembly of A.setaceus covering 710.15 Mb,accounting for 98.63%of the estimated genome size.A total of 96.85%of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes.The genome of A.setaceus was predicted to contain 28,410 genes,25,649(90.28%)of which were functionally annotated.A total of 65.59%of the genome was occupied by repetitive sequences,among which long terminal repeats were predominant(42.51%of the whole genome).Evolutionary analysis revealed an estimated divergence time of A.setaceus from its close relative A.officinalis of~9.66 million years ago,and A.setaceus underwent two rounds of whole-genome duplication.In addition,762 specific gene families,96 positively selected genes,and 76 resistance(R)genes were detected and functionally predicted in A.setaceus.These findings provide new knowledge about the characteristics and evolution of the A.setaceus genome,and will facilitate comparative genetic and genomic research on the genus Asparagus.

DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus

DNA methylation is a crucial regulatory mechanism in many biological processes.However,limited studies have dissected the contribution of DNA methylation to sexual differentiation in dioecious plants.In this study,we investigated the variances in methylation and transcriptional patterns of male and female flowers of garden asparagus.Compared with male flowers,female flowers at the same stages showed higher levels of DNA methylation.Both male and female flowers gained DNA methylation globally from the premeiotic to meiotic stages.Detailed analysis revealed that the increased DNA methylation was largely due to increased CHH methylation.Correlation analysis of differentially expressed genes and differentially methylated regions suggested that DNA methylation might not have contributed to the expression variation of the sex-determining genes SOFF and TDF1 but probably played important roles in sexual differentiation and flower development of garden asparagus.The upregulated genes AoMS1,AoLAP3,AoAMS,and AoLAP5 with varied methylated CHH regions might have been involved in sexual differentiation and flower development of garden asparagus.Plant hormone signaling genes and transcription factor genes also participated in sexual differentiation and flower development with potential epigenetic regulation.In addition,the CG and CHG methylation levels in the Y chromosome were notably higher than those in the X chromosome,implying that DNA methylation might have been involved in Y chromosome evolution.These data provide insights into the epigenetic modification of sexual differentiation and flower development and improve our understanding of sex chromosome evolution in garden asparagus.