Chromosome-level genomes of three key_231116.pptx

genomes assembly

1. Presented by: Wiwit Probowati

2. Introduction Allium species (family-Amaryllidaceae): a group of plant with tremendous value as crops, spices, medicinal material and ornamentals. The hallmark flavour  sulfur-containing compounds (allicin and isoallicin )  catalyzed by hydrolyzing enzimes such as alliinase and lacrimal factor synthase. These closely related Allium species with diverse flavour compounds evolved remains a fundamental unresolved question in plant biology and horticulture. High-quality reference genomes and mapping phenotype variation to genes is important to accelerate Allium crop breeding. A.fistulosum A.cepa A.sativum African lily (Agapanthus africanus

3. Chromosome-level genome assembly The contig N50 sizes of three Allium species were not only the highest among recently published Allium assemblies but also the highest recorded for plant with large genomes. The QV of the genome assemblies of the three Allium species and African lily (55.38-69.61) indicate very high base accuracy. Annotation of the assemblies found telomeric repeats at many chromosomal ends, suggesting the chromosome assemblies are of high quality.

4. Evolution of three Allium species Fig. 1. Evolution of Allium and African lily genomes. Overview of Allium species and African lily genomes. Interaction map of Hi-C data of four species. Maximum-likelihood phylogenetic tree from single-copy ortholog genes of ten plant species dated with fossil calibration. Synteny patterns between genomic regions from three Allium species

5. Allium -specific polyploidization events Fig.2 . Comparative genomic analyses. Synteny blocks within the African lily genome (left) and between Welsh onion and African lily genomes (right). Alignment of homologous genomic fragments among A. trichopoda , Welsh onion and African lily. Gaussian fitting of average synonymous substitution rate (Ks) distribution of gene pairs in syntenic blocks in four monocot species.

6. Evolution of allicin/ isoallicin pathway in Allium Fig.3 .Insights into allicin/ isoallicin biosynthesis. Putative biosynthetic pathway of allicin and isoallicin in Allium plants. Copy number of homologous genes involved in biosynthesis of allicin and isoallicin in 21 representative species. Characterization of alliinase gene family. Specific mutation in Allium AcpPCS1 and AcpGGT3.

7. Spatial pattern of secondary metabolism in onion bulbs Fig.4 .Spatial RNA-seq reveals spatial distribution of gene expression in metabolic process and onion bulb formation. a. Unsupervised clustering of three consecutive period onion bulbs. b,c . UMAP dimensionality reduction projection of onion bulb cell, grouped by clusters and developmental stages.. d . Flavonoid metabolism in onion epidermal cell. e,f , Spatial expression of genes ( CHS and LTP ) in different onion bulb developmental stages. g, Spongy mesophyll cell lineages visualized in spatial coordinates. h . Significant biological process GO terms enriched in top 1,000 DEGs with lowest q value in spongy mesophyll cell lineages.

8. Genes related to evolution and formation of tunicate bulbs Fig.5. Evolution of genes involved in bulb formation in Allium plants and expression pattern divergence. a. Red genes represent positively selected genes (PSGs). Orange genes represent rapidly evolving genes (REGs).

9. Bulb formation in Allium plants and expression pattern divergence Fig.5. b – i , Expression patterns of FRA and TUA during onion bulb formation based on in situ hybridization. b′ – i ′ , Expression signal intensities of FRA and TUA in onion and Welsh onion leaf sheaths in b – i were selected and transformed to pseudocolors with ImageJ. In onion, FRA transcript was observed in epidermal cells (green arrow) and two or three layers of cells (orange arrows) of the second leaf sheath, increasing to five or six layers of cells during late bulb swelling ( b , d , b′ and d′ ). TUA transcript was observed in the inner cells of the second leaf sheath at late bulb formation ( c , e , c′ and e′ ). In Welsh onion, accumulation of FRA and TUA transcripts was not observed in second leaf sheaths ( f – i , f′ – i ′ ).

10. Summary Three Allium species experienced at least four WGD events, more than other closely related lineages such as African lily, A. officinalis, Apostasia Shenzhenica , and Elaeis Guineensis . The abundant repetitive sequences in the Allium genome may be the result of hybridization and/or polyploid adaptation to different environmental conditions. genes encoding enzymes involved in the metabolic pathway of Allium -specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Onion bulb epidermal cell co-expressed many flavonoid synthesis genes, indicating that epidermal cells are the primary course of onion bulb flavonoids. This study is important fundamental update to the genetic resources and molecular mechanisms of trait evolution in Allium , which will facilitate crop breeding.