Phylogenomic analysis of the APETALA2 transcription factor subfamily across angiosperms reveals both deep conservation and lineage-specific patterns

PLETHORA transcription factors promote early embryo development through induction of meristematic potential

Plants are dependent on divisions of stem cells to establish cell lineages required for growth. During embryogenesis, early division products are considered to be stem cells, whereas during post-embryonic development, stem cells are present in meristems at the root and shoot apex. PLETHORA/AINTEGUMENTA-LIKE (PLT/AIL) transcription factors are regulators of post-embryonic meristem function and are required to maintain stem cell pools. Despite the parallels between embryonic and post-embryonic stem cells, the role of PLTs during early embryogenesis has not been thoroughly investigated. Here, we demonstrate that the PLT regulome in the zygote, and apical and basal cells is in strong congruence with that of post-embryonic meristematic cells. We reveal that out of all six PLTs, only PLT2 and PLT4/BABY BOOM (BBM) are expressed in the zygote, and that these two factors are essential for progression of embryogenesis beyond the zygote stage and first divisions. Finally, we show that other PLTs can rescue plt2 bbm defects when expressed from the PLT2 and BBM promoters, establishing upstream regulation as a key factor in early embryogenesis. Our data indicate that generic PLT factors facilitate early embryo development in Arabidopsis by induction of meristematic potential.

Genome-wide analysis of AP2/ERF transcription factors that regulate fruit development of Chinese prickly ash

BACKGROUND

AP2/ERF is a large family of plant transcription factor proteins that play essential roles in signal transduction, plant growth and development, and responses to various stresses. The AP2/ERF family has been identified and verified by functional analysis in various plants, but so far there has been no comprehensive study of these factors in Chinese prickly ash. Phylogenetic, motif, and functional analyses combined with transcriptome analysis of Chinese prickly ash fruits at different developmental stages (30, 60, and 90 days after anthesis) were conducted in this study.

RESULTS

The analysis identified 146 ZbAP2/ERF genes that could be classified into 15 subgroups. The motif analysis revealed the presence of different motifs or elements in each group that may explain the functional differences between the groups. ZbERF13.2, ZbRAP2-12, and ZbERF2.1 showed high levels of expression in the early stages of fruit development. ZbRAP2-4, and ZbERF3.1 were significantly expressed at the fruit coloring stage (R2 and G2). ZbERF16 were significantly expressed at fruit ripening and expression level increased as the fruit continued to develop. Relative gene expression levels of 6 representative ZbAP2/ERFs assessed by RT-qPCR agreed with transcriptome analysis results.

CONCLUSIONS

These genes identified by screening can be used as candidate genes that affect fruit development. The results of the analysis can help guide future genetic improvement of Chinese prickly ash and enrich our understanding of AP2/ERF transcription factors and their regulatory functions in plants.

Exploring the evolution of CHS gene family in plants

Chalcone synthase (CHS) is a key enzyme that catalyzes the first committed step of flavonoid biosynthetic pathway. It plays a vital role not only in maintaining plant growth and development, but also in regulating plant response to environmental hazards. However, the systematic phylogenomic analysis of CHS gene family in a wide range of plant species has not been reported yet. To fill this knowledge gap, a large-scale investigation of CHS genes was performed in 178 plant species covering green algae to dicotyledons. A total of 2,011 CHS and 293 CHS-like genes were identified and phylogenetically divided into four groups, respectively. Gene distribution patterns across the plant kingdom revealed the origin of CHS can be traced back to before the rise of algae. The gene length varied largely in different species, while the exon structure was relatively conserved. Selection pressure analysis also indicated the conserved features of CHS genes on evolutionary time scales. Moreover, our synteny analysis pinpointed that, besides genome-wide duplication and tandem duplication, lineage specific transposition events also occurred in the evolutionary trajectory of CHS gene family. This work provides novel insights into the evolution of CHS gene family and may facilitate further research to better understand the regulatory mechanism of traits relating to flavonoid biosynthesis in diverse plants.

Ancient Duplication and Lineage-Specific Transposition Determine Evolutionary Trajectory of ERF Subfamily across Angiosperms

AP2/ERF transcription factor family plays an important role in plant development and stress responses. Previous studies have shed light on the evolutionary trajectory of the AP2 and DREB subfamilies. However, knowledge about the evolutionary history of the ERF subfamily in angiosperms still remains limited. In this study, we performed a comprehensive analysis of the ERF subfamily from 107 representative angiosperm species by combining phylogenomic and synteny network approaches. We observed that the expansion of the ERF subfamily was driven not only by whole-genome duplication (WGD) but also by tandem duplication (TD) and transposition duplication events. We also found multiple transposition events in Poaceae, Brassicaceae, Poales, Brassicales, and Commelinids. These events may have had notable impacts on copy number variation and subsequent functional divergence of the ERF subfamily. Moreover, we observed a number of ancient tandem duplications occurred in the ERF subfamily across angiosperms, e.g., in Subgroup IX, IXb originated from ancient tandem duplication events within IXa. These findings together provide novel insights into the evolution of this important transcription factor family.

Haploid rhapsody: the molecular and cellular orchestra of in vivo haploid induction in plants

In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms underlying these HI systems remain largely unknown. This review synthesizes the current understanding of HI systems in plants (with a focus on genes and molecular mechanisms involved), including the molecular and cellular interactions which orchestrate the HI process. As most HI systems can function across taxonomic boundaries, we particularly discuss the evidence for conserved mechanisms underlying the process. These include mechanisms involved in preserving chromosomal integrity, centromere function, gamete communication and/or fusion, and maintenance of karyogamy. While significant discoveries and advances on haploid inducer systems have arisen over the past decades, we underscore gaps in understanding and deliberate on directions for further research for a more comprehensive understanding of in vivo HI processes in plants.

Origin and early divergence of tandem duplicated sorbitol transporter genes in Rosaceae: insights from evolutionary analysis of the SOT gene family in angiosperms

Sorbitol is a critical photosynthate and storage substance in the Rosaceae family. Sorbitol transporters (SOTs) play a vital role in facilitating sorbitol allocation from source to sink organs and sugar accumulation in sink organs. While prior research has addressed gene duplications within the SOT gene family in Rosaceae, the precise origin and evolutionary dynamics of these duplications remain unclear, largely due to the complicated interplay of whole genome duplications and tandem duplications. Here, we investigated the synteny relationships among all identified Polyol/Monosaccharide Transporter (PLT) genes in 61 angiosperm genomes and SOT genes in representative genomes within the Rosaceae family. By integrating phylogenetic analyses, we elucidated the lineage-specific expansion and syntenic conservation of PLTs and SOTs across diverse plant lineages. We found that Rosaceae SOTs, as PLT family members, originated from a pair of tandemly duplicated PLT genes within Class III-A. Furthermore, our investigation highlights the role of lineage-specific and synergistic duplications in Amygdaloideae in contributing to the expansion of SOTs in Rosaceae plants. Collectively, our findings provide insights into the genomic origins, duplication events, and subsequent divergence of SOT gene family members. Such insights lay a crucial foundation for comprehensive functional characterizations in future studies.

Highly differentiated genomic properties underpin the different cell walls of Poaceae and eudicots

Plant cell walls of Poaceae and eudicots differ substantially, both in the content and composition of their components. However, the genomic and genetic basis underlying these differences is not fully resolved. In this research, we analyzed multiple genomic properties of 150 cell wall gene families across 169 angiosperm genomes. The properties analyzed include gene presence/absence, copy number, synteny, occurrence of tandem gene clusters, and phylogenetic gene diversity. Results revealed a profound genomic differentiation of cell wall genes between Poaceae and eudicots, often associated with the cell wall diversity between these plant groups. For example, overall patterns of gene copy number variation and synteny were clearly divergent between Poaceae and eudicot species. Moreover, differential Poaceae-eudicot copy number and genomic contexts were observed for all the genes within the BEL1-like HOMEODOMAIN 6 regulatory pathway, which respectively induces and represses secondary cell wall synthesis in Poaceae and eudicots. Similarly, divergent synteny, copy number, and phylogenetic gene diversification were observed for the major biosynthetic genes of xyloglucans, mannans, and xylans, potentially contributing to the differences in content and types of hemicellulosic polysaccharides differences in Poaceae and eudicot cell walls. Additionally, the Poaceae-specific tandem clusters and/or higher copy number of PHENYLALANINE AMMONIA-LYASE, CAFFEIC ACID O-METHYLTRANSFERASE, or PEROXIDASE genes may underly the higher content and larger variety of phenylpropanoid compounds observed in Poaceae cell walls. All these patterns are discussed in detail in this study, along with their evolutionary and biological relevance for cell wall (genomic) diversification between Poaceae and eudicots.

Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species

Syntenic cell wall QTLs (SQTLs) can identify genetic determinants of biomass traits in understudied species based on results from model crops. However, their effective use in plant breeding requires SQTLs to display intraspecific allelic variability and to predict causative loci in other populations/species than the ones used for SQTLs identification. In this study, genome assemblies from different accessions of Arabidopsis, rapeseed, tomato, rice, Brachypodium and maize were used to evaluate the intraspecific variability of SQTLs. In parallel, a genome-wide association study (GWAS) on cell wall quality traits was performed in miscanthus to verify the colocalization between GWAS loci and miscanthus SQTLs. Finally, an analogous approach was applied on a set of switchgrass cell wall QTLs retrieved from the literature. These analyses revealed large SQTLs intraspecific genetic variability, ranging from presence-absence gene variation to SNPs/INDELs and changes in coded proteins. Cell wall genes displaying gene dosage regulation, such as PAL and CAD, displayed presence-absence variation in Brachypodium and rapeseed, while protein INDELs were detected for the Brachypodium homologs of the rice brittle culm-like 8 locus, which may likely impact cell wall quality. Furthermore, SQTLs significantly colocalized with the miscanthus and switchgrass QTLs, with relevant cell wall genes being retained in colocalizing regions. Overall, SQTLs are useful tools to screen germplasm for relevant genes and alleles to improve biomass quality and can increase the efficiency of plant breeding in understudied biomass crops.

An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea

Large-scale transcriptome analysis can provide a systems-level understanding of biological processes. To accelerate functional genomic studies in chickpea, we perform a comprehensive transcriptome analysis to generate full-length transcriptome and expression atlas of protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs) from 32 different tissues/organs via deep sequencing. The high-depth RNA-seq dataset reveal expression dynamics and tissue-specificity along with associated biological functions of PCGs and lncRNAs during development. The coexpression network analysis reveal modules associated with a particular tissue or a set of related tissues. The components of transcriptional regulatory networks (TRNs), including transcription factors, their cognate cis-regulatory motifs, and target PCGs/lncRNAs that determine developmental programs of different tissues/organs, are identified. Several candidate tissue-specific and abiotic stress-responsive transcripts associated with quantitative trait loci that determine important agronomic traits are also identified. These results provide an important resource to advance functional/translational genomic and genetic studies during chickpea development and environmental conditions.

A full-length transcriptome and expression atlas of protein-coding genes and long non-coding RNAs is generated in chickpea. Components of transcriptional regulatory networks and candidate tissue-specific transcripts associated with quantitative trait loci are identified.

Evolution of the DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN subfamily in green plants

Adapting to unfavorable environments is a necessary step in plant terrestrialization and radiation. The dehydration-responsive element-binding (DREB) protein subfamily plays a pivotal role in plant abiotic stress regulation. However, relationships between the origin and expansion of the DREB subfamily and adaptive evolution of land plants are still being elucidated. Here, we constructed the evolutionary history of the DREB subfamily by compiling APETALA2/ethylene-responsive element-binding protein superfamily genes from 169 representative species of green plants. Through extensive phylogenetic analyses and comparative genomic analysis, our results revealed that the DREB subfamily diverged from the ethylene-responsive factor (ERF) subfamily in the common ancestor of Zygnemophyceae and Embryophyta during the colonization of land by plants, followed by expansions to form three different ancient archetypal genes in Zygnemophyceae species, designated as groups archetype-I, archetype-II/III, and archetype-IV. Four large-scale expansions paralleling the evolution of land plants led to the nine-subgroup divergence of group archetype-II/III in angiosperms, and five whole-genome duplications during Brassicaceae and Poaceae radiation shaped the diversity of subgroup IIb-1. We identified a Poaceae-specific gene in subgroup IIb-1, ERF014, remaining in a Poaceae-specific microsynteny block and co-evolving with a small heat shock protein cluster. Expression analyses demonstrated that heat acclimation may have driven the neofunctionalization of ERF014s in Pooideae by engaging in the conserved heat-responsive module in Poaceae. This study provides insights into lineage-specific expansion and neofunctionalization in the DREB subfamily, together with evolutionary information valuable for future functional studies of plant stress biology.

BABY BOOM regulates early embryo and endosperm development

The zygote is a totipotent structure that develops into an embryo with all of the cells needed to produce an entire plant. The BABY BOOM (BBM) transcription factor induces spontaneous asexual embryo development on plant organs when ectopically expressed. Although BBM is at the top of a transcriptional network that promotes asexual embryo development, little is known about its expression and role during zygotic embryogenesis. Here we show in Arabidopsis that BBM regulates the progression of zygotic embryo development and embryo patterning, and division and cellularization of the filial endosperm. In line with its role as a totipotency factor, ectopic BBM expression in the egg cell is also sufficient to induce haploid embryo development in Arabidopsis and dicot crops.

The BABY BOOM (BBM) AINTEGUMENTA-LIKE (AIL) AP2/ERF domain transcription factor is a major regulator of plant cell totipotency, as it induces asexual embryo formation when ectopically expressed. Surprisingly, only limited information is available on the role of BBM during zygotic embryogenesis. Here we reexamined BBM expression and function in the model plant Arabidopsis thaliana (Arabidopsis) using reporter analysis and newly developed CRISPR mutants. BBM was expressed in the embryo from the zygote stage and also in the maternal (nucellus) and filial (endosperm) seed tissues. Analysis of CRISPR mutant alleles for BBM (bbm-cr) and the redundantly acting AIL gene PLETHORA2 (PLT2) (plt2-cr) uncovered individual roles for these genes in the timing of embryo progression. We also identified redundant roles for BBM and PLT2 in endosperm proliferation and cellularization and the maintenance of zygotic embryo development. Finally, we show that ectopic BBM expression in the egg cell of Arabidopsis and the dicot crops Brassica napus and Solanum lycopersicon is sufficient to bypass the fertilization requirement for embryo development. Together these results highlight roles for BBM and PLT2 in seed development and demonstrate the utility of BBM genes for engineering asexual embryo development in dicot species.

Identification of genes differentially expressed between prostrate shoots and erect shoots in the lycophyte Selaginella nipponica using an RNA-seq approach

Lycophytes are the earliest vascular plants and Selaginella is the most studied genus among them. Prostrate shoots are produced during early growth and erect shoots emerge later in S. nipponica, thus providing an opportunity for exploring the evolution of the mechanism underlying the transition between growth phases. Six libraries were sequenced for the prostrate and the erect shoots, and a total of 206 768 genes were identified. Some genes were differentially expressed in prostate and erect shoot, with relatively high expression in the prostate shoots being related to hormone responses and defence reactions, while higher expression in the erect shoots was related to spore formation and shoot development. Some SPL genes possessed a miR156 binding site and were highly expressed in the erect shoots, while AP2-like genes were more highly expressed in the prostrate shoots but simultaneously lacked any miR172 binding site. MiR156 was detected at a higher concentration in the prostrate shoots. Thus, the mechanism for the vegetative to reproductive transition of sporophytes probably originated in the common ancestor of vascular plants and must have experienced stepwise development during evolution.

Draft genome sequence of Indian mulberry (Morus indica) provides a resource for functional and translational genomics

Mulberry is an important crop plant for the sericulture industry. Here, we report high-quality genome sequence of a cultivated Indian mulberry (Morus indica cv K2) obtained by combining data from four different technologies, including Illumina, single-molecule real-time sequencing, chromosome conformation capture and optical mapping, with a gene completeness of 96.5%. Based on the genome sequence, we identified 49.2% of repetitive DNA and 27,435 high-confidence protein-coding genes with >90% of them supported by transcript evidence. A comparative analysis with other plant genomes identified 4.8% of species-specific genes in the M. indica genome. Transcriptome profiling revealed tissue-specific and differential expression across multiple accessions of ~4.7% and 2-5% of protein-coding genes, respectively, implicated in diverse biological processes. Whole genome resequencing of 21 accessions/species revealed ~2.5 million single nucleotide polymorphisms and ~ 0.2 million insertions/deletions. These data and results provide a comprehensive resource to accelerate the genomics research in mulberry for its improvement.

Genomic Architecture and Evolution of the Cellulose synthase Gene Superfamily as Revealed by Phylogenomic Analysis

The Cellulose synthase superfamily synthesizes cellulose and different hemicellulosic polysaccharides in plant cell walls. While much has been discovered about the evolution and function of these genes, their genomic architecture and relationship with gene (sub-)functionalization and evolution remains unclear. By using 242 genomes covering plant evolution from green algae to eudicots, we performed a large-scale analysis of synteny, phylogenetic, and functional data of the CesA superfamily. Results revealed considerable gene copy number variation across species and gene families, and also two patterns - singletons vs. tandem arrays - in chromosomic gene arrangement. Synteny analysis revealed exceptional conservation of gene architecture across species, but also lineage-specific patterns across gene (sub-)families. Synteny patterns correlated with gene sub-functionalization into primary and secondary CesAs and distinct CslD functional isoforms. Furthermore, a genomic context shift of a group of cotton secondary CesAs was associated with peculiar properties of cotton fiber synthesis. Finally, phylogenetics suggested that primary CesA sequences appeared before the secondary CesAs, while phylogenomic analyses unveiled the genomic trace of the CslD duplication that initiated the CslF family. Our results describe in detail the genomic architecture of the CesA superfamily in plants, highlighting its crucial relevance for gene diversification and sub-functionalization, and for understanding their evolution.

Phylogenomic classification and synteny network analyses deciphered the evolutionary landscape of aldo-keto reductase (AKR) gene superfamily in the plant kingdom

Aldo-keto reductase-domain (PF00248) containing proteins (AKRs) are NAD(P)(H)-dependent oxidoreductases of a multigene superfamily that mediate versatile functions in plants ranging from detoxification, metal chelation, potassium ion efflux to specialized metabolism. To uncover the complete repertoire of AKR gene superfamily in plants, a systematic kingdom-wide identification, phylogeny reconstruction, classification and synteny network clustering analyses were performed in this study using 74 diverse plant genomes. Plant AKRs were omnipresent, legitimately classified into 4 groups (based on phylogeny) and 14 subgroups (based on the ≥ 60% of protein sequence identity). Species composition of AKR subgroups highlights their distinct emergence during plant evolution. Loss of AKR subgroups among plants was apparent and that various lineage-, order/family- and species-specific losses were observed. The subgroups IA, IVB and IVF were flourished and diversified well during plant evolution, likely related to the complexity of plant's specialized metabolism and environmental adaptation. About 65% of AKRs were in genomic synteny regions across the plant kingdom and the AKRs relevant to important functions (e.g. vitamin B₆ metabolism) were in profoundly conserved angiosperm-wide synteny communities. This study underscores the evolutionary landscape of plant AKRs and provides a comprehensive resource to facilitate the functional characterization of them.

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants

Multidrug and toxic compound extrusion (MATE) transporters comprise a multigene family that mediates multiple functions in plants through the efflux of diverse substrates including organic molecules, specialized metabolites, hormones, and xenobiotics. MATE classification based on genome-wide studies remains ambiguous, likely due to a lack of large-scale phylogenomic studies and/or reference sequence datasets. To resolve this, we established a phylogeny of the plant MATE gene family using a comprehensive kingdom-wide phylogenomic analysis of 74 diverse plant species. We identified more than 4,000 MATEs, which were classified into 14 subgroups based on a systematic bioinformatics pipeline using USEARCH, blast+ and synteny network tools. Our classification was performed using a four-step process, whereby MATEs sharing ≥ 60% protein sequence identity with a ≤ 1E-05 threshold at different sequence lengths (either full-length, ≥ 60% length, or ≥ 150 amino acids) or retaining in the similar synteny blocks were assigned to the same subgroup. In this way, we assigned subgroups to 95.8% of the identified MATEs, which we substantiated using synteny network clustering analysis. The subgroups were clustered under four major phylogenetic groups and named according to their clockwise appearance within each group. We then generated a reference sequence dataset, the usefulness of which was demonstrated in the classification of MATEs in additional species not included in the original analysis. Approximately 74% of the plant MATEs exhibited synteny relationships with angiosperm-wide or lineage-, order/family-, and species-specific conservation. Most subgroups evolved independently, and their distinct evolutionary trends were likely associated with the development of functional novelties or the maintenance of conserved functions. Together with the systematic classification and synteny network profiling analyses, we identified all the major evolutionary events experienced by the MATE gene family in plants. We believe that our findings and the reference dataset provide a valuable resource to guide future functional studies aiming to explore the key roles of MATEs in different aspects of plant physiology. Our classification framework can also be readily extendable to other (super) families.

A conserved superlocus regulates above- and belowground root initiation

Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato (Solanum lycopersicum) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS (SBRL). Evolutionary analysis reveals that SBRL's function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.

Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants

In comparative genomics, the study of synteny can be a powerful method for exploring genome rearrangements, inferring genomic ancestry, defining orthology relationships, determining gene and genome duplications, and inferring gene positional conservation patterns across taxa. In this chapter, we present a step-by-step protocol for microsynteny network (SynNet) analysis, as an alternative to traditional methods of synteny comparison, where nodes in the network represent protein-coding genes and edges represent the pairwise syntenic relationships. The SynNet pipeline consists of six main steps: (1) pairwise genome comparisons between all the genomes being analyzed, (2) detection of inter- and intrasynteny blocks, (3) generation of an entire synteny database (i.e., edgelist), (4) network clustering, (5) phylogenomic profiling of the gene family of interest, and (6) evolutionary inference. The SynNet approach facilitates the rapid analysis and visualization of synteny relationships (from specific genes, specific gene families up to all genes) across a large number of genomes.

Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants

Nitrate transporter 2 (NRT2) and NRT3 or nitrate-assimilation-related 2 (NAR2) proteins families form a two-component, high-affinity nitrate transport system, which is essential for the acquisition of nitrate from soils with low N availability. An extensive phylogenomic analysis across land plants for these families has not been performed. In this study, we performed a microsynteny and orthology analysis on the NRT2 and NRT3 genes families across 132 plants (Sensu lato) to decipher their evolutionary history. We identified significant differences in the number of sequences per taxonomic group and different genomic contexts within the NRT2 family that might have contributed to N acquisition by the plants. We hypothesized that the greater losses of NRT2 sequences correlate with specialized ecological adaptations, such as aquatic, epiphytic, and carnivory lifestyles. We also detected expansion on the NRT2 family in specific lineages that could be a source of key innovations for colonizing contrasting niches in N availability. Microsyntenic analysis on NRT3 family showed a deep conservation on land plants, suggesting a high evolutionary constraint to preserve their function. Our study provides novel information that could be used as guide for functional characterization of these gene families across plant lineages.

Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses

In response to various environmental stresses, plants have evolved a wide range of defense mechanisms, resulting in the overexpression of a series of stress-responsive genes. Among them, there is certain set of genes that encode for intrinsically disordered proteins (IDPs) that repair and protect the plants from damage caused by environmental stresses. Group II LEA (late embryogenesis abundant) proteins compose the most abundant and characterized group of IDPs; they accumulate in the late stages of seed development and are expressed in response to dehydration, salinity, low temperature, or abscisic acid (ABA) treatment. The physiological and biochemical characterization of group II LEA proteins has been carried out in a number of investigations because of their vital roles in protecting the integrity of biomolecules by preventing the crystallization of cellular components prior to multiple stresses. This review describes the distribution, structural architecture, and genomic diversification of group II LEA proteins, with some recent investigations on their regulation and molecular expression under various abiotic stresses. Novel aspects of group II LEA proteins in Phoenix dactylifera and in orthodox seeds are also presented. Genome-wide association studies (GWAS) indicated a ubiquitous distribution and expression of group II LEA genes in different plant cells. In vitro experimental evidence from biochemical assays has suggested that group II LEA proteins perform heterogenous functions in response to extreme stresses. Various investigations have indicated the participation of group II LEA proteins in the plant stress tolerance mechanism, spotlighting the molecular aspects of group II LEA genes and their potential role in biotechnological strategies to increase plants' survival in adverse environments.

The Evolution of euAPETALA2 Genes in Vascular Plants: From Plesiomorphic Roles in Sporangia to Acquired Functions in Ovules and Fruits

The field of evolutionary developmental biology can help address how morphological novelties evolve, a key question in evolutionary biology. In Arabidopsis thaliana, APETALA2 (AP2) plays a role in the development of key plant innovations including seeds, flowers, and fruits. AP2 belongs to the AP2/ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR family which has members in all viridiplantae, making it one of the oldest and most diverse gene lineages. One key subclade, present across vascular plants is the euAPETALA2 (euAP2) clade, whose founding member is AP2. We reconstructed the evolution of the euAP2 gene lineage in vascular plants to better understand its impact on the morphological evolution of plants, identifying seven major duplication events. We also performed spatiotemporal expression analyses of euAP2/TOE3 genes focusing on less explored vascular plant lineages, including ferns, gymnosperms, early diverging angiosperms and early diverging eudicots. Altogether, our data suggest that euAP2 genes originally contributed to spore and sporangium development, and were subsequently recruited to ovule, fruit and floral organ development. Finally, euAP2 protein sequences are highly conserved; therefore, changes in the role of euAP2 homologs during development are most likely due to changes in regulatory regions.

Genome-wide investigation and expression analysis of APETALA-2 transcription factor subfamily reveals its evolution, expansion and regulatory role in abiotic stress responses in Indica Rice (Oryza sativa L. ssp. indica)

Rice is an important cereal crop that serves as staple food for more than half of the world population. Abiotic stresses resulting from changing climatic conditions are continuously threating its yield and production. Genes in APETALA-2 (AP2) family encode transcriptional regulators implicated during regulation of developmental processes and abiotic stress responses but their identification and characterization in indica rice was still missing. In this context, twenty-six genes distributed among eleven chromosomes in Indica rice encoding AP2 transcription-factor subfamily were identified and their diverse haplotypes were studied. Phylogenetic analysis of OsAP2 TF family-members grouped them into three clades indicating conservation of clades among cereals. Segmental duplications were observed to be principal route of evolution, supporting the higher positive selection-pressure, which were estimated to be originated about 10.57 to 56.72 million years ago (MYA). Conserved domain analysis and intron-exon distribution pattern of identified OsAP2s revealed their exclusive distribution among the specific clades of the phylogenetic tree. Moreover, the members of osa-miR172 family were also identified potentially targeting four OsAP2 genes. The real-time quantitative expression profiling of OsAP2s under heat stress conditions in contrasting indica rice genotypes revealed the differential expression pattern of OsAP2s (6 genes up-regulated and 4 genes down-regulated) in stress- and genotype-dependent manner. These findings unveiled the evolutionary pathways of AP2-TF in rice, and can help the functional characterization under developmental and stress responses.