Role In Somatic Embryogenesis Research Articles

Regulation of regeneration in Arabidopsis thaliana

We employed several algorithms with high efficacy to analyze the public transcriptomic data, aiming to identify key transcription factors (TFs) that regulate regeneration in Arabidopsis thaliana. Initially, we utilized CollaborativeNet, also known as TF-Cluster, to construct a collaborative network of all TFs, which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder (CoSE) algorithms. Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration. We further applied principal component analysis and gene ontology (GO) enrichment analysis to reduce the subnetworks from nine to three, namely subnetworks 1, 12, and 17. Searching for TF-binding sites in the promoters of the co-expressed and co-regulated (CCGs) genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each subnetwork. Finally, six potential candidate TFs—WOX9A, LEC2, PGA37, WIP5, PEI1, and AIL1 from subnetwork 1—were identified, and their roles in somatic embryogenesis (GO:0010262) and regeneration (GO:0031099) were discussed, so were the TFs in Subnetwork 12 and 17 associated with regeneration. The TFs identified were also assessed using the CIS-BP database and Expression Atlas. Our analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to regeneration. The tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest.

Transcriptome analysis revealed enrichment pathways and regulation of gene expression associated with somatic embryogenesis in Camellia sinensis

The high frequency, stable somatic embryo system of tea has still not been established due to the limitations of its own characteristics and therefore severely restricts the genetic research and breeding process of tea plants. In this study, the transcriptome was used to illustrate the mechanisms of gene expression regulation in the somatic embryogenesis of tea plants. The number of DEGs for the (IS intermediate stage)_PS (preliminary stage), ES (embryoid stage)_IS and ES_PS stages were 109, 2848 and 1697, respectively. The enrichment analysis showed that carbohydrate metabolic processes were considerably enriched at the ES_IS stage and performed a key role in somatic embryogenesis, while enhanced light capture in photosystem I could provide the material basis for carbohydrates. The pathway analysis showed that the enriched pathways in IS_PS process were far less than those in ES_IS or ES_PS, and the photosynthesis and photosynthetic antenna protein pathway of DEGs in ES_IS or ES_PS stage were notably enriched and up-regulated. The key photosynthesis and photosynthesis antenna protein pathways and the Lhcb1 gene were discovered in tea plants somatic embryogenesis. These results were of great significance to clarify the mechanism of somatic embryogenesis and the breeding research of tea plants.

GmBBM7 promotes callus and root growth during somatic embryogenesis of soybean (Glycine max)

The BABY BOOM (BBM) subfamily of the AP2/ERF transcription factor family is the main regulator of totipotency in plant cells and plays an important role in regulating cell proliferation and plant growth and development. Previously, we identified GmBBM7, a key gene of the soybean BBM gene subfamily (GmBBM family). In this study, we aimed to analyze its molecular characteristics and role in somatic embryogenesis in soybean. First, we identified 17 members of GmBBM family. Phylogenetic and collinear analyses revealed that the GmBBM family genes mainly exhibited a strong genetic relationship with the those of PvBBM family, the BBM family of common bean (Phaseolus vulgaris). Analysis of the promoters revealed that GmBBM family genes were mainly regulated by plant hormones. The expression of GmBBM7 varied in various tissues of soybean. Particularly, it was higher in the roots, immature embryos, grains and callus. Subcellular localization analysis indicated that GmBBM7 encodes a nuclear protein. Furthermore, overexpressed GmBBM7 could significantly enhance callus formation by regulating the levels of gibberellin A1, A3 and A7; abscisic acid; and salicylic acid and could promote root growth and development. In summary, GmBBM7 is an important regulatory gene for somatic embryogenesis and root elongation in soybean. GmBBM7 overexpression in soybean could increase the callus formation rate and density through hormonal pathways and could increase root growth. This study provided theoretical basis for efficient breeding of soybean via gene editing, transgenic and other techniques.

Construction of ceRNA Networks at Different Stages of Somatic Embryogenesis in Garlic.

LncRNA (long non-coding RNA) and mRNA form a competitive endogenous RNA (ceRNA) network by competitively binding to common miRNAs. This network regulates various processes of plant growth and development at the post-transcriptional level. Somatic embryogenesis is an effective means of plant virus-free rapid propagation, germplasm conservation, and genetic improvement, which is also a typical process to study the ceRNA regulatory network during cell development. Garlic is a typical asexual reproductive vegetable. Somatic cell culture is an effective means of virus-free rapid propagation in garlic. However, the ceRNA regulatory network of somatic embryogenesis remains unclear in garlic. In order to clarify the regulatory role of the ceRNA network in garlic somatic embryogenesis, we constructed lncRNA and miRNA libraries of four important stages (explant stage: EX; callus stage: AC; embryogenic callus stage: EC; globular embryo stage: GE) in the somatic embryogenesis of garlic. It was found that 44 lncRNAs could be used as precursors of 34 miRNAs, 1511 lncRNAs were predicted to be potential targets of 144 miRNAs, and 45 lncRNAs could be used as eTMs of 29 miRNAs. By constructing a ceRNA network with miRNA as the core, 144 miRNAs may bind to 1511 lncRNAs and 12,208 mRNAs. In the DE lncRNA-DE miRNA-DE mRNA network of adjacent stages of somatic embryo development (EX-VS-CA, CA-VS-EC, EC-VS-GE), by KEGG enrichment of adjacent stage DE mRNA, plant hormone signal transduction, butyric acid metabolism, and C5-branched dibasic acid metabolism were significantly enriched during somatic embryogenesis. Since plant hormones play an important role in somatic embryogenesis, further analysis of plant hormone signal transduction pathways revealed that the auxin pathway-related ceRNA network (lncRNAs-miR393s-TIR) may play a role in the whole stage of somatic embryogenesis. Further verification by RT-qPCR revealed that the lncRNA125175-miR393h-TIR2 network plays a major role in the network and may affect the occurrence of somatic embryos by regulating the auxin signaling pathway and changing the sensitivity of cells to auxin. Our results lay the foundation for studying the role of the ceRNA network in the somatic embryogenesis of garlic.

Large-Scale Quantitative Proteomic Analysis during Different Stages of Somatic Embryogenesis in Larix olgensis.

Larix olgensis is an economically important tree species native to northeastern China. The use of somatic embryogenesis (SE) is efficient and enables the rapid production of varieties with desirable qualities. Here, isobaric labeling via tandem mass tags was used to conduct a large-scale quantitative proteomic analysis of proteins in three critically important stages of SE in L. olgensis: the primary embryogenic callus, the single embryo, and the cotyledon embryo. We identified 6269 proteins, including 176 shared differentially expressed proteins across the three groups. Many of these proteins are involved in glycolipid metabolism, hormone response/signal transduction, cell synthesis and differentiation, and water transport; proteins involved in stress resistance and secondary metabolism, as well as transcription factors, play key regulatory roles in SE. The results of this study provide new insights into the key pathways and proteins involved in SE in Larix. Our findings have implications for the expression of totipotency, the preparation of synthetic seeds, and genetic transformation.

Transcriptome analysis reveals differentially expressed genes involved in somatic embryogenesis and podophyllotoxin biosynthesis of Sinopodophyllum hexandrum (Royle) T. S. Ying.

Sinopodophyllum hexandrum (Royle) T. S. Ying, an important source of podophyllotoxin (PTOX), has become a rare and endangered plant because of over-harvesting. Somatic embryogenesis (SE) is the main way of seedling rapid propagation and germplasm enhancement, but the regeneration of S. hexandrum has not been well established, and the PTOX biosynthesis abilities at different SE stages remain unclear. Therefore, it is extremely important to elucidate the SE mechanism of S. hexandrum and clarify the biosynthesis variation of PTOX. In this study, the transcriptomes of S. hexandrum at different SE stages were sequenced, the contents of PTOX and 4'-demethylepipodophyllotoxin were assayed, and the transcript expression patterns were validated by qRT-PCR. The results revealed that plant hormone (such as auxins, abscisic acid, zeatin, and gibberellins) related pathways were significantly enriched among different SE stages, indicating these plant hormones play important roles in SE of S. hexandrum; the expression levels of a series of PTOX biosynthesis related genes as well as PTOX and 4'-demethylepipodophyllotoxin contents were much higher in embryogenic callus stage than in the other stages, suggesting embryogenic callus stage has the best PTOX biosynthesis ability among different SE stages. This study will contribute to germplasm conservation and fast propagation of S. hexandrum, and facilitate the production of PTOX.

MtCLE08, MtCLE16, and MtCLE18 Transcription Patterns and Their Possible Functions in the Embryogenic Calli of Medicago truncatula.

CLE peptides are well-known hormonal regulators of plant development, but their role in somatic embryogenesis remains undetermined. CLE genes are often regulated by WOX transcription factors and, in their turn, regulate the expression level of WOX genes. In this study, we used in vitro cultivation, as well as qPCR and transcriptomic analysis, to find CLE peptides which could regulate the MtWOX9-1 gene, stimulating somatic embryogenesis in Medicago truncatula. Three CLE peptides were found which could probably be such regulators, but none of them was found to influence MtWOX9-1 expression in the embryogenic calli. Nevertheless, overexpression of one of CLE genes under study, MtCLE16, decreased somatic embryogenesis intensity. Additionally, overexpression of MtCLE08 was found to suppress expression of MtWOX13a, a supposed antagonist of somatic embryo development. Our findings can be helpful for the search for new regeneration regulators which could be used for plant transformation.

Genome-wide identification and expression profiling of WUSCHEL-related homeobox (WOX) genes confer their roles in somatic embryogenesis, growth and abiotic stresses in banana.

The online version contains supplementary material available at 10.1007/s13205-022-03387-w.

Insights into the Histone Acetylation-Mediated Regulation of the Transcription Factor Genes That Control the Embryogenic Transition in the Somatic Cells of Arabidopsis.

Somatic embryogenesis (SE), which is a process that involves the in vitro-induced embryogenic reprogramming of plant somatic cells, requires dynamic changes in the cell transcriptome. These changes are fine-tuned by many genetic and epigenetic factors, including posttranslational histone modifications such as histone acetylation. Antagonistically acting enzymes, histone acetyltransferases (HATs) and deacetylases (HDACs), which control histone acetylation in many developmental processes, are believed to control SE. However, the function of specific HAT/HDACs and the genes that are subjected to histone acetylation-mediated regulation during SE have yet to be revealed. Here, we present the global and gene-specific changes in histone acetylation in Arabidopsis explants that are undergoing SE. In the TSA (trichostatin A)-induced SE, we demonstrate that H3 and H4 acetylation might control the expression of the critical transcription factor (TF) genes of a vital role in SE, including LEC1, LEC2 (LEAFY COTYLEDON 1; 2), FUS3 (FUSCA 3) and MYB118 (MYB DOMAIN PROTEIN 118). Within the HATs and HDACs, which mainly positively regulate SE, we identified HDA19 as negatively affecting SE by regulating LEC1, LEC2 and BBM. Finally, we provide some evidence on the role of HDA19 in the histone acetylation-mediated regulation of LEC2 during SE. Our results reveal an essential function of histone acetylation in the epigenetic mechanisms that control the TF genes that play critical roles in the embryogenic reprogramming of plant somatic cells. The results implicate the complexity of Hac-related gene regulation in embryogenic induction and point to differences in the regulatory mechanisms that are involved in auxin- and TSA-induced SE.

Identification and expression analysis of histone modification gene (HM) family during somatic embryogenesis of oil palm

BackgroundOil palm (Elaeis guineensis, Jacq.) is an important vegetable oil-yielding plant. Somatic embryogenesis is a promising method to produce large-scale elite clones to meet the demand for palm oil. The epigenetic mechanisms such as histone modifications have emerged as critical factors during somatic embryogenesis. These histone modifications are associated with the regulation of various genes controlling somatic embryogenesis. To date, none of the information is available on the histone modification gene (HM) family in oil palm.ResultsWe reported the identification of 109 HM gene family members including 48 HMTs, 27 HDMs, 13 HATs, and 21 HDACs in the oil palm genome. Gene structural and motif analysis of EgHMs showed varied exon–intron organization and with conserved motifs among them. The identified 109 EgHMs were distributed unevenly across 16 chromosomes and displayed tandem duplication in oil palm genome. Furthermore, relative expression analysis showed the differential expressional pattern of 99 candidate EgHM genes at different stages (non-embryogenic, embryogenic, somatic embryo) of somatic embryogenesis process in oil palm, suggesting the EgHMs play vital roles in somatic embryogenesis. Our study laid a foundation to understand the regulatory roles of several EgHM genes during somatic embryogenesis.ConclusionsA total of 109 histone modification gene family members were identified in the oil palm genome via genome-wide analysis. The present study provides insightful information regarding HM gene’s structure, their distribution, duplication in oil palm genome, and also their evolutionary relationship with other HM gene family members in Arabidopsis and rice. Finally, our study provided an essential role of oil palm HM genes during somatic embryogenesis process.

Caffeate may play an important role in the somatic embryogenesis of oil palm (Elaeis guineensis Jacq.)

Somatic embryogenesis (SE) is a key step in plant regeneration and propagation, but the mechanisms underlying SE in oil palm still stay unclear. Integrated analysis of metabolome and transcriptome data showed that 13 metabolites are specifically accumulated in somatic embryo, of which caffeate was 16.6-fold (p = 0.0002) higher than in callus. Moreover, caffeate was significantly correlated with phytohormone signaling genes including ethylene receptor (ETR2-2), auxin efflux carrier component 3a (PIN3A), auxin response factor (ARF15-2), and several SE transcription factors (TFs) including WUSCHEL-related homeobox (WOX), VIVIPAROUS1(VP1), BABY BOOM2 (BBM2). Furthermore, staining and microscopic observation showed that phenolic acids highly accumulated in the center of newly formed callus clusters and lignin is predominant in somatic embryo than in callus, indicated that caffeate (the major phenolic acids in glycosylated form and the precursor of lignin biosynthesis) may play an important role in SE. Our results provide a better understanding of the SE mechanism in oil palm.

Reactive oxygen species, nitric oxide and plant cell death associated with caspase-like protease activity during somatic embryogenesis in Fraxinus mandshurica

Programmed cell death occurs in browning explants of Fraxinus mandshurica during somatic embryogenesis, but the underlying mechanism is unclear. In this study, single cotyledons of zygotic embryos of F. mandshurica were used as explants. Mitochondrial structure and function, caspase-3-like protease activity, hydrogen peroxide metabolism, and nitric oxide accumulation induced by high concentrations of sucrose and plant growth regulators were studied. The results show that plant growth regulators induced somatic embryogenesis and also promoted explant browning. High sucrose concentrations had similar effects. High concentrations of sucrose and plant growth regulators led to the accumulation of hydrogen peroxide and nitric oxide which induced changes in mitochondrial structure and function such as modifications in mitochondrial morphology, increased membrane permeability, decreased membrane potential, and the release of cytochrome c into the cytoplasm. An increase in caspase-3-like protease activity triggered programmed cell death in some browning explant cells. During somatic embryogenesis there were increased activities of superoxide dismutase, peroxidase, and catalase, which are associated with hydrogen peroxide metabolism and jointly maintain reactive oxygen species levels. Intracellular nitric oxide synthase and nitrate reductase activities were not significantly correlated with nitric oxide content. Instead, intracellular nitric oxide may be derived from non-enzymatic reactions. Our results indicate that hydrogen peroxide and nitric oxide may function as signals, playing key roles in somatic embryogenesis and programmed cell death of explant cells of F. mandshurica. The interaction between nitric oxide and reactive oxygen species determines the occurrence of programmed cell death in explant cells; somatic embryogenesis and programmed cell death are positively regulated by hydrogen peroxide. However, the regulation of nitric oxide is complex.

Genome-wide identification and expression analysis of Argonaute gene family from longan embryogenic callus

Argonaute (AGO) proteins are the core of the RNA-induced gene silencing complex which regulate a wide variety of processes in plants, from organ development to abiotic stress responses. They have been identified in many plants, but little is known in longan (Dimocarpus longan Lour.), and how AGO functions in the signaling pathways in plant embryos in response to changing environmental stimuli remains unclear. In the present research, a genome-wide analysis of the AGO gene family members and their roles in somatic embryogenesis (SE), zygotic embryogenesis (ZE), tissue developmental processes, and responses to hormones, light and abiotic stress in longan were conducted. Ten longan AGO genes were identified genome-wide and divided into four clades. They were distributed on chromosomes 1, 4, 8, 10, 12, 13, 14, and 15, and had 2–23 introns. The expression profiling implied that DIAGOs regulated early and middle embryogenesis, as well as developmental processes of seed, flower, and stem in longan. In addition, the transcript levels of DIAGOs in response to exogenous hormones, light and abiotic stress showed differences in expression patterns. These results provide the useful information for further elucidation of RNAi-mediated gene silencing in longan embryogenic callus (EC).

Influence of exogenous polyamines on somatic embryogenesis and regeneration of fresh and long-term cultures of three elite indica rice cultivars

The influence of putrescine (Put), spermidine (Spd), and spermine (Spm) on somatic embryogenesis (SE) and plant regeneration of three indica rice cultivars (ASD16, IR64, and ADT43) were evaluated since polyamines (PAs) are reported to play vital roles in SE and plant regeneration. Significant increases in the regeneration potential of the rice cultivars upon polyamine treatments were observed. Put (1.0 mM) induced the highest regeneration frequencies, somatic embryos, and shoot numbers. PAs influenced the fresh weights of the suspension cultures. Spd was found to be detrimental to cultivar ADT43 towards embryogeneicity, regeneration, and somatic embryo induction. Among the cultivars, ASD16 was found to respond superiorly to the polyamine treatment. Experiments with long-term cultures of the rice revealed that Put and Spm enhanced the regeneration potential, and the highest frequencies were recorded for ASD16 and IR64. Results indicate that PAs can be effectively used as growth modulators to achieve success in in vitro tissue and genetic manipulation studies with elite recalcitrant indica rice cultivars.

Retraction Note to: In vitro somatic embryogenesis from immature female flower of Musa AAB cv. Chenichampa and molecular analysis of transcript factors (TFs) during somatic embryogenesis

Somatic embryogenesis (SE) is a process where somatic embryos can form differentiated tissues and regenerate into new plants. Efficient SE and liquid culture system for large-scale production of banana cv. Chenichampa is presented. The embryo maturation media (M3) was modified with different organic additives and high-frequency somatic embryos were observed in M3 media supplemented with CH: Gln (100:150 mg/L) resulting in a tenfold increase in somatic embryo formation as compared to the control. The generated plantlets were hardened and polymerase chain reaction (PCR) with SSR primers were used to confirm the genetic fidelity of the plantlets. To understand the molecular mechanism of SE, expression patterns of transcript factors (TFs) in respect of embryogenic calli (EC) and embryogenic cell suspension (ECS) was also studied. Transcript factor (TF) such as BBM has been reported to play a significant part in converting explants to EC. The higher expression of TFs MaBBM1, MaBBM2, MaWUS2, and MaVP1 in the EC and MaBBM2 and MaWUS2 in ECS, suggested that these genes could play a crucial role in SE. The protocol developed in this commercially important banana cv. Chenichampa could be highly useful for large-scale micropropagation and genetic manipulation studies which can be adapted to other cultivars lacking in male flowers. An efficient micropropagation system using SE for banana cultivar Chenichampa (Musa AAB) is presented. Differential expression profiles of TFs during various stages of SE studied. Organic additives enhanced the SE and this optimized protocol will serve as a platform for developing efficient propagation system for banana cultivars that lack male flowers.

Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.).

Transcriptome analysis of maize embryogenic callus and somatic embryos reveals associated genes reprogramming, hormone signaling pathways and transcriptional regulation involved in somatic embryogenesis in maize. Somatic embryos are widely utilized in propagation and genetic engineering of crop plants. In our laboratory, an elite maize inbred line Y423 that could generate intact somatic embryos was obtained and applied to genetic transformation. To enhance our understanding of regulatory mechanisms during maize somatic embryogenesis, we used RNA-based sequencing (RNA-seq) to characterize the transcriptome of immature embryo (IE), embryogenic callus (EC) and somatic embryo (SE) from maize inbred line Y423. The number of differentially expressed genes (DEGs) in three pairwise comparisons (IE-vs-EC, IE-vs-SE and EC-vs-SE) was 5767, 7084 and 1065, respectively. The expression patterns of DEGs were separated into eight major clusters. Somatic embryogenesis associated genes were mainly grouped into cluster A or B with an expression trend toward up-regulation during dedifferentiation. GO annotation and KEGG pathway analysis revealed that DEGs were implicated in plant hormone signal transduction, stress response and metabolic process. Among the differentially expressed transcription factors, the most frequently represented families were associated with the common stress response or related to cell differentiation, embryogenic patterning and embryonic maturation processes. Genes include hormone response/transduction and stress response, as well as several transcription factors were discussed in this study, which may be potential candidates for further analyses regarding their roles in somatic embryogenesis. Furthermore, the temporal expression patterns of candidate genes were analyzed to reveal their roles in somatic embryogenesis. This transcriptomic data provide insights into future functional studies, which will facilitate further dissections of the molecular mechanisms that control maize somatic embryogenesis.

Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis.

Plant somatic embryogenesis refers to a phenomenon where embryos develop from somatic cells in the absence of fertilization. Previous studies have revealed that the phytohormone auxin plays a crucial role in somatic embryogenesis by inducing a cell totipotent state, although its underlying mechanism is poorly understood. Here, we show that auxin rapidly rewires the cell totipotency network by altering chromatin accessibility. The analysis of chromatin accessibility dynamics further reveals a hierarchical gene regulatory network underlying somatic embryogenesis. Particularly, we find that the embryonic nature of explants is a prerequisite for somatic cell reprogramming. Upon cell reprogramming, the B3-type totipotent transcription factor LEC2 promotes somatic embryo formation by direct activation of the early embryonic patterning genes WOX2 and WOX3. Our results thus shed light on the molecular mechanism by which auxin promotes the acquisition of plant cell totipotency and establish a direct link between cell totipotent genes and the embryonic development pathway.

Dataset of transcriptome assembly of date palm embryogenic calli and functional annotation.

Date palm (Phoenix dactylifera L.; 2n = 36; Arecaceae), cultivated in tropical and sub-tropical regions worldwide, is a staple food for people in the Middle East region and has economic value throughout the world. Tissue culture is considered as a feasible technique for the large-scale multiplication of elite date palm varieties. In this article, we report the transcriptome assembly from the embryogenic calli of Khalas variety of date palm. A total of 50,852,331 paired-end (PE) raw reads were acquired using an Illumina sequencing platform. Reference-based assembly, with date palm genome, resulted in 53251 transcripts. A total of 63888 Gene Ontology (GO) terms could be annotated from the assembled transcriptome. Also, transcription factor families and small RNAs were annotated from the assembled transcriptome. Results of the pathway analysis revealed that a total of 2584 transcripts were involved in various metabolic pathways. Transcripts with possible roles in somatic embryogenesis were also identified. The dataset provides insights into the expression pattern of various genes during early somatic embryogenesis in date palm.

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

BackgroundThe 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.ResultsA 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.ConclusionsThe 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.

Full-Length Transcriptome Analysis of the ABCB, PIN/PIN-LIKES, and AUX/LAX Families Involved in Somatic Embryogenesis of Lilium pumilum DC. Fisch.

Plant cell totipotency is one of the 25 major topics in current scientific research, and somatic embryos are good experimental material for studying cell totipotency. Polar auxin transport plays an important regulatory role in somatic embryogenesis (SE). However, little is known about the auxin transport genes and their regulatory mechanisms in Lilium SE. In this study, we applied single-molecule real-time (SMRT) sequencing to Lilium pumilum DC. Fisch. for the first time and obtained a total of 119,649 transcripts, of which 14 encoded auxin transport genes. Correlation analyses between somatic embryo induction and gene expression under different treatments revealed that auxin transport genes, especially ATP-binding cassette (ABC) transporter B family member 21 (ABCB21) and PIN-FORMED (PIN) LIKES 7 (PILS7), may be key players in SE, and the necessary duration of picloram (PIC) treatment to induce SE is as short as 3 days. Our research provides valuable genetic information on Lilium pumilum, elucidating the candidate auxin transport genes involved in SE and their influencing factors. This study lays a foundation for elucidating the regulatory mechanism of auxin transport in SE.