De novo transcriptome assembly reveals characteristics of flower sex determination of Excoecaria agallocha

Abstract

Key message MADS-box genes family may play important roles in the flower sex determination in Excoecaria agallocha. A total of 73 MADS-box genes were identified in E. agallocha. De novo transcriptome assembly analysis suggested that AP1/FUL, AP3/PI, AGL104, and SOC1 plays potential roles in E. agallocha flower sex determination. Context Excoecaria agallocha is a dioecious species containing both male and female individuals producing unisexual flowers. The underlying mechanisms regulating inflorescence differentiation in these species remains poorly understood. Aims Flower development influences reproduction and breeding in E.agallocha, which contributes to ecological restoration in the intertidal zone. Methods We performed de novo transcriptome assembly analysis on male and female flowers and leaves from E. agallocha. Results We identified a total of 73 MADS-box genes in the E. agallocha genome, which we grouped into five distinct classes (MIKCc, Mα, Mβ, Mγ, MIKC*) after phylogenetic comparisons with J. curcas homologs. We analyzed expression profiles and suggested AP1/FUL, AP3/PI, AGL104, and SOC1 as candidate regulators of sex determination. In addition, several EaMADS genes were significantly upregulated in flowers compared to leaves. Conclusion Our study represents the first detailed, comprehensive evaluation of the regulation of MADS-box genes associated with sex determination in E. agallocha. The assembled transcriptomic profiles increase the genetic information available for this species and constitute an important contribution to functional studies of inflorescence genes. In turn, this will help exploring the molecular mechanisms underlying the evolution of E. agallocha.

Genome assembly of the milky mangroveExcoecaria agallocha

“…Haplotypic duplications were removed using “purge_dups” based on the depth of HiFi reads (Guan et al, 2020). Furthermore, proximity ligation data sequenced from the Omni-C library were employed to scaffold the assembly with YaHS (Zhou et al, 2022).…”

“…These include a transcriptomic study on the flower sex determination of this dioecious species (Zhou et al, 2022) and the assembly of its chloroplast genome (Shi et al, 2020).…”

“…To date, a few molecular and genomic studies have been conducted on E. agallocha . These include a transcriptomic study on the flower sex determination of this dioecious species (Zhou et al, 2022) and the assembly of its chloroplast genome (Shi et al, 2020). However, the genome of this mangrove species remained missing.…”

“…Zhou et al, 2022).Gene model prediction was run by funannotate (Palmer & Stajich, 2020) ES --optimize_augustus --organism other --max_intronlen 350000". The predicted gene models from various prediction sources including GeneMark, high-quality…”