The chromosome-level genome of Eucommia ulmoides provides insights into sex differentiation and α-linolenic acid biosynthesis

Abstract

Eucommia ulmoides Oliver is a typical dioecious plant endemic to China that has great medicinal and economic value. Here, we report a high-quality chromosome-level female genome of E. ulmoides obtained by PacBio and Hi-C technologies. The size of the female genome assembly was 1.01 Gb with 17 pseudochromosomes and 31,665 protein coding genes. In addition, Hi-C technology was used to reassemble the male genome released in 2018. The reassembled male genome was 1.24 Gb with the superscaffold N50 (48.30 Mb), which was increased 25.69 times, and the number of predicted genes increased by 11,266. Genome evolution analysis indicated that E. ulmoides has undergone two whole-genome duplication events before the divergence of female and male, including core eudicot γ whole-genome triplication event (γ-WGT) and a recent whole genome duplication (WGD) at approximately 27.3 million years ago (Mya). Based on transcriptome analysis, EuAP3 and EuAG may be the key genes involved in regulating the sex differentiation of E. ulmoides. Pathway analysis showed that the high expression of ω-3 fatty acid desaturase coding gene EU0103017 was an important reason for the high α-linolenic acid content in E. ulmoides. The genome of female and male E. ulmoides presented here is a valuable resource for the molecular biological study of sex differentiation of E. ulmoides and also will provide assistance for the breeding of superior varieties.

Keywords: Eucommia ulmoides Oliver; MADS-box genes; genome; sex differentiation; whole-genome duplication; α-linolenic acid biosynthesis.

Figure 1

Morphological characteristic of Eucommia ulmoides. (A) Mature plant, (B) male inflorescence, (C) female inflorescence, (D) fruit.

Figure 2

Internal anatomical structure and external morphological characteristics of male and female flower buds at different differentiation stages. Br, Bract; Ca, Carp; Mic, Microsporocyte; Pis, Pistil, SAM, Stem Apical Meristem; Sq, Squama; Sta, Stamen; Sti, Stigma. (A1-A5): The external morphology structure of female flower bud; (B1-B5): The anatomic structure of female flower bud; (C1-C5): The external morphology structure of male flower bud; (D1-D5): The anatomic structure of male flower bud.

Figure 3

Genome evolutionary analysis. (A) Distribution of insertion times for LTR-RTs. (B) Ks value distribution in Female V1 and Male V2 genome. The divergence line represents Ks value distribution of syntenic blocks between male and female. (C) Genomic alignments of chromosomes and superscaffolds between Female V1 and Male V2.

Figure 4

Landscape of Female V1 and Male V2 genome. The circle from outside to inside represents, (A) Chromosomes of Female V1 and Superscaffolds of Male V2, (B) gene density, (C) GC content, (D) repeat abundance, (E) synteny information. All distributions were drawn in a window size of 1 Mb.

Figure 5

Heatmap of sex determination genes expression data in different stages of flower bud development in Female and male E. ulmoides. FS1: female floral organ induction stage flower bud, MS1: male floral organ induction stage flower bud, FS2: female floral organ morphological differentiation initial stage flower bud, MS2: and male floral organ morphological differentiation initial stage flower bud, FS3: female floral organ maturity stage flower bud, MS3: male floral organ maturity stage flower bud. Various color blocks represent the normalized gene expression levels of candidate genes involved in sex determination at different stages of flower bud development in Female and male E. ulmoides. The six boxes in one row of each heatmap (left to right) correspond to the expression levels in FS1, MS1, FS2, MS2, FS3, and MS3. Each row in the heatmap corresponds to one gene.

Figure 6

The reconstructed pathway of α-linolenic acid biosynthesis and metabolism in E. ulmoides. FAB2, Aacyl-ACP desaturase; FATA, acyl-ACP thioesterase; Δ12-FAD, omega-6 fatty acid desaturase; Δ15-FAD, omega-3 fatty acid desaturase; LOX, lipoxygenase; DOX, alpha-dioxygenase. Various color blocks represent the normalized gene expression levels of candidate genes related to α-linolenic acid biosynthesis and metabolism in E. ulmoides. The four boxes in one row of each heatmap (left to right) correspond to the expression levels in fruit, stem, leaf, and bark. Each row in the heatmap corresponds to one gene.