The AP2-like gene OitaAP2 is alternatively spliced and differentially expressed in inflorescence and vegetative tissues of the orchid Orchis italica

Improvement of RNA In Situ Hybridisation for Grapevine Fruits and Ovules

The European grapevine (Vitis vinifera L.) is one of the world's most widely cultivated and economically important fruit crops. Seedless fruits are particularly desired for table grapes, with seedlessness resulting from stenospermocarpy being an important goal for cultivar improvement. The establishment of an RNA in situ hybridisation (ISH) system for grape berries and ovules is, therefore, important for understanding the molecular mechanisms of ovule abortion in stenospermocarpic seedless cultivars. We improved RNA in situ hybridisation procedures for developing berries and ovules by targeting two transcription factor genes, VvHB63 and VvTAU, using two seeded varieties, 'Red Globe' and 'Pinot Noir', and two seedless cultivars, 'Flame Seedless' and 'Thompson Seedless'. Optimisation focused on the time of proteinase K treatment, probe length, probe concentration, hybridisation temperature and post-hybridisation washing conditions. The objectives were to maximise hybridisation signals and minimise background interference, while still preserving tissue integrity. For the target genes and samples tested, the best results were obtained with a pre-hybridisation proteinase K treatment of 30 min, probe length of 150 bp and concentration of 100 ng/mL, hybridisation temperature of 50 °C, three washes with 0.2× saline sodium citrate (SSC) solution and blocking with 1% blocking reagent for 45 min during the subsequent hybridisation. The improved ISH system was used to study the spatiotemporal expression patterns of genes related to ovule development at a microscopic level.

Orchid NAC Transcription Factors: A Focused Analysis of CUPULIFORMIS Genes

Plant transcription factors are involved in different developmental pathways. NAC transcription factors (No Apical Meristem, Arabidopsis thaliana Activating Factor, Cup-shaped Cotyledon) act in various processes, e.g., plant organ formation, response to stress, and defense mechanisms. In Antirrhinum majus, the NAC transcription factor CUPULIFORMIS (CUP) plays a role in determining organ boundaries and lip formation, and the CUP homologs of Arabidopsis and Petunia are involved in flower organ formation. Orchidaceae is one of the most species-rich families of angiosperms, known for its extraordinary diversification of flower morphology. We conducted a transcriptome and genome-wide analysis of orchid NACs, focusing on the No Apical Meristem (NAM) subfamily and CUP genes. To check whether the CUP homologs could be involved in the perianth formation of orchids, we performed an expression analysis on the flower organs of the orchid Phalaenopsis aphrodite at different developmental stages. The expression patterns of the CUP genes of P. aphrodite suggest their possible role in flower development and symmetry establishment. In addition, as observed in other species, the orchid CUP1 and CUP2 genes seem to be regulated by the microRNA, miR164. Our results represent a preliminary study of NAC transcription factors in orchids to understand the role of these genes during orchid flower formation.

Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology

Background

The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. As an essential aquatic horticultural model plant, lotus has an increasingly prominent economic and research value.

Results

We have identified and analysed the AP2/ERF gene family in the lotus. Initially, 121 AP2/ERF family genes were identified. By analysing their gene distribution and protein structure, and their expression patterns during the development of lotus rhizome, combined with previous studies, we obtained an SNP (megascaffold_20:3578539) associated with lotus rhizome phenotype. This SNP was in the NnADAP gene of the AP2 subfamily, and the changes in SNP (C/T) caused amino acid conversion (proline/leucine). We constructed a population of 95 lotus varieties for SNP verification. Through population typing experiments, we found that the group with SNP CC had significantly larger lotus rhizome and higher soluble sugar content among the population.

Conclusions

In conclusion, we speculate that the alteration of the SNP in the NnADAP can affect the size and sugar content of the lotus rhizome.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07473-w.

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

Background

The APETALA2/ethylene responsive factor (AP2/ERF) superfamily members are transcription factors that regulate diverse developmental processes and stress responses in plants. They have been identified in many plants. However, little is known about the AP2/ERF superfamily in longan (Dimocarpus longan Lour.), which is an important tropical/subtropical evergreen fruit tree that produces a variety of bioactive compounds with rich nutritional and medicinal value. We conducted a genome-wide analysis of the AP2/ERF superfamily and its roles in somatic embryogenesis (SE) and developmental processes in longan.

Results

A genome-wide survey of the AP2/ERF superfamily was carried out to discover its evolution and function in longan. We identified 125 longan AP2/ERF genes and classified them into the ERF (101 members), AP2 (19 members), RAV (four members) families, and one Soloist. The AP2 and Soloist genes contained one to ten introns, whereas 87 genes in the ERF and RAV families had no introns. Hormone signaling molecules such as methyl jasmonate (MeJA), abscisic acid (ABA), gibberellin, auxin, and salicylic acid (SA), and stress response cis-acting element low-temperature (55) and defense (49) boxes also were identified. We detected diverse single nucleotide polymorphisms (SNPs) between the ‘Hong He Zi’ (HHZ) and ‘SI JI MI’ (SJM) cultivars. The number of insertions and deletions (InDels) was far fewer than SNPs. The AP2 family members exhibited more alternative splicing (AS) events in different developmental processes of longan than members of the other families. Expression pattern analysis revealed that some AP2/ERF members regulated early SE and developmental processes in longan seed, root, and flower, and responded to exogenous hormones such as MeJA, SA, and ABA, and 2,4-D, a synthetic auxin. Protein interaction predictions indicated that the Baby Boom (BBM) transcription factor, which was up-regulated at the transcriptional level in early SE, may interact with the LALF/AGL15 network.

Conclusions

The comprehensive analysis of molecular evolution and expression patterns suggested that the AP2/ERF superfamily may plays an important role in longan, especially in early SE, and in seed, root, flower, and young fruit. This systematic analysis provides a foundation for further functional characterization of the AP2/ERF superfamily with the aim of longan improvement.

The MADS-box genes expressed in the inflorescence of Orchis italica (Orchidaceae)

The Orchidaceae family, which is one of the most species-rich flowering plant families, includes species with highly diversified and specialized flower shapes. The aim of this study was to analyze the MADS-box genes expressed in the inflorescence of Orchis italica, a wild Mediterranean orchid species. MADS-box proteins are transcription factors involved in various plant biological processes, including flower development. In the floral tissues of O. italica, 29 MADS-box genes are expressed that are classified as both class I and II. Class I MADS-box genes include one Mβ-type gene, thereby confirming the presence of this type of MADS-box genes in orchids. The class II MIKC* gene is highly expressed in the column, which is consistent with the conserved function of the MIKC* genes in gametophyte development. In addition, homologs of the SOC, SVP, ANR1, AGL12 and OsMADS32 genes are expressed. Compared with previous knowledge on class II MIKC^C genes of O. italica involved in the ABCDE model of flower development, the number of class B and D genes has been confirmed. In addition, 4 class A (AP1/FUL) transcripts, 2 class E (SEP) transcripts, 2 new class C (AG) transcripts and 1 new AGL6 transcript have been identified. Within the AP1/FUL genes, the sequence divergence, relaxation of purifying selection and expression profiles suggest a possible functional diversification within these orchid genes. The detection of only two SEP transcripts in O. italica, in contrast with the 4 genes found in other orchids, suggests that only two SEP genes could be present in the subfamily Orchidoideae. The expression pattern of the MIKC^C genes of O. italica indicates that low levels at the boundary of the domain of a given MADS-box gene can overlap with the expression of genes belonging to a different functional A-E class in the adjacent domain, thereby following a “fading borders” model.

Evolutionary Conservation of the Orchid MYB Transcription Factors DIV, RAD, and DRIF

The MYB transcription factors DIVARICATA (DIV), DIV-and-RAD-Interacting-Factor (DRIF), and the small interfering peptide RADIALIS (RAD) can interact, forming a regulatory module that controls different plant developmental processes. In the snapdragon Antirrhinum majus, this module, together with the TCP transcription factor CYCLOIDEA (CYC), is responsible for the establishment of floral dorsoventral asymmetry. The spatial gene expression pattern of the OitDIV, OitDRIF, and OitRAD homologs of Orchis italica, an orchid with zygomorphic flowers, has suggested a possible conserved role of these genes in bilateral symmetry of the orchid flower. Here, we have identified four DRIF genes of orchids and have reconstructed their genomic organization and evolution. In addition, we found snapdragon transcriptional cis-regulatory elements of DIV and RAD loci generally conserved within the corresponding orchid orthologues. We have tested the biochemical interactions among OitDIV, OitDRIF1, and OitRAD of O. italica, showing that OitDRIF1 can interact both with OitDIV and OitRAD, whereas OitDIV and OitRAD do not directly interact, as in A. majus. The analysis of the quantitative expression profile of these MYB genes revealed that in zygomorphic orchid flowers, the DIV, DRIF1, and RAD transcripts are present at higher levels in the lip than in lateral inner tepals, whereas in peloric orchid flowers they show similar expression levels. These results indicate that MYB transcription factors could have a role in shaping zygomorphy of the orchid flower, potentially enriching the underlying orchid developmental code.

Transcriptome-Wide Identification and Expression Analysis of DIVARICATA- and RADIALIS-Like Genes of the Mediterranean Orchid Orchis italica

Bilateral symmetry of flowers is a relevant novelty that has occurred many times throughout the evolution of flowering plants. In Antirrhinum majus, establishment of flower dorso-ventral asymmetry is mainly due to interaction of TCP (CYC and DICH) and MYB (DIV, RAD, and DRIF) transcription factors. In the present study, we characterized 8 DIV-, 4 RAD-, and 2 DRIF-like genes from the transcriptome of Orchis italica, an orchid species with bilaterally symmetric and resupinate flowers. We found a similar number of DIV- and RAD-like genes within the genomes of Phalaenopsis equestris and Dendrobium catenatum orchids. Orchid DIV- and RAD-like proteins share conserved motifs whose distribution reflects their phylogeny and analysis of the genomic organization revealed a single intron containing many traces of transposable elements. Evolutionary analysis has shown that purifying selection acts on the DIV- and RAD-like coding regions in orchids, with relaxation of selective constraints in a branch of the DIV-like genes. Analysis of the expression patterns of DIV- and RAD-like genes in O. italica revealed possible redundant functions for some of them. In the perianth of O. italica, the ortholog of DIV and DRIF of A. majus are expressed in all tissues, whereas RAD is mainly expressed in the outer tepals and lip. These data allow for proposal of an evolutionary conserved model in which the expression of the orthologs of the DIV, RAD, and DRIF genes might be related to establishment of flower bilateral symmetry in the nonmodel orchid species O. italica.

Differential isoform expression and protein localization from alternatively spliced Apetala2 in peanut under drought stress

APETALA2 (AP2) belongs to the AP2/Ethylene Responsive Factor (ERF) family and regulates expression levels of downstream stress responsive genes as a transcription factor. In this study, we cloned six different isoforms of AhAP2 from peanut (Arachis hypogaea). Four isoforms (AhAP2.1, AhAP2.2, AhAP2.3 and AhAP2.4) had both AP2/ERF DNA binding domains and ERF-associated amphiphilic repression (EAR) motifs. Two isoforms (AhAP2.5 and AhAP2.6) only had an EAR suppressor domain. After agroinfiltration, AhAP2.1, AhAP2.3, and AhAP2.4 fused to yellow fluorescent protein (YFP) showed localization to the nucleolus, which is the site of transcription and ribosome biogenesis. AhAP2.2-YFP showed a dispersed signal in the nucleus. AhAP2.5 and AhAP2.6 fused to YFP localized to both the nucleus and cytoplasm. In addition, increased levels of AhAP2.1 and AhAP2.2 transcripts were observed in drought-treated peanut leaves, suggesting differential transcriptional regulation under drought stress conditions.

De novo transcriptome assembly from inflorescence of Orchis italica: analysis of coding and non-coding transcripts

The floral transcriptome of Orchis italica, a wild orchid species, was obtained using Illumina RNA-seq technology and specific de novo assembly and analysis tools. More than 100 million raw reads were processed resulting in 132,565 assembled transcripts and 86,079 unigenes with an average length of 606 bp and N50 of 956 bp. Functional annotation assigned 38,984 of the unigenes to records present in the NCBI non-redundant protein database, 32,161 of them to Gene Ontology terms, 15,775 of them to Eukaryotic Orthologous Groups (KOG) and 7,143 of them to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The in silico expression analysis based on the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was confirmed by real-time RT-PCR experiments on 10 selected unigenes, which showed high and statistically significant positive correlation with the RNA-seq based expression data. The prediction of putative long non-coding RNAs was assessed using two different software packages, CPC and Portrait, resulting in 7,779 unannotated unigenes that matched the threshold values for both of the analyses. Among the predicted long non-coding RNAs, one is the homologue of TAS3, a long non-coding RNA precursor of trans-acting small interfering RNAs (ta-siRNAs). The differential expression pattern observed for the selected putative long non-coding RNAs suggests their possible functional role in different floral tissues.

The analysis of the inflorescence miRNome of the orchid Orchis italica reveals a DEF-like MADS-box gene as a new miRNA target

Plant microRNAs (miRNAs) are small, regulatory non-coding RNAs involved in a wide range of biological processes, from organ development to response to stimuli. In recent years, an increasing number of studies on model plant species have highlighted the evolutionary conservation of a high number of miRNA families and the existence of taxon-specific ones. However, few studies have examined miRNAs in non-model species such as orchids, which are characterized by highly diversified floral structures and pollination strategies. Therefore, we analysed a small RNA library of inflorescence tissue of the Mediterranean orchid Orchis italica to increase the knowledge on miRNAs in a non-model plant species. The high-throughput sequencing and analysis of a small RNA library of inflorescence of O. italica revealed 23 conserved and 161 putative novel miRNA families. Among the putative miRNA targets, experimental validation demonstrated that a DEF-like MADS-box transcript is cleaved by the homolog of miR5179 of O. italica. The presence of conserved miRNA families in the inflorescence of O. italica indicates that the basic developmental flower regulatory mechanisms mediated by miRNAs are maintained through evolution. Because, according to the "orchid code" theory, DEF-like genes exert a key function in the diversification of tepals and lip, the cleavage-mediated inhibitory activity of miR5179 on a OitaDEF-like transcript suggests that, in orchids, miRNAs play an important role in the diversification of the perianth organs.