Segmental Duplications Research Articles

Identification and characterization analysis of the HDM gene family in melon (Cucumis melo L.).

Histone demethylase (HDM) play crucial roles in regulating plant growth and environmental adaptation. In this study, the HDM gene family in melon was identified by bioinformatics methods and the expression patterns of the CmHDM family members in different melon tissues were analyzed using transcriptome data. The results showed that 20 CmHDM genes were identified in the melon genome, which were unevenly distributed across each chromosome. These members fall into two major categories: LSD1 and JmjC. The JmjC group could be further divided into five subgroups with different numbers. The results of collinearity analysis of intraspecific and interspecific relationships showed that there were only one pair of segmental duplication in melon HDM genes, and more collinearity in genetic relationship of HDM genes between melon and tomato. The numbers of conserved domains, exons and introns in each member vary and various cis-acting elements responding to hormones and environmental signals existed in the respective promoter regions. Expression analysis showed that the respective gene members were expressed at different levels in male flowers, female flowers, roots, stems, leaves, ovary, and mature fruits of melon. These results will contribute to the understanding on the potential functions of the HDM genes and their potential functions in regulating melon growth and environmental adaptation.

Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs

SQUAMOSA PROMOTER BINDING PROTEIN-LIKEs (SPLs) encode plant-specific transcription factors that regulate plant growth and development, stress response, and metabolite accumulation. However, there is limited information on Scutellaria baicalensis SPLs. In this study, 14 SbSPLs were identified and divided into 8 groups based on phylogenetic relationships. SbSPLs in the same group had similar structures. Abscisic acid-responsive (ABRE) and MYB binding site (MBS) cis-acting elements were found in the promoters of 8 and 6 SbSPLs. Segmental duplications and transposable duplications were the main causes of SbSPL expansion. Expression analysis based on transcriptional profiling showed that SbSPL1, SbSPL10, and SbSPL13 were highly expressed in roots, stems, and flowers, respectively. Expression analysis based on quantitative real-time polymerase chain reaction (RT‒qPCR) showed that most SbSPLs responded to low temperature, drought, abscisic acid (ABA) and salicylic acid (SA), among which the expression levels of SbSPL7/9/10/12 were significantly upregulated in response to abiotic stress. These results indicate that SbSPLs are involved in the growth, development and stress response of S. baicalensis. In addition, 8 Sba-miR156/157 s were identified, and SbSPL1-5 was a potential target of Sba-miR156/157 s. The results of target gene prediction and coexpression analysis together indicated that SbSPLs may be involved in the regulation of L-phenylalanine (L-Phe), lignin and jasmonic acid (JA) biosynthesis. In summary, the identification and characterization of the SbSPL gene family lays the foundation for functional research and provides a reference for improved breeding of S. baicalensis stress resistance and quality traits.

Genome-wide analysis of the switchgrass YABBY family and functional characterization of PvYABBY14 in response to ABA and GA stress in Arabidopsis

BackgroundThe small YABBY plant-specific transcription factor has a prominent role in regulating plant growth progress and responding to abiotic stress.ResultsHere, a total of 16 PvYABBYs from switchgrass (Panicum virgatum L.) were identified and classified into four distinct subgroups. Proteins within the same subgroup exhibited similar conserved motifs and gene structures. Synteny analyses indicated that segmental duplication contributed to the expansion of the YABBY gene family in switchgrass and that complex duplication events occurred in rice, maize, soybean, and sorghum. Promoter regions of PvYABBY genes contained numerous cis-elements related to stress responsiveness and plant hormones. Expression profile analysis indicated higher expression levels of many PvYABBY genes during inflorescence development and seed maturation, with lower expression levels during root growth. Real-time quantitative PCR analysis demonstrated the sensitivity of multiple YABBY genes to PEG, NaCl, ABA, and GA treatments. The overexpression of PvYABBY14 in Arabidopsis resulted in increased root length after treatment with GA and ABA compared to wild-type plants.ConclusionsTaken together, our study provides the first genome-wide overview of the YABBY transcription factor family, laying the groundwork for understanding the molecular basis and regulatory mechanisms of PvYABBY14 in response to ABA and GA responses in switchgrass.

Comprehensive bioinformation analysis of homeodomain-leucine zipper gene family and expression pattern of HD-Zip I under abiotic stress in Salix suchowensis

BackgroundHomeodomain-leucine zipper (HD-Zip) transcription factors are plant-specific and play important roles in plant defense against environmental stresses. Identification and functional studies have been carried out in model plants such as rice, Arabidopsis thaliana, and poplar, but comprehensive analysis on the HD-Zip family of Salix suchowensis have not been reported.ResultsA total of 55 HD-Zip genes were identified in the willow genome, unevenly distributed on 18 chromosomes except for chromosome 19. And segmental duplication events containing SsHD-Zip were detected on all chromosomes except chromosomes 13 and 19. The SsHD-Zip were classified into 4 subfamilies subfamilies (I-IV) according to the evolutionary analysis, and members of each subfamily shared similar domain structure and gene structure. The combination of GO annotation and promoter analysis showed that SsHD-Zip genes responded to multiple abiotic stresses. Furthermore, the results of qPCR analysis showed that the SsHD-Zip I gene exhibited different degrees of expression under salt stress, PEG treatment and heat treatment. Moreover, there was a synergistic effect between SsHD-Zip I genes under stress conditions based on coregulatory networks analysis.ConclusionsIn this study, HD-Zip transcription factors were systematically identified and analyzed at the whole genome level. These results preliminarily clarified the structural characteristics and related functions of willow HD-Zip family members, and it was found that SsHox34, SsHox36 and SsHox51 genes were significantly involved in the response to various stresses. Together, these findings laid the foundation for further research on the resistance functions of willow HD-Zip genes.

Functional diversification of miR172 isoforms in tomato under abiotic stress

Plant gene families have expanded many folds as opposed to animals to compensate for being sessile as well as having unique features like ability to photosynthesise. While different protein families are well characterised in plants, similar knowledge on miRNA families is still in its infancy. The MIR172 family plays important role in various plant development processes including vegetative to reproductive phase change, floral patterning, nodulation, and fruit ripening as well as also in response to different environmental cues. However, in-depth analysis of this family in tomato (Solanum lycopersicum) is limited. In this study, we identified four new MIR172 loci (Sly-MIR172a1/a2/e/f) and two new isoforms, other than those reported at the miRBase repository. The MIR172 family has expanded by segmental duplication events and is conserved between the wild (S. pennellii and S. pimpinellifolium) and the cultivated tomato varieties. However, phylogenetic analysis showed that S. pennellii formed the most divergent member within each clade and S. pimpinellifolium is closer to the cultivated varieties. Additionally, investigations in 42 plant species highlighted that miR172a/b is the most abundant form in the plant kingdom. In addition to the classical target Apetala2 (AP2), degradome analysis identified SEC14p-like phosphatidylinositol transfer family protein (SEC14p) as a novel target of Sly-miR172 that was validated using precursor:effector and target:reporter transient assays. Further, we report dual mode of Sly-miR172-mediated silencing of targets Sly-AP2 and Sly-SEC14p by post-transcriptional transcript cleavage as well as translational repression. Different members of Sly-MIR172s:Sly-AP2s and Sly-MIR172s:Sly-SEC14p exhibit inverse expression correlation in response to different abiotic stresses, suggesting their role in stress response. Functional investigation of MIR172 showed that tomato plants performed better in different abiotic stresses (heat, drought, and salt) upon MIR172 overexpression or target knock-down by virus-induced-gene-silencing. Conversely, when miRNA is chelated using short-tandem-target-mimic, the plants exhibit sensitivity to these stresses. Thus, Sly-miR172 acts as a positive regulator while its targets Sly-AP2a and Sly-SEC14p as negative regulators of different abiotic stresses.

In Silico Identification and Characterization of Rare Cold Inducible 2 (RCI2) Gene Family in Cotton.

RCI2/PMP3s are involved in biotic and abiotic stresses and have an influence on the regulation of many genes. RCI2/PMP3 genes, which particularly encode small membrane proteins of the PMP3 family, are involved in abiotic stress responses in plants. In this work, in silico studies were used to investigate RCI2's potential function in stress tolerance and organogenesis. We conducted an extensive study of the RCI2 gene family and revealed 36 RCI2 genes from cotton species that were distributed over 36 chromosomes of the cotton genome. Functional and phylogenetic examination of the RCI2/PMP3 gene family has been studied in Arabidopsis, but in cotton, the RCI2/PMP3 genes have not yet been studied. Phylogenetic and sequencing studies revealed that cotton RCI2s are conserved, with most of them categorized into six distinct clades. A chromosome distribution and localization study indicated that cotton RCI2 genes were distributed unevenly on 36 chromosomes with segmental duplications, suggesting that the cotton RCI2 family is evolutionarily conserved. Many cis-elements related to stress responsiveness, development, and hormone responsiveness were detected in the promoter regions of the cotton RCI2. Moreover, the 36 cotton RCI2s revealed tissue-specific expression patterns in the development of cotton performed by transcriptome analysis. Gene structure analysis indicated that nearly all RCI2 genes have two exons and one intron. All of the cotton RCI2 genes were highly sensitive to drought, abscisic acid, salt, and cold treatments, demonstrating that they may be employed as genetic objects to produce stress-resistant plants.

Comprehensive analysis of sesame LRR-RLKs: structure, evolution and dynamic expression profiles under Macrophomina phaseolina stress.

Leucine-rich repeat receptor-like kinases (LRR-RLKs) can participate in the regulation of plant growth and development, immunity and signal transduction. Sesamum indicum, one of the most important oil crops, has a significant role in promoting human health. In this study, 175 SiLRR-RLK genes were identified in S. indicum, and they were subdivided into 12 subfamilies by phylogenetic analysis. Gene duplication analysis showed that the expansion of the SiLRR-RLK family members in the sesame was mainly due to segmental duplication. Moreover, the gene expansion of subfamilies IV and III contributed to the perception of stimuli under M. phaseolina stress in the sesame. The collinearity analysis with other plant species revealed that the duplication of SiLRR-RLK genes occurred after the differentiation of dicotyledons and monocotyledons. The expression profile analysis and functional annotation of SiLRR-RLK genes indicated that they play a vital role in biotic stress. Furthermore, the protein-protein interaction and coexpression networks suggested that SiLRR-RLKs contributed to sesame resistance to Macrophomina phaseolina by acting alone or as a polymer with other SiLRR-RLKs. In conclusion, the comprehensive analysis of the SiLRR-RLK gene family provided a framework for further functional studies on SiLRR-RLK genes.

Cytogenetic Analysis of the Fish Genus Carassius Indicates Divergence, Fission, and Segmental Duplication as Drivers of Tandem Repeat and Microchromosome Evolution.

Fishes of the genus Carassius are useful experimental vertebrate models for the study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Those Carassius polyploids with ≥150 chromosomes have microchromosomes, but the origin of microchromosomes, especially in European populations, is unknown. We used cytogenetics to study evolution of tandem repeats (U1 and U2 small nuclear DNAs and H3 histone) and microchromosomes in Carassius from the Czech Republic. We tested the hypotheses whether the number of tandem repeats was affected by polyploidization or divergence between species and what mechanism drives evolution of microchromosomes. Tandem repeats were found in tetraploid and hexaploid Carassius gibelio, and tetraploid Carassius auratus and Carassius carassius in conserved numbers, with the exception of U1 small nuclear DNA in C. auratus. This conservation indicates reduction and/or loss in the number of copies per locus in hexaploids and may have occurred by divergence rather than polyploidization. To study the evolution of microchromosomes, we used the whole microchromosome painting probe from hexaploid C. gibelio and hybridized it to tetraploid and hexaploid C. gibelio, and tetraploid C. auratus and C. carassius. Our results revealed variation in the number of microchromosomes in hexaploids and indicated that the evolution of the Carassius karyotype is governed by macrochromosome fissions followed by segmental duplication in pericentromeric areas. These are potential mechanisms responsible for the presence of microchromosomes in Carassius hexaploids. Differential efficacy of one or both of these mechanisms in different tetraploids could ensure variability in chromosome number in polyploids in general.

Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum

BackgroundSugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes.ResultsHere, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases.ConclusionsThis investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.

GhBRX.1, GhBRX.2, and GhBRX4.3 improve resistance to salt and cold stress in upland cotton.

Abiotic stress during growth readily reduces cotton crop yield. The different survival tactics of plants include the activation of numerous stress response genes, such as BREVIS RADIX (BRX). In this study, the BRX gene family of upland cotton was identified and analyzed by bioinformatics method, three salt-tolerant and cold-resistant GhBRX genes were screened. The expression of GhBRX.1, GhBRX.2 and GhBRXL4.3 in upland cotton was silenced by virus-induced gene silencing (VIGS) technique. The physiological and biochemical indexes of plants and the expression of related stress-response genes were detected before and after gene silencing. The effects of GhBRX.1, GhBRX.2 and GhBRXL4.3 on salt and cold resistance of upland cotton were further verified. We discovered 12, 6, and 6 BRX genes in Gossypium hirsutum, Gossypium raimondii and Gossypium arboreum, respectively. Chromosomal localization indicated that the retention and loss of GhBRX genes on homologous chromosomes did not have a clear preference for the subgenomes. Collinearity analysis suggested that segmental duplications were the main force for BRX gene amplification. The upland cotton genes GhBRX.1, GhBRX.2 and GhBRXL4.3 are highly expressed in roots, and GhBRXL4.3 is also strongly expressed in the pistil. Transcriptome data and qRT‒PCR validation showed that abiotic stress strongly induced GhBRX.1, GhBRX.2 and GhBRXL4.3. Under salt stress and low-temperature stress conditions, the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) and the content of soluble sugar and chlorophyll decreased in GhBRX.1-, GhBRX.2- and GhBRXL4.3-silenced cotton plants compared with those in the control (TRV: 00). Moreover, GhBRX.1-, GhBRX.2- and GhBRXL4.3-silenced cotton plants exhibited greater malondialdehyde (MDA) levels than did the control plants. Moreover, the expression of stress marker genes (GhSOS1, GhSOS2, GhNHX1, GhCIPK6, GhBIN2, GhSnRK2.6, GhHDT4D, GhCBF1 and GhPP2C) decreased significantly in the three target genes of silenced plants following exposure to stress. These results imply that the GhBRX.1, GhBRX.2 and GhBRXL4.3 genes may be regulators of salt stress and low-temperature stress responses in upland cotton.

Local Genomic Instability of the SpTransformer Gene Family in the Purple Sea Urchin Inferred from BAC Insert Deletions.

The SpTransformer (SpTrf) gene family in the purple sea urchin, Strongylocentrotus purpuratus, encodes immune response proteins. The genes are clustered, surrounded by short tandem repeats, and some are present in genomic segmental duplications. The genes share regions of sequence and include repeats in the coding exon. This complex structure is consistent with putative local genomic instability. Instability of the SpTrf gene cluster was tested by 10 days of growth of Escherichia coli harboring bacterial artificial chromosome (BAC) clones of sea urchin genomic DNA with inserts containing SpTrf genes. After the growth period, the BAC DNA inserts were analyzed for size and SpTrf gene content. Clones with multiple SpTrf genes showed a variety of deletions, including loss of one, most, or all genes from the cluster. Alternatively, a BAC insert with a single SpTrf gene was stable. BAC insert instability is consistent with variations in the gene family composition among sea urchins, the types of SpTrf genes in the family, and a reduction in the gene copy number in single coelomocytes. Based on the sequence variability among SpTrf genes within and among sea urchins, local genomic instability of the family may be important for driving sequence diversity in this gene family that would be of benefit to sea urchins in their arms race with marine microbes.

Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC.

Phosphoenolpyruvate carboxylase (PEPC) gene family plays a crucial role in both plant growth and response to abiotic stress. Approximately half of the Orchidaceae species are estimated to perform CAM pathway, and the availability of sequenced orchid genomes makes them ideal subjects for investigating the PEPC gene family in CAM plants. In this study, a total of 33 PEPC genes were identified across 15 orchids. Specifically, one PEPC gene was found in Cymbidium goeringii and Platanthera guangdongensis; two in Apostasia shenzhenica, Dendrobium chrysotoxum, D. huoshanense, Gastrodia elata, G. menghaiensis, Phalaenopsis aphrodite, Ph. equestris, and Pl. zijinensis; three in C. ensifolium, C. sinense, D. catenatum, D. nobile, and Vanilla planifolia. These PEPC genes were categorized into four subgroups, namely PEPC-i, PEPC-ii, and PEPC-iii (PTPC), and PEPC-iv (BTPC), supported by the comprehensive analyses of their physicochemical properties, motif, and gene structures. Remarkably, PEPC-iv contained a heretofore unreported orchid PEPC gene, identified as VpPEPC4. Differences in the number of PEPC homolog genes among these species were attributed to segmental duplication, whole-genome duplication (WGD), or gene loss events. Cis-elements identified in promoter regions were predominantly associated with light responsiveness, and circadian-related elements were observed in each PEPC-i and PEPC-ii gene. The expression levels of recruited BTPC, VpPEPC4, exhibited a lower expression level than other VpPEPCs in the tested tissues. The expression analyses and RT-qPCR results revealed diverse expression patterns in orchid PEPC genes. Duplicated genes exhibited distinct expression patterns, suggesting functional divergence. This study offered a comprehensive analysis to unveil the evolution and function of PEPC genes in Orchidaceae.

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus

Suncus etruscus is one of the world’s smallest mammals, with an average body mass of about 2 grams. The Etruscan shrew’s small body is accompanied by a very high energy demand and numerous metabolic adaptations. Here we report a chromosome-level genome assembly using PacBio long read sequencing, 10X Genomics linked short reads, optical mapping, and Hi-C linked reads. The assembly is partially phased, with the 2.472 Gbp primary pseudohaplotype and 1.515 Gbp alternate. We manually curated the primary assembly and identified 22 chromosomes, including X and Y sex chromosomes. The NCBI genome annotation pipeline identified 39,091 genes, 19,819 of them protein-coding. We also identified segmental duplications, inferred GO term annotations, and computed orthologs of human and mouse genes. This reference-quality genome will be an important resource for research on mammalian development, metabolism, and body size control.

Genome-Wide Identification and Expression Profile Analysis of Sugars Will Eventually Be Exported Transporter (SWEET) Genes in Zantedeschia elliottiana and Their Responsiveness to Pectobacterium carotovora subspecies Carotovora (Pcc) Infection.

SWEET, sugars will eventually be exported transporter, is a novel class of sugar transporter proteins that can transport sugars across membranes down a concentration gradient. It plays a key role in plant photosynthetic assimilates, phloem loading, nectar secretion from nectar glands, seed grouting, pollen development, pathogen interactions, and adversity regulation, and has received widespread attention in recent years. To date, systematic analysis of the SWEET family in Zantedeschia has not been documented, although the genome has been reported in Zantedeschia elliottiana. In this study, 19 ZeSWEET genes were genome-wide identified in Z. elliottiana, and unevenly located in 10 chromosomes. They were further clustered into four clades by a phylogenetic tree, and almost every clade has its own unique motifs. Synthetic analysis confirmed two pairs of segmental duplication events of ZeSWEET genes. Heatmaps of tissue-specific and Pectobacterium carotovora subsp. Carotovora (Pcc) infection showed that ZeSWEET genes had different expression patterns, so SWEETs may play widely varying roles in development and stress tolerance in Zantedeschia. Moreover, quantitative reverse transcription-PCR (qRT-PCR) analysis revealed that some of the ZeSWEETs responded to Pcc infection, among which eight genes were significantly upregulated and six genes were significantly downregulated, revealing their potential functions in response to Pcc infection. The promoter sequences of ZeSWEETs contained 51 different types of the 1380 cis-regulatory elements, and each ZeSWEET gene contained at least two phytohormone responsive elements and one stress response element. In addition, a subcellular localization study indicated that ZeSWEET07 and ZeSWEET18 were found to be localized to the plasma membrane. These findings provide insights into the characteristics of SWEET genes and contribute to future studies on the functional characteristics of ZeSWEET genes, and then improve Pcc infection tolerance in Zantedeschia through molecular breeding.

Genome-wide identification and characterization of TCP gene family in Dendrobium nobile and their role in perianth development.

TCP is a widely distributed, essential plant transcription factor that regulates plant growth and development. An in-depth study of TCP genes in Dendrobium nobile, a crucial parent in genetic breeding and an excellent model material to explore perianth development in Dendrobium, has not been conducted. We identified 23 DnTCP genes unevenly distributed across 19 chromosomes and classified them as Class I PCF (12 members), Class II: CIN (10 members), and CYC/TB1 (1 member) based on the conserved domain and phylogenetic analysis. Most DnTCPs in the same subclade had similar gene and motif structures. Segmental duplication was the predominant duplication event for TCP genes, and no tandem duplication was observed. Seven genes in the CIN subclade had potential miR319 and -159 target sites. Cis-acting element analysis showed that most DnTCP genes contained many developmental stress-, light-, and phytohormone-responsive elements in their promoter regions. Distinct expression patterns were observed among the 23 DnTCP genes, suggesting that these genes have diverse regulatory roles at different stages of perianth development or in different organs. For instance, DnTCP4 and DnTCP18 play a role in early perianth development, and DnTCP5 and DnTCP10 are significantly expressed during late perianth development. DnTCP17, 20, 21, and 22 are the most likely to be involved in perianth and leaf development. DnTCP11 was significantly expressed in the gynandrium. Specially, MADS-specific binding sites were present in most DnTCP genes putative promoters, and two Class I DnTCPs were in the nucleus and interacted with each other or with the MADS-box. The interactions between TCP and the MADS-box have been described for the first time in orchids, which broadens our understanding of the regulatory network of TCP involved in perianth development in orchids.

Genome-Wide Identification and Characterization of the TIFY Gene Family and Their Expression Patterns in Response to MeJA and Aluminum Stress in Centipedegrass (Eremochloa ophiuroides)

The TIFY family is a group of novel plant-specific transcription factors involved in plant development, signal transduction, and responses to stress and hormones. TIFY genes have been found and functionally characterized in a number of plant species. However, there is no information about this family in warm-season grass plants. The current study identified 24 TIFY genes in Eremochloa ophiuroides, a well-known perennial warm-season grass species with a high tolerance to aluminum toxicity and good adaptability to the barren acidic soils. All of the 24 EoTIFYs were unevenly located on six out of nine chromosomes and could be classified into two subfamilies (ZIM/ZML and JAZ), consisting of 3 and 21 genes, respectively, with the JAZ subfamily being further divided into five subgroups (JAZ I to JAZ V). The amino acids of 24 EoTIFYs showed apparent differences between the two subfamilies based on the analysis of gene structures and conserved motifs. MCScanX analysis revealed the tandem duplication and segmental duplication of several EoTIFY genes occurred during E. ophiuroides genome evolution. Syntenic analyses of TIFY genes between E. ophiuroides and other five plant species (including A. thaliana, O. sativa, B. distachyon, S. biocolor, and S. italica) provided valuable clues for understanding the potential evolution of the EoTIFY family. qRT-PCR analysis revealed that EoTIFY genes exhibited different spatial expression patterns in different tissues. In addition, the expressions of EoTIFY genes were highly induced by MeJA and all of the EoTIFY family members except for EoJAZ2 displayed upregulated expression by MeJA. Ten EoTIFY genes (EoZML1, EoZML1, EoJAZ1, EoJAZ3, EoJAZ5, EoJAZ6, EoJAZ8, EoJAZ9, EoJAZ10, and EoJAZ21) were observed to be highly expressed under both exogenous MeJA treatment and aluminum stress, respectively. These results suggest that EoTIFY genes play a role in the JA-regulated pathway of plant growth and aluminum resistance as well. The results of this study laid a foundation for further understanding the function of TIFY genes in E. ophiuroides, and provided useful information for future aluminum tolerance related breeding and gene function research in warm-season grass plants.

Characterization of NAC Gene Family in Ammopiptanthus mongolicus and Functional Analysis of AmNAC24, an Osmotic and Cold-Stress-Induced NAC Gene.

The NAC family of transcription factors (TFs) is recognized as a significant group within the plant kingdom, contributing crucially to managing growth and development processes in plants, as well as to their response and adaptation to various environmental stressors. Ammopiptanthus mongolicus, a temperate evergreen shrub renowned for its remarkable resilience to low temperatures and drought stress, presents an ideal subject for investigating the potential involvement of NAC TFs in stress response mechanisms. Here, the structure, evolution, and expression profiles of NAC family TFs were analyzed systematically, and a cold and osmotic stress-induced member, AmNAC24, was selected and functionally characterized. A total of 86 NAC genes were identified in A. mongolicus, and these were divided into 15 groups. Up to 48 and 8 NAC genes were generated by segmental duplication and tandem duplication, respectively, indicating that segmental duplication is a predominant mechanism in the expansion of the NAC gene family in A. mongolicus. A considerable amount of NAC genes, including AmNAC24, exhibited upregulation in response to cold and osmotic stress. This observation is in line with the detection of numerous cis-acting elements linked to abiotic stress response in the promoters of A. mongolicus NAC genes. Subcellular localization revealed the nuclear residence of the AmNAC24 protein, coupled with demonstrable transcriptional activation activity. AmNAC24 overexpression enhanced the tolerance of cold and osmotic stresses in Arabidopsis thaliana, possibly by maintaining ROS homeostasis. The present study provided essential data for understanding the biological functions of NAC TFs in plants.

Genome-wide identification and analysis of WD40 proteins reveal that NtTTG1 enhances drought tolerance in tobacco (Nicotiana tabacum)

BackgroundWD40 proteins, which are highly prevalent in eukaryotes, play important roles in plant development and stress responses. However, systematic identification and exploration of WD40 proteins in tobacco have not yet been conducted.ResultsIn this study, a total of 399 WD40 regulatory genes were identified in common tobacco (Nicotiana tabacum). Gene structure and motif analysis revealed structural and functional diversity among different clades of tobacco WD40 regulatory genes. The expansion of tobacco WD40 regulatory genes was mainly driven by segmental duplication and purifying selection. A potential regulatory network of NtWD40s suggested that NtWD40s might be regulated by miRNAs and transcription factors in various biological processes. Expression pattern analysis via transcriptome analysis and qRT-PCR revealed that many NtWD40s exhibited tissue-specific expression patterns and might be involved in various biotic and abiotic stresses. Furthermore, we have validated the critical role of NtTTG1, which was located in the nuclei of trichome cells, in enhancing the drought tolerance of tobacco plants.ConclusionsOur study provides comprehensive information to better understand the evolution of WD40 regulatory genes and their roles in different stress responses in tobacco.

Genome-wide identification of GATA transcription factor family and the effect of different light quality on the accumulation of terpenoid indole alkaloids in Uncaria rhynchophylla.

Uncaria rhynchophylla is an evergreen vine plant, belonging to the Rubiaceae family, that is rich in terpenoid indole alkaloids (TIAs) that have therapeutic effects on hypertension and Alzheimer's disease. GATA transcription factors (TF) are a class of transcription regulators that participate in the light response regulation, chlorophyll synthesis, and metabolism, with the capability to bind to GATA cis-acting elements in the promoter region of target genes. Currently the charactertics of GATA TFs in U. rhynchophylla and how different light qualities affect the expression of GATA and key enzyme genes, thereby affecting the changes in U. rhynchophylla alkaloids have not been investigated. In this study, 25 UrGATA genes belonging to four subgroups were identified based on genome-wide analysis. Intraspecific collinearity analysis revealed that only segmental duplications were identified among the UrGATA gene family. Collinearity analysis of GATA genes between U. rhynchophylla and four representative plant species, Arabidopsis thaliana, Oryza sativa, Coffea Canephora, and Catharanthus roseus was also performed. U. rhynchophylla seedlings grown in either red lights or under reduced light intensity had altered TIAs content after 21 days. Gene expression analysis reveal a complex pattern of expression from the 25 UrGATA genes as well as a number of key TIA enzyme genes. UrGATA7 and UrGATA8 were found to have similar expression profiles to key enzyme TIA genes in response to altered light treatments, implying that they may be involved in the regulation TIA content. In this research, we comprehensively analyzed the UrGATA TFs, and offered insight into the involvement of UrGATA TFs from U. rhynchophylla in TIAs biosynthesis.

Duplication of a chromosome 2 segment in production CHO cell lines correlates with age-related growth improvement.

Monitoring the stability of recombinant Chinese Hamster Ovary (CHO) cell lines is essential to ensure the selection of production cell lines suitable for biomanufacturing. It has been frequently observed that recombinant CHO cell lines develop phenotypic changes upon aging, such as accelerated cell growth in late generation cultures. However, the mechanism responsible for age-correlated changes is poorly understood. In this study, we investigated the molecular mechanisms underlying the age-correlated cell growth improvement in Pfizer's platform fed-batch production process, by examining multiple cell lines derived from different CHO expression systems, expressing a variety of monoclonal antibodies (mAbs). Comprehensive whole-genome resequencing analysis revealed duplication of a continuous 50.2 Mbp segment in chromosome 2 (Chr2) specific to clones that showed age-correlated growth change as compared to clones that did not exhibit age-correlated growth change. Moreover, such age- and growth-related Chr2 duplication was independent of the presence or type of recombinant monoclonal antibody expression. When we compared transcriptome profiles from low-growth and high-growth cell lines, we found that>95% of the genes overexpressed in high-growth cell lines were in the duplicated Chr2 segment. To the best of our knowledge, this is the first report of large genomic duplication, specific to Chr2, being associated with age-correlated growth change. Investigation of the cause-and-effect relationship between the genes identified in the duplicated regions and age-correlated growth change is underway. We are confident that this effort will lead to improved cell line screening and targeted rational cell line engineering efforts to develop cell lines with improved stability performance.