Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization

Identification and Characterization of EIN3/EIL Transcription Factor Family Members in Pinus massoniana Lamb

Transcription factors refer to types of proteins that perform significant functions in the process of gene expression regulation. The ethylene insensitive 3/ethylene insensitive 3-like (EIN3/EIL) family, functioning as significant transcription factors regulating ethylene, plays a critical role in the growth and development of plants and participates in the plant's response to diverse environmental stresses. Pinus massoniana is an excellent native tree with high economic and ecological value. However, the study of EIN3/EIL genes in gymnosperms, for instance, P. massoniana, is still relatively limited. In this research, four putative EIN3/EIL genes were identified in the transcriptome of P. massoniana. Bioinformatics analysis showed that PmEIL genes contain a highly conserved EIN3 domain and other structural features of acidic, proline-rich and glutamine-rich sites. The molecular evolution tree analysis demonstrated that the EIN3/EIL family was partitioned into three categories (A, B, and C), and the number, type, and distribution of conserved motifs grouped in one category were similar. The results of qRT-PCR indicated that the expression levels of PmEIL genes were markedly elevated in needles compared to other tissues. Through the analysis of expression patterns of the PmEIL genes under various stress treatments, it was found that the PmEIL genes could participate in plant hormone stimulation induction, osmosis, drought and other response processes. In addition, PmEIL is a nuclear localization protein. PmEIL1, PmEIL3, and PmEIL4 are transcriptional activators, while PmEIL2 is a transcriptional suppressor. This research provides a basis for further elucidating the function of EIN3/EIL transcription factors in growth, development and stress response of P. massoniana.

An EIL Family Transcription Factor From Switchgrass Affects Sulphur Assimilation and Root Development in Arabidopsis

Sulphur limitation 1 (SLIM1), a member of ethylene-insensitive3-like (EIN3/EIL) protein family, is recognised as the pivotal transcription factor regulating sulphur assimilation, essential for maintaining sulphur homoeostasis in Arabidopsis. However, the function of its monocot homologues is largely unknown. In this study, we identified PvEIL3a, a homologous gene of AtSLIM1, from switchgrass (Panicum virgatum L.), a significant perennial bioenergy crop. Our results demonstrated that introducing PvEIL3a into Arabidopsis slim1 mutants significantly increased the expression of genes responsive to sulphur deficiency, and transgenic plants exhibited shortened root length and delayed development. Moreover, PvEIL3a activated the expression of AtAPR1, AtSULTR1;1 and AtBGLU30, which plays an important role in sulphur assimilation and glucosinolate metabolism. Results of transcriptome and metabonomic analysis further indicated a perturbation in the metabolic pathways of tryptophan-dependent indole glucosinolates (IGs), camalexin and auxin. In addition, PvEIL3a conservatively regulated sulphur assimilation and the biosynthesis of tryptophan pathway-derived secondary metabolites, which reduced the biosynthesis of indole-3-acetic acid (IAA) and inhibited the root elongation of transgenic Arabidopsis. In conclusion, this study highlights the functional difference of the ethylene-insensitive 3-like (EIL) family gene in monocot and dicot plants, thereby deepening the understanding of the specific biological roles of EIL3 in monocot plant species.

The Stilbene Synthase Family in Arachis: A Genome-Wide Study and Functional Characterization in Response to Stress

Peanut (Arachis hypogaea) and its wild relatives are among the few species that naturally synthesize resveratrol, a well-known stilbenoid phytoalexin that plays a crucial role in plant defense against biotic and abiotic stresses. Resveratrol has received considerable attention due to its health benefits, such as preventing and treating various human diseases and disorders. Chalcone (CHS) and Stilbene (STS) Synthases are plant-specific type III Polyketide Synthases (PKSs) that share the same substrates and are key branch enzymes in the biosynthesis of flavonoids and stilbenoids, respectively. Although resveratrol accumulation in response to external stimulus has been described in peanut, there are no comprehensive studies of the CHS and STS gene families in the genus Arachis. In the present study, we identified and characterized 6 CHS and 46 STS genes in the tetraploid peanut and an average of 4 CHS and 22 STS genes in three diploid wild species (Arachis duranensis, Arachis ipaënsis and Arachis stenosperma). The CHS and STS gene and protein structures, chromosomal distributions, phylogenetic relationships, conserved amino acid domains, and cis-acting elements in the promoter regions were described for all Arachis species studied. Based on gene expression patterns of wild A. stenosperma STS genes in response to different biotic and abiotic stresses, we selected the candidate AsSTS4 gene, which is strongly induced by ultraviolet (UV) light exposure, for further functional investigation. The AsSTS4 overexpression in peanut hairy roots significantly reduced (47%) root-knot nematode infection, confirming that stilbene synthesis activation in transgenic plants can increase resistance to pathogens. These findings contribute to understanding the role of resveratrol in stress responses in Arachis species and provide the basis for genetic engineering for improved production of valuable secondary metabolites in plants.

Unleashing the Potential of EIL Transcription Factors in Enhancing Sweet Orange Resistance to Bacterial Pathologies: Genome-Wide Identification and Expression Profiling

The ETHYLENE INSENSITIVE3-LIKE (EIL) family is one of the most important transcription factor (TF) families in plants and is involved in diverse plant physiological and biochemical processes. In this study, ten EIL transcription factors (CsEILs) in sweet orange were systematically characterized via whole-genome analysis. The CsEIL genes were unevenly distributed across the four sweet orange chromosomes. Putative cis-acting regulatory elements (CREs) associated with CsEIL were found to be involved in plant development, as well as responses to biotic and abiotic stress. Notably, quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that CsEIL genes were widely expressed in different organs of sweet orange and responded to both high and low temperature, NaCl treatment, and to ethylene-dependent induction of transcription, while eight additionally responded to Xanthomonas citri pv. Citri (Xcc) infection, which causes citrus canker. Among these, CsEIL2, CsEIL5 and CsEIL10 showed pronounced upregulation. Moreover, nine genes exhibited differential expression in response to Candidatus Liberibacter asiaticus (CLas) infection, which causes Citrus Huanglongbing (HLB). The genome-wide characterization and expression profile analysis of CsEIL genes provide insights into the potential functions of the CsEIL family in disease resistance.

Genome-wide characterization of the NLR gene family in tomato (Solanum lycopersicum) and their relatedness to disease resistance

Nucleotide-binding leucine-rich-repeat receptors (NLR), the largest group of genes associated with plant disease resistance (R), have attracted attention due to their crucial role in protecting plants from pathogens. Genome-wide studies of NLRs have revealed conserved domains in the annotated tomato genome. The 321 NLR genes identified in the tomato genome have been randomly mapped to 12 chromosomes. Phylogenetic analysis and classification of NLRs have revealed that 211 genes share full-length domains categorized into three major clades (CNL, TNL, and RNL); the remaining 110 NLRs share partial domains and are classified in CN, TN, and N according to their motifs and gene structures. The cis-regulatory elements of NLRs exhibit the maximum number of these elements and are involved in response to biotic and abiotic stresses, pathogen recognition, and resistance. Analysis of the phylogenetic relationship between tomato NLRs and orthologs in other species has shown conservation among Solanaceae members and variation with A. thaliana. Synteny and Ka/Ks analyses of Solanum lycopersicum and Solanum tuberosum orthologs have underscored the importance of NLR conservation and diversification from ancestral species millions of years ago. RNA-seq data and qPCR analysis of early and late blight diseases in tomatoes revealed consistent NLR expression patterns, including upregulation in infected compared to control plants (with some exceptions), suggesting the role of NLRs as key regulators in early blight resistance. Moreover, the expression levels of NLRs associated with late blight resistance (Solyc04g007060 [NRC4] and Solyc10g008240 [RIB12]) suggested that they regulate S. lycopersicum resistance to P. infestans. These findings provide important fundamental knowledge for understanding NLR evolution and diversity and will empower the broader characterization of disease resistance genes for pyramiding through speed cloning to develop disease-tolerant varieties.

Origin, Expansion, and Divergence of ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE Transcription Factors During Streptophytes Evolution

The transition of plants to land required several regulatory adaptive mechanisms. Little is known about these mechanisms, but they no doubt involved the evolution of transcription factor (TF) families. ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) transcription factors (TFs) are core components of the ethylene signaling pathway that play important roles in almost every aspect of plant development and environmental responses by regulating the transcription of numerous genes. However, the evolutionary history of EIN3/EIL TFs, which are present in a wide range of streptophytes, is still not clear. Here, to explore the evolution and functions of EIN3/EIL TFs, we performed phylogenetic analysis of these TFs and investigated their gene and protein structures as well as sequence features. Our results suggest that the EIN3/EIL TF family was already was already present in the ancestor of streptophyte algae. Phylogenetic analysis divided the EIN3/EIL TFs into three groups (Group A-C). Analysis of gene and protein structure revealed that most of the structural features of these TFs had already formed in ancient lineages. Further investigation suggested that all groups have undergone several duplication events related to whole-genome duplications in plants, generating multiple, functionally diverse gene copies. Therefore, as plants colonized terrestrial habitats and evolved key traits, the EIN3/EIL TF family expanded broadly via multiple duplication events, which could have promoted their fundamental neo- and sub-functionalization to help plants adapt to terrestrial life. Our findings shed light on the functional evolution of the EIN3/EIL TF family in the streptophytes.

Comprehensive Evolutionary Analysis of CPP Genes in Brassica napus L. and Its Two Diploid Progenitors Revealing the Potential Molecular Basis of Allopolyploid Adaptive Advantage Under Salt Stress

Allopolyploids exist widely in nature and have strong environmental adaptability. The typical allopolyploid Brassica napus L. is a widely cultivated crop, but whether it is superior to its diploid progenitors in abiotic stress resistance and the key genes that may be involved are not fully understood. Cystein-rich polycomb-like protein (CPP) genes encode critical transcription factors involved in the response of abiotic stress, including salt stress. To explore the potential molecular basis of allopolyploid adaptation to salt stress, we comprehensively analyzed the characteristics and salt stress response of the CPP genes in B. napus and its two diploid progenitors in this study. We found some molecular basis that might be associated with the adaptability of B. napus, including the expansion of the CPP gene family, the acquisition of introns by some BnCPPs, and abundant cis-acting elements upstream of BnCPPs. We found two duplication modes (whole genome duplication and transposed duplication) might be the main reasons for the expansion of CPP gene family in B. napus during allopolyploidization. CPP gene expression levels and several physiological indexes were changed in B. napus and its diploid progenitors after salt stress, suggesting that CPP genes might play important roles in the response of salt stress. We found that some BnCPPs might undergo new functionalization or subfunctionalization, and some BnCPPs also show biased expression, which might contribute to the adaptation of B. napus under saline environment. Compared with diploid progenitors, B. napus showed stronger physiological responses, and BnCPP gene expression also showed higher changes after salt stress, indicating that the allopolyploid B. napus had an adaptive advantage under salt stress. This study could provide evidence for the adaptability of polyploid and provide important clues for the study of the molecular mechanism of salt stress resistance in B. napus.

Clone and Function Verification of the OPR gene in Brassica napus Related to Linoleic Acid Synthesis

BACKGROUND

Fatty acid composition and content affect rapeseed oil quality. Fatty acid synthesis-related genes in rapeseed have been studied globally by researchers. Nevertheless, rapeseed oil is mainly composed of seven different fatty acids (FA), and each fatty acid was regulated by different genes. Furthermore, different FA affect each other, which needs continuous and in-depth research to obtain more clear results in Brassica napus.

RESULTS

In this paper, broad-scale miRNA expression profiles were constructed and 21 differentially expressed miRNAs were detected. GO enrichment analysis showed that most up-regulated proteins were involved in transcription factor activity and catalytic activity. KEGG pathway enrichment analysis indicated that 20 pathways involving 36 target genes were enriched, of which the bna00592 pathway may be involved in fatty acid metabolism. The results were verified using a quantitative real-time PCR (RT-qPCR) analysis, we found that the target gene of bna-miR156b > c > g was the OPR (12-oxo-phytodienoic acid reductase). Four copies of OPR gene were found, and the over-expression vectors (pCAMBIA1300-35 s-OPR and pCAMBIA1300-RNAi-OPR) were constructed to verify their functions. In T1 and T2 generation, the content of linoleic acid (LA) increased significantly in OE but deceased in OPRi.

CONCLUSIONS

This is the first study to provide four copies of the OPR gene that regulates LA metabolism, can be used for the molecular mechanism of LA and optimizing fatty acid profiles in oilseed for breeding programs.

Genome-Wide Identification of the TIFY Gene Family in Brassiceae and Its Potential Association with Heavy Metal Stress in Rapeseed

The TIFY gene family plays important roles in various plant biological processes and responses to stress and hormones. The chromosome-level genome of the Brassiceae species has been released, but knowledge concerning the TIFY family is lacking in the Brassiceae species. The current study performed a bioinformatics analysis on the TIFY family comparing three diploid (B. rapa, B. nigra, and B. oleracea) and two derived allotetraploid species (B. juncea, and B. napus). A total of 237 putative TIFY proteins were identified from five Brassiceae species, and classified into ten subfamilies (six JAZ types, one PPD type, two TIFY types, and one ZML type) based on their phylogenetic relationships with TIFY proteins in A. thaliana and Brassiceae species. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the TIFY family genes during the process of polyploidization, and most of these TIFY family genes (TIFYs) were subjected to purifying selection after duplication based on Ka/Ks values. The spatial and temporal expression patterns indicated that different groups of BnaTIFYs have distinct spatiotemporal expression patterns under normal conditions and heavy metal stresses. Most of the JAZIII subfamily members were highest in all tissues, but JAZ subfamily members were strongly induced by heavy metal stresses. BnaTIFY34, BnaTIFY59, BnaTIFY21 and BnaTIFY68 were significantly upregulated mostly under As3+ and Cd2+ treatment, indicating that they could be actively induced by heavy metal stress. Our results may contribute to further exploration of TIFYs, and provided valuable information for further studies of TIFYs in plant tolerance to heavy metal stress.

Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp

The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant's adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.

Identification and Analysis of the EIN3/EIL Gene Family in Populus × xiaohei T. S. Hwang et Liang: Expression Profiling during Stress

The ethylene-insensitive 3-like (EIN3/EIL) gene family, as a transcriptional activator in plants, not only plays an important role in the ethylene-signaling pathway in regulating plant growth and development but also participates in the defense against various biotic and abiotic stresses. However, there are few studies on the functions of EIN3/EIL genes in woody plants. Populus × xiaohei is a kind of tree species with strong drought resistance and salt-alkali tolerance and, thus, is an ideal subject for studying abiotic stress mechanisms in trees. Eight EIN3/EIL genes were cloned from Populus × xiaohei. Bioinformatic analysis showed that the PsnEIN3/EIL gene contained a highly conserved EIN3 domain, N-terminal sites rich in proline and glutamine, and other EIN3/EIL family structural characteristics. The results of a multi-species phylogenetic analysis showed that the family EIN3/EIL proteins were divided into three groups (A, B, and C). EIL3 and EIL4 belonged to groups A and B, while EIL2 and EIN3 generally belonged to group C. Analysis of tissue expression characteristics showed that PsnEIN3/EIL was expressed in different tissues and was involved in the development of stem nodes and leaves. The response analysis of the expression of PsnEIN3/EIL under abscisic acid (ABA) and abiotic stresses (salts, heavy metals, alkaline conditions, and drought) showed changes in expression, suggesting that PsnEIN3/EIL may be involved in the processes of plant hormone responses to salts, heavy metals, alkaline conditions, and drought. This study provides a foundation for further elucidation of the functions of EIN3/EIL genes in forest growth and development and abiotic stress responses.

The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus

Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes occurred in allopolyploids. What evolutionary changes of transcripts have taken place in Brassica napus during the early establishment and subsequent evolution was a fascinating scientific question. Here, we study this issue using a set of materials (natural, resynthesized B. napus and their progenitors/parents) by long-read RNA sequencing technology. The results showed that more genes were up-regulated in resynthesized B. napus compared with its two parents, and more up-regulated expressed genes were observed in natural B. napus compared with resynthesized B. napus. The presence of up-regulation genes in organism may help it adapt to the influence of "genomic shock" and cope with natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of novel isoforms were identified in all materials, which could improve the reference genome information of B. napus. We found that the isoform numbers, the number of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, which may involve in the adaptation of plants to natural environment. In addition, all identified isoforms were functional annotated by searching 7 databases. In general, this study could improve our overall understanding of the full-length transcriptome of B. napus, and help us recognize the significant gene expression changes and isoform abundance changes occurred in allopolyploid B. napus during evolution.

Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations

We provided a study on homeologous gene evolution of homeologous genes by comparing Brassica genomes. Polyploidy has played fundamental roles during the evolution of plants. Following polyploidization, many duplicated genes are diversified or lost in a process termed diploidization. Understanding the retention and diversification of homeologs after polyploidization will help elucidate the process of diploidization. Here, we investigated the evolution of homeologous genes in Brassica genomes and observed similarly asymmetrical gene retention among different functional groups and consistent retention after recurrent polyploidizations. In the comparative analysis of Brassica diploid genomes, we found that preferentially retained genes show different patterns on sequence and expression divergence: genes with the function of 'biosynthetic process' and 'transport' were under much stronger purifying selection, while transcriptional regulatory genes diverged much faster than other genes. Duplicate pairs of the former two functional groups show conserved high expression patterns, while most of transcriptional regulatory genes are simultaneously lowly expressed. Furthermore, homeologs in diploids and allotetraploids showed similar loss and retention patterns: duplicates in progenitor genomes were more likely to be retained and accumulated fewer substitutions. However, transcriptional regulation is also enriched in the genes that do not have any non-synonymous mutations in the Brassica allotetraploids, indicating that some of these genes were under strong purifying selection. Overall, our study provided insight into the evolution of homeologs genes during diploidization process.

Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus

DNA binding with one finger (DOF) proteins are plant-specific transcription factors that play roles in diverse plant functions. However, little is known about the DOF protein repertoire of the allopolyploid crop, Brassica napus. This in silico study identified 117 Brassica napus Dof genes (BnaDofs) and classified them into nine groups (A, B1, B2, C1, C2.1, C2.2, C3, D1, and D2), based on phylogenetic analysis. Most members belonging to a particular group displayed conserved gene structural organisation and protein motif distribution. Evolutionary analysis exemplified that the divergence of the Brassica genus from Arabidopsis, the whole-genome triplication event, and the hybridisation of Brassica oleracea and Brassica rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of the Dof transcription factor (TF) gene family in B. napus. So far, this is the largest number of Dof genes reported in a single eudicot species. Functional annotation of BnaDof proteins, cis-element analysis of their promoters, and transcriptomic analysis suggested potential roles in organ development, the transition from the vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness, as well as potential regulatory roles in abiotic stress. Overall, our results provide a comprehensive understanding of the molecular structure, evolution, and possible functional roles of Dof genes in plant development and abiotic stress response.

Genome-wide mining and comparative analysis of fatty acid elongase gene family in Brassica napus and its progenitors

Very long chain fatty acids (VLCFAs) that are structural components of cell membrane lipid, cuticular waxes and seed oil, play crucial roles in plant growth, development and stress response. Fatty acid elongases (FAEs) comprising KCS and ELO, are key enzymes for VLCFA biosynthesis in plants. Although reference genomes of Brassica napus and its parental speices both have been sequenced, whole-genome analysis of FAE gene family in these Brassica speices is not reported. Here, 58, 33 and 30 KCS genes were identified in B. napus, B. rapa and B. oleracea genomes, respectively, whereas 14, 6 and 8 members were obtained for ELO genes. These KCS genes were unevenly located in 37 chromosomes and 3 scaffolds of 3 Brassica species, while these ELO genes were mapped to 19 chromosomes. The KCS and ELO proteins were divided into 8 and 4 subclasses, respectively. Gene structure and protein motifs remained highly conserved in each KCS or ELO subclass. Most promoters of KCS and ELO genes harbored various plant growth-, phytohormone-, and stress response-related cis-acting elements. 20 SSR loci existed in the KCS and ELO genes/promoters. The whole-genome duplication and segmental duplication mainly contributed to expansion of KCS and ELO genes in these genomes. Transcriptome analysis showed that KCS and ELO genes in 3 Brassica species were expressed in various tissues/organs with different levels, whereas 1 BnELO gene and 6 BnKCS genes might be pathogen-responsive genes. The qRT-PCR assay showed that BnKCS22 and BnELO04 responded to various phytohormone treatments and abiotic stresses. This work lays the foundation for further function identification of KCS and ELO genes in B. napus and its progenitors.

Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance

Phosphorus transporter (PHT) genes encode H2PO4-/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1-PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.

Sequential Paleotetraploidization shaped the carrot genome

BACKGROUND

Carrot (Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrences, and nature of these events are not clearly defined.

RESULTS

Using a previously published comparative genomics pipeline, we reanalysed the carrot genome and characterized genomic fractionation, as well as gene loss and retention, after each of the two tetraploidization events and inferred a dominant and sensitive subgenome for each event. In particular, we found strong evidence of two sequential tetraploidization events, with one (Dc-α) approximately 46-52 million years ago (Mya) and the other (Dc-β) approximately 77-87 Mya, both likely allotetraploidization in nature. The Dc-β event was likely common to all Apiales plants, occurring around the divergence of Apiales-Bruniales and after the divergence of Apiales-Asterales, likely playing an important role in the derivation and divergence of Apiales species. Furthermore, we found that rounds of polyploidy events contributed to the expansion of gene families responsible for plastidial methylerythritol phosphate (MEP), the precursor of carotenoid accumulation, and shaped underlying regulatory pathways. The alignment of orthologous and paralogous genes related to different events of polyploidization and speciation constitutes a comparative genomics platform for studying Apiales, Asterales, and many other related species.

CONCLUSIONS

Hierarchical inference of homology revealed two tetraploidization events that shaped the carrot genome, which likely contributed to the successful establishment of Apiales plants and the expansion of MEP, upstream of the carotenoid accumulation pathway.

Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.