Gene Subfamily Research Articles

The LEA2 gene sub-family: Characterization, evolution, and potential functions in Camellia oleifera seed development and stress response

Camellia oleifera (C. oleifera) is a woody plant that is important economically due to its oil production. Late embryonic abundant (LEA) proteins are hydrophilic and thermostable proteins that accumulate during the late stages of embryo development, serving vital functions in plant development, seed oil accumulation, and stress responses. However, it remains unclear how LEAs regulate seed size, oil accumulation, and stress responses in C. oleifera. In our study, 47 LEA genes were identified across the C. oleifera genome, which were named based on their chromosomal distribution and separated into LEA2 subgroups. Ancient duplication events resulted in 3 tandem and 8 segmental duplications in the C. oleifera genome. Further analysis of genetic structure, motifs, and cis-elements demonstrated that the evolutionary relationships of the LEA gene family in C. oleifera are highly conserved with many of the LEA genes located in the chloroplast. WGCNA was used to identify modules containing co-expressed genes in different seed developmental stages, and the regulatory network revealed that CoLEA6, CoLEA26, CoLEA17, and CoLEA22 were the hub genes, acting alongside the genes involved in plant growth and abiotic stress. The qPCR analysis of 8 C. oleifera LEA genes under simulated drought stress conditions and gradient shade was conducted, and indicated that CoLEAs responded to drought and shade stresses. Overall, CoLEA22 may be critical for responses to abiotic stress and seed development. This study enable valuable insights into the roles of LEA genes in C. oleifera and establishes a foundation for further research on their function in regulating seed development, oil accumulation and stress response.

Genome-wide identification and characterization of the kinesin gene family in upland cotton (Gossypium hirsutum L.)

Kinesin (KIN) genes play vital functions in plant development and the stress response. However, no comprehensive analysis of this gene family has been reported for cotton. In the present study, we performed a genome-wide investigation and comprehensive analysis of KIN genes in Gossypium hirsutum. A total of 172 putative GhKIN genes were identified in the cotton genome, classified into eight subfamilies (KIN1-KIN8) according to a phylogenetic tree. The GhKINs showed an uneven distribution on chromosomes. Gene duplication analysis indicated that segmental duplication was the only driving force for the expansion of the GhKIN gene family. Segmental duplication gene pairs all have undergone purification selection in the process of evolution. Different subfamily genes had differences in gene structure and motif composition, but the same subfamily showed some similarity. The promoter regions of GhKIN genes contained abundant stress- and hormone-related cis-elements. Based on the published RNA-seq data, 56 common potential candidate genes among these 172 GhKINs were used to identify the spatiotemporal expression patterns in different tissues and abiotic stress response patterns under different treatments (drought, salt, heat and cold). Real-time fluorescence quantitative PCR (RTqPCR) analysis further revealed the expression patterns of 15 GhKINs under drought and salt stress. GhKIN14 and 27 were downregulated under both stress conditions, while GhKIN18, 65, 101, 106, and 137 were upregulated at certain time points. Weighted gene coexpression network analysis (WGCNA) showed that five GhKIN genes, GhKIN13, GhKIN14, GhKIN27, GhKIN140 and GhKIN152, may be important genes regulating the salt stress response. Our study comprehensively analyzes the GhKIN genes in Gossypium hirsutum, providing a new perspective on the functional roles of GhKINs in cotton development and stress adaptation.

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.

Genome-Wide Identification and Expression Profiling of B3 Transcription Factor Genes in Prunus armeniaca

The B3 superfamily, which belongs to the plant-specific transcription factors, is widely involved in multiple biological processes. In apricot (Prunus armeniaca), the classification, structure, and function of the B3 superfamily are not yet clear. In this study, a total of 75 B3 genes were identified from the apricot genome. The apricot B3 superfamily can be divided into five subfamilies, i.e., REM, ARF, ABI3, RAV, and HSI, and genes in the same subfamily have similar structures. The distribution of B3 genes on chromosomes presents a clustering phenomenon. Tandem duplication is the main mode of apricot B3 family expansion, and gene duplication mainly occurs in the REM and ARF subfamilies. Many B3 genes originated from a common ancestor of Arabidopsis and apricot before lineage divergence, and ancestor genes expanded fewer times in apricot than in Arabidopsis. Gene ontology analysis showed that apricot B3 genes were closely related to vernalization, flower development, and shoot system development. PaABI3-1 and PaABI3-2 might play a positive regulation role in the transcription of PaOleosin, which encodes a lipid body protein. This study lays a foundation for the further study of the B3 superfamily function in apricot, especially the specific functions of the ABI3 subfamily in apricot kernel oil storage.

Comparing genomes of Fructus Amomi-producing species reveals genetic basis of volatile terpenoid divergence.

Wurfbainia longiligularis and Wurfbainia villosa are both rich in volatile terpenoids and are two primary plant sources of Fructus Amomi used for curing gastrointestinal diseases. Metabolomic profiling has demonstrated that bornyl diphosphate (BPP)-related terpenoids are more abundant in the W. villosa seeds and have a wider tissue distribution in W. longiligularis. To explore the genetic mechanisms underlying the volatile terpenoids divergence, a high-quality chromosome-level genome of W. longiligularis (2.29 Gb, contig N50 of 80.39 Mb) was assembled. Functional characterization of 17 terpene synthases (WlTPSs) revealed that WlBPPS, along with WlTPS 24/26/28 with bornyl diphosphate synthase (BPPS) activity, contribute to the wider tissue distribution of BPP-related terpenoids in W. longiligularis compared to W. villosa. Furthermore, transgenic Nicotiana tabacum showed that the GCN4-motif element positively regulates seed expression of WvBPPS and thus promotes the enrichment of BPP-related terpenoids in W. villosa seeds. Systematic identification and analysis of candidate TPS in 29 monocot plants from 16 families indicated that substantial expansion of TPS-a and TPS-b subfamily genes in Zingiberaceae may have driven increased diversity and production of volatile terpenoids. Evolutionary analysis and functional identification of BPPS genes showed that BPP-related terpenoids may be distributed only in the Zingiberaceae of monocot plants. This research provides valuable genomic resources for breeding and improving Fructus Amomi with medicinal and edible value and sheds light on the evolution of terpenoid biosynthesis in Zingiberaceae.

Transcriptomic Profiling Highlights the ABA Response Role of BnSIP1-1 in Brassica napus.

BnSIP1-1 is the first identified SIP1 (6b Interacting Protein1) subfamily gene of the trihelix transcription factor family from Brassica napus (B. napus). We previously used a reverse genetic method to reveal its abiotic stress response function in endowing plants resistance to drought and salinity, as well as ABA (Abscisic acid). However, the molecular mechanisms of BnSIP1-1 are unclear. In this study, the global transcriptome files of BnSIP1-1-overexpressing transgenic and wildtype B. napus seedlings under ABA treatment were constructed using RNA-seq. A total of 1823 and 5512 DEGs (Differentially Expressed Genes) were identified in OE vs. WT and OE_ABA vs. WT_ABA comparison groups, which included 751 and 2567 up-regulated DEGs, and 1072 and 2945 down-regulated DEGs, separately. The impact of overexpressed BnSIP1-1 on plants was amplified by ABA, indicating BnSIP1-1 was an ABA-conditioned responsive gene. More interestingly, we found the reasons for BnSIP1-1 increasing plants' insensitivity to ABA were not by regulating ABA synthesis and catabolism, but by manipulating ABA transportation, ABA signal perception and transduction, inositol phosphate metabolism, as well as endomembrane trafficking, indirectly suggesting this gene may play roles upstream of the core ABA response pathway. Our results provided new insights into improving the knowledge about the function of BnSIP1-1 and the ABA signaling mechanism in B. napus.

Genome-Wide Investigation of BAM Gene Family in Annona atemoya: Evolution and Expression Network Profiles during Fruit Ripening

β-amylase proteins (BAM) are important to many aspects of physiological process such as starch degradation. However, little information was available about the BAM genes in Annona atemoya, an important tropical fruit. Seven BAM genes containing the conservative domain of glycoside hydrolase family 14 (PF01373) were identified with Annona atemoya genome, and these BAM genes can be divided into four groups. Subcellular localization analysis revealed that AaBAM3 and AaBAM9 were located in the chloroplast, and AaBAM1.2 was located in the cell membrane and the chloroplast. The AaBAMs belonging to Subfamily I contribute to starch degradation have the higher expression than those belonging to Subfamily II. The analysis of the expression showed that AaBAM3 may function in the whole fruit ripening process, and AaBAM1.2 may be important to starch degradation in other organs. Temperature and ethylene affect the expression of major AaBAM genes in Subfamily I during fruit ripening. These expressions and subcellular localization results indicating β-amylase play an important role in starch degradation.

The soybean NADPH oxidase gene GmRbohK is crucial for nodule formation in symbiosis

Plants regulate various biological activities in cells by producing reactive oxygen species (ROS) as signal molecules. Plant NADPH oxidases, respiratory burst oxidase homologues (Rbohs), are the main source of ROS and participate in a variety of plant physiological processes. However, there are few studies regarding the function of Rbohs in rhizobium–legume symbiotic nodulation. A Rbohs subfamily gene GmRbohK was cloned and the gene expression and its subcellular localization were studied. The GmRbohK gene was highly expressed in soybean roots and nodules and greatly induced by rhizobia. GmRbohK was located at the cell membrane of Arabidopsis protoplasts. Moreover, RNA interference (RNAi) of GmRbohK resulted in a decrease in the number of nodules and nitrogenase activity. Meanwhile, the expression levels of nodulation marker genes decreased in association with the decrease in GmRbohK expression level. RNAi of GmRbohK inhibited the production of ROS and blocked infection events at the initial stage of nodule formation. Further analysis of nodule tissue sections revealed that RNAi of GmRbohK significantly reduced the number of bacteroids in the nodule infection area. In conclusion, GmRbohK is heavily involved in the regulation of soybean nodule formation.

Formation mechanism of glandular trichomes involved in the synthesis and storage of terpenoids in lavender

BackgroundLavender (genus Lavandula, family Lamiaceae) is an aromatic plant widely grown as an ornamental plant. The chemical composition of lavender is characterized by monoterpenoids, sesquiterpenoids, and other compounds, which are primarily synthesized and stored in epidermal secretory structures called glandular trichomes (GTs). Volatile organic compounds (VOCs) are responsible for the aroma characteristics of plant oil that drive consumer preference. Aroma is usually regarded as a characteristic trait for the classification of aromatic plants. Interestingly, VOCs are synthesized and stored in GTs. Lamiaceae species such as purple perilla, peppermint, basil, thyme, and oregano usually possess two types of GTs: peltate glandular trichomes (PGTs) and capitate glandular trichomes (CGTs). But the development process of PGTs in lavender has been reported in only a few studies to date.ResultsIn this study, we identified and quantified the VOCs in four lavender cultivars by headspace-solid phase micro extraction-gas chromatography mass spectrometry (HS–SPME–GC–MS). A total of 66 VOCs were identified in these four cultivars, the most prominent of which were linalyl acetate and linalool, and flowers were the main site of accumulation of these VOCs. Here, we examined the developmental process of PGTs, including the formation of their base, body, and apex. The apex cells contained secretory cavities, which produced VOCs. Based on the reference genome sequence of the lavender cultivar ‘Jingxun 2’, several R2R3-MYB subfamily genes related to GT formation were identified. These results will guide the engineering of GTs and molecular breeding of lavender for improving the VOC content.ConclusionsIn this study, we identified the VOCs in four lavender cultivars. We analyzed the formation of GTs, and compared the number and diameter size of PGTs among four lavender cultivars. Additionally, we identified four candidate genes belonging to the R2R3-MYB family.

General aspects on skin development in vertebrates with emphasis on sauropsids epidermis

General cellular aspects of skin development in vertebrates are presented with emphasis on the epidermis of sauropsids. Anamniote skin develops into a multilayered mucogenic and soft keratinized epidermis made of Intermediate Filament Keratins (IFKs) that is reinforced in most fish and few anurans by dermal bony and fibrous scales. In amniotes, the developing epidermis in contact with the amniotic fluid initially transits through a mucogenic phase recalling that of their anamniotes progenitors. A new gene cluster termed EDC (Epidermal Differentiation Complex) evolved in amniotes contributing to the origin of the stratum corneum. The EDC contains numerous genes coding for over 100 types of corneous proteins (CPs). In sauropsids 2–8 layers of embryonic epidermis accumulate soft keratins (IFKs) but do not form a compact corneous layer. The embryonic epidermis of reptiles and birds produces small amount of other, poorly known proteins in addition to IFKs and mucins. In the following development, a resistant corneous layer is formed underneath the embryonic epidermis that is shed before hatching. The definitive corneous epidermis of sauropsids is mainly composed of CBPs (Corneous beta proteins, formerly indicated as beta-keratins) derived from the EDC. CBPs belong to a gene sub-family of CPs unique for sauropsids, contain an inner amino acid region formed by beta-sheets, are rich in cysteine and glycine, and make most of the protein composition of scales, claws, beaks and feathers. In mammalian epidermis CPs missing the beta-sheet region are instead produced, and include loricrin, involucrin, filaggrin and various cornulins. Small amount of CPs accumulate in the 2–3 layers of mammalian embryonic epidermis and their appendages, that is replaced with the definitive corneous layers before birth. Differently from sauropsids, mammals utilize KAPs (keratin associated proteins) rich in cysteine and glycine for making the hard corneous material of hairs, claws, hooves, horns, and occasionally also scales.

Genome-Wide Identification, Characterization and Expression Analysis of Plant Nuclear Factor (NF-Y) Gene Family Transcription Factors in Saccharum spp.

Plant nuclear factor (NF-Y) is a transcriptional activating factor composed of three subfamilies: NF-YA, NF-YB, and NF-YC. These transcriptional factors are reported to function as activators, suppressors, and regulators under different developmental and stress conditions in plants. However, there is a lack of systematic research on the NF-Y gene subfamily in sugarcane. In this study, 51 NF-Y genes (ShNF-Y), composed of 9 NF-YA, 18 NF-YB, and 24 NF-YC genes, were identified in sugarcane (Saccharum spp.). Chromosomal distribution analysis of ShNF-Ys in a Saccharum hybrid located the NF-Y genes on all 10 chromosomes. Multiple sequence alignment (MSA) of ShNF-Y proteins revealed conservation of core functional domains. Sixteen orthologous gene pairs were identified between sugarcane and sorghum. Phylogenetic analysis of NF-Y subunits of sugarcane, sorghum, and Arabidopsis showed that ShNF-YA subunits were equidistant while ShNF-YB and ShNF-YC subunits clustered distinctly, forming closely related and divergent groups. Expression profiling under drought treatment showed that NF-Y gene members were involved in drought tolerance in a Saccharum hybrid and its drought-tolerant wild relative, Erianthus arundinaceus. ShNF-YA5 and ShNF-YB2 genes had significantly higher expression in the root and leaf tissues of both plant species. Similarly, ShNF-YC9 had elevated expression in the leaf and root of E. arundinaceus and in the leaf of a Saccharum hybrid. These results provide valuable genetic resources for further sugarcane crop improvement programs.

Whole genome sequencing and analysis of Armillaria gallica Jzi34 symbiotic with Gastrodia elata

BackgroundArmillaria species are plant pathogens, but a few Armillaria species can establish a symbiotic relationship with Gastrodia elata, a rootless and leafless orchid, that is used as a Chinese herbal medicine. Armillaria is a nutrient source for the growth of G. elata. However, there are few reports on the molecular mechanism of symbiosis between Armillaria species and G. elata. The genome sequencing and analysis of Armillaria symbiotic with G. elata would provide genomic information for further studying the molecular mechanism of symbiosis.ResultsThe de novo genome assembly was performed with the PacBio Sequel platform and Illumina NovaSeq PE150 for the A. gallica Jzi34 strain, which was symbiotic with G. elata. Its genome assembly contained ~ 79.9 Mbp and consisted of 60 contigs with an N50 of 2,535,910 bp. There were only 4.1% repetitive sequences in the genome assembly. Functional annotation analysis revealed a total of 16,280 protein coding genes. Compared with the other five genomes of Armillaria, the carbohydrate enzyme gene family of the genome was significantly contracted, while it had the largest set of glycosyl transferase (GT) genes. It also had an expansion of auxiliary activity enzymes AA3-2 gene subfamily and cytochrome P450 genes. The synteny analysis result of P450 genes reveals that the evolutionary relationship of P450 proteins between A. gallica Jzi34 and other four Armillaria was complex.ConclusionsThese characteristics may be beneficial for establishing a symbiotic relationship with G. elata. These results explore the characteristics of A. gallica Jzi34 from a genomic perspective and provide an important genomic resource for further detailed study of Armillaria. This will help to further study the symbiotic mechanism between A. gallica and G. elata.

Genetic characterization of C. elegans TMED genes.

p24/transmembrane Emp24 domain (TMED) proteins are a set of evolutionarily conserved, single pass transmembrane proteins that have been shown to facilitate protein secretion and selection of cargo proteins to transport vesicles in the cellular secretion pathway. However, their functions in animal development are incompletely understood. The C. elegans genome encodes eight identified TMED genes, with at least one member from each defined subfamily (α, β, γ, δ). TMED gene mutants exhibit a shared set of defects in embryonic viability, animal movement, and vulval morphology. Two γ subfamily genes, tmed-1 and tmed-3, exhibit the ability to compensate for each other, as defects in movement and vulva morphology are only apparent in double mutants. TMED mutants also exhibit a delay in breakdown of basement membrane during vulva development. The results establish a genetic and experimental framework for the study of TMED gene function in C. elegans, and argue that a functional protein from each subfamily is important for a shared set of developmental processes. A specific function for TMED genes is to facilitate breakdown of the basement membrane between the somatic gonad and vulval epithelial cells, suggesting a role for TMED proteins in tissue reorganization during animal development.

Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple

Sucrose phosphate synthase (SPS) is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality. However, studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are still lacking. In the present study, a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1. The gene structures and their promoter cis-elements, protein conserved motifs, subcellular localizations, physiological functions and biochemical properties were analyzed. A chromosomal location and gene-duplication analysis demonstrated that whole-genome duplication (WGD) and segmental duplication played vital roles in MdSPS gene family expansion. The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have undergone strong purifying selection during domestication. Furthermore, three SPS gene subfamilies were classified based on phylogenetic relationships, and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies. In addition, a major gene related to sucrose accumulation (MdSPSA2.3) was identified according to the highly consistent trends in the changes of its expression in four apple varieties (‘Golden Delicious’, ‘Fuji’, ‘Qinguan’ and ‘Honeycrisp’) and the correlation between gene expression and soluble sugar content during fruit development. Furthermore, the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit. The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.

Genome-wide characterization, phylogenetic and expression analysis of ABCG gene subfamily in cucumber (Cucumis sativus L.).

The ABCG is the largest subfamily of the ABC family with extensive functions, and only a few members have been identified in detail. However, more and more studies have shown that the members of this family are very important and are involved in many life processes such as plant development and response to various stresses. Cucumber is an important vegetable crops around the world. The cucumber development is essential for its production and quality. Meanwhile, various stresses have caused serious losses of cucumber. However, the ABCG genes were not well characterized and functioned in cucumber. In this study, the cucumber CsABCG gene family were identified and characterized, and their evolutionary relationship and functions were analyzed. The cis-acting elements and expression analysis showed that they played important role in development and responding to various biotic and abiotic stresses in cucumber. Phylogenetic analysis, sequence alignment and MEME (Multiple Em for Motif Elicitation) analysis indicated that the functions of ABCG proteins in different plants are evolutionarily conserved. Collinear analysis revealed that the ABCG gene family was highly conserved during the evolution. In addition, the potential binding sites of the CsABCG genes targeted by miRNA were predicted. These results will lay a foundation for further research on the function of the CsABCG genes in cucumber.

Zona pellucida family genes in Chinese pond turtle: identification, expression profiles, and role in the spermatozoa acrosome reaction†.

The zona pellucida (ZP) is an extracellular matrix that surrounds all vertebrate eggs, and it is involved in fertilization and species-specific recognition. Numerous in-depth studies of the ZP proteins of mammals, birds, amphibians, and fishes have been conducted, but systematic investigation of the ZP family genes and their role during fertilization in reptiles has not been reported to date. In this study, we identified six turtle ZP (Tu-ZP) gene subfamilies (Tu-ZP1, Tu-ZP2, Tu-ZP3, Tu-ZP4, Tu-ZPD, and Tu-ZPAX) based on whole genome sequence data from Mauremys reevesii. We found that Tu-ZP4 had large segmental duplication and was distributed on three chromosomes, and we also detected gene duplication in the other Tu-ZP genes. To evaluate the role of Tu-ZP proteins in sperm-egg binding, we assessed the expression pattern of these Tu-ZP proteins and their ability to induce the spermatozoa acrosome reaction in M. reevesii. In conclusion, this is the first report of the existence of gene duplication of Tu-ZP genes and that Tu-ZP2, Tu-ZP3, and Tu-ZPD can induce acrosome exocytosis of spermatogenesis in the reptile.

Systematic analysis of MYB transcription factors and the role of LuMYB216 in regulating anthocyanin biosynthesis in the flowers of flax (Linum usitatissimum L.)

Anthocyanin is an important pigment that affects plant color and nutritional quality. MYBs play an important role in plant anthocyanin synthesis and accumulation. However, the regulatory function of MYB transcription factors in anthocyanin synthesis in flax flowers is still unclear. In this study, 402 MYB transcription factors were identified in the flax genome. These MYB members are unevenly distributed on 15 chromosomes. The R2R3-LuMYB members were divided into 32 phylogenetic subfamilies. qRT-PCR analysis showed that seven R2R3-LuMYB genes in the adjacent subfamily of the evolutionary tree had similar expression patterns, among which LuMYB216 was highly expressed in the petals of different colors. Moreover, gene editing of LuMYB216 in flax showed that the petal color, anther color and seed coat color of mutant plants were significantly lighter than those of wild-type plants, and the anthocyanin content of lumyb216 mutant plants was significantly reduced. Correlation analysis indicated that LuMYB216 was significantly positively correlated with the upstream regulator bHLH30. This study systematically analyzed the MYB gene family in flax, laying a foundation for studying the regulation of LuMYB216 in flax flower anthocyanin synthesis.

Identification and transcriptome data analysis of ARF family genes in five Orchidaceae species

The Orchidaceae is a large family of perennial herbs especially noted for the exceptional diversity of specialized flowers. Elucidating the genetic regulation of flowering and seed development of orchids is an important research goal with potential utility in orchid breeding programs. Auxin Response Factor (ARF) genes encode auxin-responsive transcription factors, which are involved in the regulation of diverse morphogenetic processes, including flowering and seed development. However, limited information on the ARF gene family in the Orchidaceae is available. In this study, 112 ARF genes were identified in the genomes of 5 orchid species (Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis aphrodite, Phalaenopsis equestris and Vanilla planifolia,). These genes were grouped into 7 subfamilies based on their phylogenetic relationships. Compared with the ARF family in model plants, such as Arabidopsis thaliana and Oryza sativa, one group of ARF genes involved in pollen wall synthesis has been lost during evolution of the Orchidaceae. This loss corresponds with absence of the exine in the pollinia. Through mining of the published genomic and transcriptomic data for the 5 orchid species: the ARF genes of subfamily 4 may play an important role in flower formation and plant growth, whereas those of subfamily 3 are potentially involved in pollen wall development. the study results provide novel insights into the genetic regulation of unique morphogenetic phenomena of orchids, which lay a foundation for further analysis of the regulatory mechanisms and functions of sexual reproduction-related genes in orchids.

Genome-Wide Characterization of the R2R3-MYB Gene Family in Diospyros oleifera

The MYB gene family is one of the largest transcription factor families, which is clustered into four subfamilies according to the number of imperfect amino acid sequences repeats in their conserved MYB domain. R2R3-MYB is the largest subfamily that plays a diverse role in plant growth and development as well as adversity stresses. Diospyros has a wide range of applications in biomedical science and the food, wood, and chemical industries. Among these species, Diospyros oleifera can be used as a model plant for the Diospyros genus and the Ebenaceae family. Although the genome sequence of Diospyros oleifera was recently published in our previous work, bioinformatics and expression pattern analysis of the MYB gene family are limited. Here, we present the findings of a genome-wide analysis and the expression profiles of the R2R3-MYB transcription factor in Diospyros oleifera. A total of 129 R2R3-MYB genes were identified and classified into 28 groups (C1–C28) which had conserved motifs. The subfamily genes were unevenly distributed in 15 chromosomes; chromosome 6 and 7 have the most DoMYB genes. A total of 44 fragment replication events containing 57 DoMYB genes were identified using synteny analysis. In addition, collinear analysis revealed that 70 (54%) pairs of R2R3-MYB genes of Diospyros oleifera were collinear with Arabidopsis thaliana. Upon combining the data from RNA-seq and qRT-PCR, four key genes were screened and identified to correlate with the soluble tannin content during fruit development. DoMYB22 may be related to the synthesis of soluble tannin in persimmon. These results lay an important foundation for further studies on the R2R3-MYB gene function in persimmon fruit development.

Cassava MeRS40 is required for the regulation of plant salt tolerance

Soil salinity affects the expression of serine/arginine-rich (SR) genes and isoforms by alternative splicing, which in turn regulates the adaptation of plants to stress. We previously identified the cassava spliceosomal component 35 like (SCL) and SR subfamilies, belonging to the SR protein family, which are extensively involved in responses to abiotic stresses. However, the post-transcriptional regulatory mechanism of cassava arginine/serine-rich (RS) subfamily in response to salt stress remains to be explored. In the current study, we identified 37 genes of the RS subfamily from 11 plant species and systematically investigated the transcript levels of the RS40 and RS31 genes under diverse abiotic stress conditions. Subsequently, an analysis of the conserved protein domains revealed that plant RS subfamily genes were likely to preserve their conserved molecular functions and played critical functional roles in responses to abiotic stresses. Importantly, we found that overexpression of MeRS40 in Arabidopsis enhanced salt tolerance by maintaining reactive oxygen species homeostasis and up-regulating the salt-responsive genes. However, overexpression of MeRS40 gene in cassava reduced salt tolerance due to the depression of its endogenous gene expression by negative autoregulation of its own pre-mRNA. Moreover, the MeRS40 protein interacted with MeU1-70Ks (MeU1-70Ka and MeU1-70Kb) in vivo and in vitro, respectively. Therefore, our ?ndings highlight the critical role of cassava SR proteins in responses to salt stress in plants.