Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses

Abstract

Eucommia ulmoides is a model representative of the dioecious plants with sex differentiation at initiation. Nevertheless, the genetic mechanisms of sexual dimorphism and sex determination in E. ulmoides remain poorly understood. In this study de novo transcriptome sequencing on Illumina platform generated >45 billion high-quality bases from fresh leaves of six male and female individuals of E. ulmoides. A total of 148,595 unigenes with an average length of 801 base-pairs (bp) were assembled. Through comparative transcriptome analyses, 116 differentially expressed genes (DEGs) between the males and the females were detected, including 73 male-biased genes and 43 female-biased genes. Of these DEGs, three female-biased genes were annotated to be related with the sexually dimorphic gutta content in E. ulmoides. One male-biased DEG was identified as putative MADS box gene APETALA3, a B class floral organ identity gene in the flowering plants. SNPs calling analyses further confirmed that the APETALA3-like gene was probably involved in the sex determination in E. ulmoides. Four other male-biased DEGs were potential sex-associated genes as well with segregated SNPs in accord with sex type. In addition, the SNPs density was 1.02 per kilobase (kb) in the expressed genes of E. ulmoides, implying a relatively high genetic diversity.

Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

“…In this study we found that the transition SNPs (34) were indeed more frequently detected than the transversion SNPs (6). Previous studies have reported a high level of nuclear genetic diversity at the population level of E. ulmoides [ 18 , 54 ]. In this study, we revealed that the frequency of plastid SNPs were 0.46 per kb at the whole cp genome level, lower than the average of 1.02 per kb in the nuclear genes of E. ulmoides [ 54 ].…”

“…Previous studies have reported a high level of nuclear genetic diversity at the population level of E. ulmoides [ 18 , 54 ]. In this study, we revealed that the frequency of plastid SNPs were 0.46 per kb at the whole cp genome level, lower than the average of 1.02 per kb in the nuclear genes of E. ulmoides [ 54 ]. The difference of SNP frequency between the cp genome and the nuclear genes could be caused by insufficient sampling in this study and/or different variation rates between the plastid and nuclear sequences.…”

“…Moreover, plastome is inherited uniparentally in general, which might introduce biases to species phylogeny inference [ 71 , 72 ]. Analyses using orthologous nuclear genes are also needed for studying the evolutionary history of E. ulmoides among the flowering plants [ 54 ].…”

Molecular Sex Identification in the Hardy Rubber Tree (Eucommia ulmoides Oliver) via ddRAD Markers

“…Nonrecombining male-specific regions including many genes have also been characterized in C. papaya [28], P. trichocarpa [29], and S. latifolia [30]. Recently, one putative MADS box APETALA3-like gene, with male-biased expression, was identified to be probably involved in the sex determination in E. ulmoides based on transcriptomic analysis [31]. Nevertheless, to our knowledge, the sex determination mechanism in E. ulmoides is still in the dark to date.…”

Comparative Transcriptome Analysis Identified Differentially Expressed Genes between Male and Female Flowers of Zanthoxylum armatum var. novemfolius

“…One class of TFs is MADS-box, now known as the homeotic genes of ABCDE model for flower organ identification, which explains how the combination of different genes determines the identification of four flower organs. MADS-box genes regulate the early stage of flower development and help determine the characteristics of floral organs [48,49]. Some MADS-box genes were identified in the transcriptome data.…”