Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species

Asparagus kiusianus is a disease-resistant dioecious plant species and a wild relative of garden asparagus (A. officinalis). To enhance A. kiusianus genomic resources, advance plant science, and facilitate asparagus breeding, we determined the genome sequences of the male and female lines of A. kiusianus. Genome sequence reads obtained with a linked-read technology were assembled into four haplotype-phased contig sequences (~1.6 Gb each) for the male and female lines. The contig sequences were aligned onto the chromosome sequences of garden asparagus to construct pseudomolecule sequences. Approximately 55,000 potential protein-encoding genes were predicted in each genome assembly, and ~70% of the genome sequence was annotated as repetitive. Comparative analysis of the genomes of the two species revealed structural and sequence variants between the two species as well as between the male and female lines of each species. Genes with high sequence similarity with the male-specific sex determinant gene in A. officinalis, MSE1/AoMYB35/AspTDF1, were presented in the genomes of the male line but absent from the female genome assemblies. Overall, the genome sequence assemblies, gene sequences, and structural and sequence variants determined in this study will reveal the genetic mechanisms underlying sexual differentiation in plants, and will accelerate disease-resistance breeding in garden asparagus.

Genetic diversity and phylogenetic analysis in Asian and European Asparagus subgenus species

Garden asparagus (Asparagus officinalis L.) is a diploid (2n = 2x = 20), perennial and dioecious species belonging to Asparagus subgenus and worldwide cultivated as a vegetable crop. A narrow genetic base has been pointed out for the current cultivars. Crop wild related species (CWR) could be a valuable genetic resource in this crop but they have been underused up to now. To investigate the phylogenetic relationships between CWR asparagus species from different origin and A. officinalis L., 12 EST-SSR markers were used to assess the genetic variability of 20 accessions. These accessions belong to 10 Asparagus spp. from Asparagus subgenus including wild and naturalized A. officinalis L. (2x, 4x, 8x, 10x) and CWR species with European (A. tenuifolius Lam. (2x), A. pseudoscaber Grec. (6x), A. macrorrhizus Pedrol & al. (12x), A. prostratus Dumort (4x), A. brachyphyllus Turcz. (6x), A. maritimus (L.) Mill. (6x)) and Asian distribution (A. verticillatus L. (2x), A. persicus Baker (2x), A. breslerianus Schult. & Schult. (8x)). A. albus L. (2x) from the Protasparagus subgenus was used as outgroup. As a result, a total of 248 alleles were obtained and specific alleles of accessions were detected among them. After cluster analysis the accessions did not group by their geographical origin. All wild polyploid accessions with European and Asian distributions were grouped together with A. officinalis L. Hence, that cluster could be considered as the ‘officinalis group’ suggesting a monophyletic origin. The diploid accessions of A. verticillatus L. and A. persicus Baker clustered together and were the most genetically distant respect to ‘officinalis group’. The results obtained in this study may provide useful information to design new crosses among accessions aimed to develop new asparagus germplasm or pre-breeding populations.

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.

TGIF-DB: terse genomics interface for developing botany

Objectives Pearl millet (Pennisetum glaucum) is a staple cereal crop for semi-arid regions. Its whole genome sequence and deduced putative gene sequences are available. However, the functions of many pearl millet genes are unknown. Situations are similar for other crop species such as garden asparagus (Asparagus officinalis), chickpea (Cicer arietinum) and Tartary buckwheat (Fagopyrum tataricum). The objective of the data presented here was to improve functional annotations of genes of pearl millet, garden asparagus, chickpea and Tartary buckwheat with gene annotations of model plants, to systematically provide such annotations as well as their sequences on a website, and thereby to promote genomics for those crops. Data description Sequences of genomes and transcripts of pearl millet, garden asparagus, chickpea and Tartary buckwheat were downloaded from a public database. These transcripts were associated with functional annotations of their Arabidopsis thaliana and rice (Oryza sativa) counterparts identified by BLASTX. Conserved domains in protein sequences of those species were identified by the HMMER scan with the Pfam database. The resulting data was deposited in the figshare repository and can be browsed on the Terse Genomics Interface for Developing Botany (TGIF-DB) website (http://webpark2116.sakura.ne.jp/rlgpr/).