Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

Background Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which leads to management problems regarding the plantations maintenance, harvest and processing of grains. Therefore, an efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. A key process on somatic embryogenesis induction is the auxin homeostasis performed by Gretchen Hagen 3 (GH3) proteins through amino acid conjugation. In this study, the GH3 family members were identified on C. canephora genome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point a GH3 gene as a potential regulator of auxin homeostasis during early somatic embryogenesis in C. arabica plants. Results We have searched within the published C. canephora genome and found 17 GH3 family members. We checked the conserved domains for GH3 proteins and clustered the members in three main groups according to phylogenetic relationships. We identified amino acids sets in four GH3 proteins that are related to acidic amino acid conjugation to auxin, and using a transcription factor (TF) network approach followed by RT-qPCR we analyzed their possible transcriptional regulators and expression profiles in cells with contrasting embryogenic potential in C. arabica. The CaGH3.15 expression pattern is the most correlated with embryogenic potential and with CaBBM, a C. arabica ortholog of a major somatic embryogenesis regulator. Conclusion Therefore, one out of the GH3 members may be influencing on coffee somatic embryogenesis by auxin conjugation with acidic amino acids, which leads to the phytohormone degradation. It is an indicative that this gene can serve as a molecular marker for coffee cells with embryogenic potential and needs to be further studied on how much determinant it is for this process. This work, together with future studies, can support the improvement of coffee clonal propagation through in vitro derived somatic embryos.

Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor superfamily in Dimocarpus longan Lour

Backgroud: APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors perform indispensable roles in various biological processes, and it has been identified in many plants. However, little is known about the AP2/ERF superfamily in longan (Dimocarpus longan Lour.). The release of the whole-genome sequence of longan provided us an opportunity to perform a genome-wide investigation of AP2/ERF superfamily. Results: In the present study, we performed a genome-wide survey of AP2/ERF superfamily longan (DlAP2/ERF), including the gene structure, motif composition, phylogenetic, cis-acting element, single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), alternative splicing (AS) events and the expression patterns. In total, 125 DlAP2/ERF genes were identified and classified into four families, including AP2 (19 members), ERF (101 members), RAV (four members) and Soliost (one member) in the longan genome. The AP2 and soloist genes possessed one to ten introns, while 87 genes within the ERF and RAV family had no introns. A large number of hormone signaling and stress response cis-acting elements were also identified. Besides, a large number of SNPs existed in the DlAP2/ERF superfamily, they may be deverse in the early somatic embryogenesis and stem of longan. However, the numbers of InDels was far less than SNPs. In addition, the AP2 family members existed a large number of AS events in different developmental processes of longan. Expression patterns analysis revealed that the AP2 family may promote the early somatic embryogenesis of longan, and DlAP2/ERF genes were specifically expressed in various organs such as seed, root, flower and young-fruit. The DlAP2/ERF genes can response to exogenous phytohormones, such as 2,4-Dichlorophenoxyacetic acid (2,4-D), Abscisic acid (ABA), Methyl jasmonate (MeJA) and Salicylic acid (SA). Protein interactions prediction indicated that the Baby Boom (BBM) protein may interacted with LALF/AGL15 network and was up-regulated expression at the transcriptional level in the early somatic embryogenesis of longan. Conclusions: A comprehensive analysis of molecular evolution and expression patterns showed that AP2/ERF superfamily played an important role in longan, especially in the early somatic embryogenesis, seed, root, flower and young-fruit. This systematic analysis provided the foundation for further functional characterization of AP2/ERF superfamily with an aim of longan improvement.