TriticeaeSSRdb: a comprehensive database of simple sequence repeats in Triticeae.

Microsatellites, known as simple sequence repeats (SSRs), are short tandem repeats of 1 to 6 nucleotide motifs found in all genomes, particularly eukaryotes. They are widely used as co-dominant markers in genetic analyses and molecular breeding. Triticeae, a tribe of grasses, includes major cereal crops such as bread wheat, barley, and rye, as well as abundant forage and lawn grasses, playing a crucial role in global food production and agriculture. To enhance genetic work and expedite the improvement of Triticeae crops, we have developed TriticeaeSSRdb, an integrated and user-friendly database. It contains 3,891,705 SSRs from 21 species and offers browsing options based on genomic regions, chromosomes, motif types, and repeat motif sequences. Advanced search functions allow personalized searches based on chromosome location and length of SSR. Users can also explore the genes associated with SSRs, design customized primer pairs for PCR validation, and utilize practical tools for whole-genome browsing, sequence alignment, and in silico SSR prediction from local sequences. We continually update TriticeaeSSRdb with additional species and practical utilities. We anticipate that this database will greatly facilitate trait genetic analyses and enhance molecular breeding strategies for Triticeae crops. Researchers can freely access the database at http://triticeaessrdb.com/.

OrangeExpDB: an integrative gene expression database for Citrus spp.

BACKGROUND: Citrus is a major fruit crop, and RNA-sequencing (RNA-seq) data can be utilized to investigate its gene functions, heredity, evolution, development, and the detection of genes linked to essential traits or resistance to pathogens. However, it is challenging to use the public RNA-seq datasets for researchers without bioinformatics training, and expertise. RESULTS: OrangeExpDB is a web-based database that integrates transcriptome data of various Citrus spp., including C. limon (L.) Burm., C. maxima (Burm.) Merr., C. reticulata Blanco, C. sinensis (L.) Osbeck, and Poncirus trifoliata (L.) Raf., downloaded from the NCBI SRA database. It features a blast tool for browsing and searching, enabling quick download of expression matrices for different transcriptome samples. Expression of genes of interest can be easily generated by searching gene IDs or sequence similarity. Expression data in text format can be downloaded and presented as a heatmap, with additional sample information provided at the bottom of the webpage. CONCLUSIONS: Researchers can utilize OrangeExpDB to facilitate functional genomic analysis and identify key candidate genes, leveraging publicly available citrus RNA-seq datasets. OrangeExpDB can be accessed at http://www.orangeexpdb.com/ .

The complete chloroplast genome and phylogenetic analysis of Bauhinia glauca subsp. hupehana (Craib) T. C. Chen 1988.

Bauhinia glauca subsp. hupehana (Craib) T. C. Chen 1988, a member of the Leguminosae family, Cercidoideae subfamily, and Bauhinia genus, has a rich history of traditional usage in Chinese medicine. Renowned for its analgesic properties, it is commonly employed for managing inflammation and pain. This study aimed to sequence the complete chloroplast genome of B. glauca subsp. hupehana using Illumina paired-end sequencing data. The chloroplast genome spans 156,967 bp and consists of four main regions: the large single-copy (LSC) region (89,185 bp), the small single-copy (SSC) region (19,146 bp), and a pair of inverted repeats (IRs) (24,318 bp). The overall GC content of the chloroplast genome is 36.19%, with specific values of 33.99%, 29.79%, and 42.76% for the LSC, SSC, and IR regions, respectively. A total of 128 genes were annotated in the chloroplast genome, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that B. glauca subsp. hupehana is closely related to Bauhinia racemose, indicating a sister taxon relationship between the two species. This study significantly contributes to the chloroplast genomic resource for Bauhinia, laying the groundwork for future phylogenetic investigations within the genus.

Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.).

Drought is one of the major environmental constraints for wheat production world-wide. As the progenitor and genetic reservoir of common wheat, emmer wheat is considered as an invaluable gene pool for breeding drought-tolerant wheat. Combining GWAS and eGWAS analysis of 107 accessions, we identified 86 QTLs, 105 462 eQTLs as well as 68 eQTL hotspots associating with drought tolerance (DT) in emmer wheat. A complex regulatory network composed of 185 upstream regulator and 2432 downstream drought-responsive candidates was developed, of which TtOTS1 was found to play a negative effect in determining DT through affecting root development. This study sheds light on revealing the genetic basis underlying DT, which will provide the indispensable genes and germplasm resources for elite drought tolerance wheat improvement and breeding.

Dynamics of Microbial Community Structure, Function and Assembly Mechanism with Increasing Stand Age of Slash Pine (Pinus elliottii) Plantations in Houtian Sandy Area, South China.

Establishing slash pine plantations is the primary method for restoring sandification land in the Houtian area of South China. However, the microbial variation pattern with increasing stand age remains unclear. In this study, we investigated microbial community structure and function in bare sandy land and four stand age gradients, exploring ecological processes that determine their assembly. We did not observe a significant increase in the absolute abundance of bacteria or fungi with stand age. Bacterial communities were dominated by Chloroflexi, Actinobacteria, Proteobacteria, and Acidobacteria; the relative abundance of Chloroflexi significantly declined while Proteobacteria and Acidobacteria significantly increased with stand age. Fungal communities showed succession at the genus level, with Pisolithus most abundant in soils of younger stands (1- and 6-year-old). Turnover of fungal communities was primarily driven by stochastic processes; both deterministic and stochastic processes influenced the assembly of bacterial communities, with the relative importance of stochastic processes gradually increasing with stand age. Bacterial and fungal communities showed the strongest correlation with the diameter at breast height, followed by soil available phosphorus and water content. Notably, there was a significant increase in the relative abundance of functional groups involved in nitrogen fixation and uptake as stand age increased. Overall, this study highlights the important effects of slash pine stand age on microbial communities in sandy lands and suggests attention to the nitrogen and phosphorus requirements of slash pine plantations in the later stages of sandy management.

Comparative Analysis Reveals Different Evolutionary Fates and Biological Functions in Wheat Duplicated Genes (Triticum aestivum L.).

Wheat (Triticum aestivum L.) is a staple food crop that provides 20% of total human calorie consumption. Gene duplication has been considered to play an important role in evolution by providing new genetic resources. However, the evolutionary fates and biological functions of the duplicated genes in wheat remain to be elucidated. In this study, the resulting data showed that the duplicated genes evolved faster with shorter gene lengths, higher codon usage bias, lower expression levels, and higher tissue specificity when compared to non-duplicated genes. Our analysis further revealed functions of duplicated genes in various biological processes with significant enrichment to environmental stresses. In addition, duplicated genes derived from dispersed, proximal, tandem, transposed, and whole-genome duplication differed in abundance, evolutionary rate, gene compactness, expression pattern, and genetic diversity. Tandem and proximal duplicates experienced stronger selective pressure and showed a more compact gene structure with diverse expression profiles than other duplication modes. Moreover, genes derived from different duplication modes showed an asymmetrical evolutionary pattern for wheat A, B, and D subgenomes. Several candidate duplication hotspots associated with wheat domestication or polyploidization were characterized as potential targets for wheat molecular breeding. Our comprehensive analysis revealed the evolutionary trajectory of duplicated genes and laid the foundation for future functional studies on wheat.

The evolutionary patterns, expression profiles, and genetic diversity of expanded genes in barley.

Gene duplication resulting from whole-genome duplication (WGD), small-scale duplication (SSD), or unequal hybridization plays an important role in the expansion of gene families. Gene family expansion can also mediate species formation and adaptive evolution. Barley (Hordeum vulgare) is the world's fourth largest cereal crop, and it contains valuable genetic resources due to its ability to tolerate various types of environmental stress. In this study, 27,438 orthogroups in the genomes of seven Poaceae were identified, and 214 of them were significantly expanded in barley. The evolutionary rates, gene properties, expression profiles, and nucleotide diversity between expanded and non-expanded genes were compared. Expanded genes evolved more rapidly and experienced lower negative selection. Expanded genes, including their exons and introns, were shorter, they had fewer exons, their GC content was lower, and their first exons were longer compared with non-expanded genes. Codon usage bias was also lower for expanded genes than for non-expanded genes; the expression levels of expanded genes were lower than those of non-expanded genes, and the expression of expanded genes showed higher tissue specificity than that of non-expanded genes. Several stress-response-related genes/gene families were identified, and these genes could be used to breed barley plants with greater resistance to environmental stress. Overall, our analysis revealed evolutionary, structural, and functional differences between expanded and non-expanded genes in barley. Additional studies are needed to clarify the functions of the candidate genes identified in our study and evaluate their utility for breeding barley plants with greater stress resistance.

BarleyExpDB: an integrative gene expression database for barley.

BACKGROUND: RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge amounts of histological data remains a great challenge for wet labs and field researchers who lack bioinformatics experience and computational resources. RESULTS: We present BarleyExpDB, an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley at different growth and developmental stages, tissues, and stress conditions, as well as differential expression of mutants and populations to build a platform for barley expression and visualization. The expression of a gene of interest can be easily queried by searching by known gene ID or sequence similarity. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Proteins Families Database, and Simple Modular Architecture Research Tool annotations. CONCLUSIONS: BarleyExpDB will serve as a valuable resource for the barley research community to leverage the vast publicly available RNA-seq datasets for functional genomics research and crop molecular breeding.

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat.

Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.

Genome-wide characterization of R2R3-MYB gene family in Santalum album and their expression analysis under cold stress.

Sandalwood (Santalum album) is a high-value multifunctional tree species that is rich in aromatic substances and is used in medicine and global cosmetics. Due to the scarcity of land resources in tropical and subtropical regions, land in temperate regions is a potential resource for the development of S. album plantations in order to meet the needs of S. album production and medicine. The R2R3-MYB transcription factor family is one of the largest in plants and plays an important role in the response to various abiotic stresses. However, the R2R3-MYB gene family of S. album has not been studied. In this study, 144 R2R3-MYB genes were successfully identified in the assembly genome sequence, and their characteristics and expression patterns were investigated under various durations of low temperature stress. According to the findings, 31 of the 114 R2R3-MYB genes showed significant differences in expression after cold treatment. Combining transcriptome and weighted gene co-expression network analysis (WGCNA) revealed three key candidate genes (SaMYB098, SaMYB015, and SaMYB068) to be significantly involved in the regulation of cold resistance in S. album. The structural characteristics, evolution, and expression pattern of the R2R3-MYB gene in S. album were systematically examined at the whole genome level for the first time in this study. It will provide important information for future research into the function of the R2R3-MYB genes and the mechanism of cold stress response in S. album.

The barley DIR gene family: An expanded gene family that is involved in stress responses.

Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.

Multi-omics reveals the key and specific miRNA-mRNA modules underlying salt tolerance in wild emmer wheat (Triticum dicoccoides L.).

BACKGROUND: Salt stress is one of the most destructive environmental factors limiting crop growth and development. MicroRNAs (miRNAs) are a class of conserved endogenous small non-coding RNAs, playing the crucial role in regulating salt response and tolerance in plants. However, the miRNAs in wild emmer wheat, especially the key and specific salt-responsive miRNAs are not well studied. RESULTS: Here, we performed small RNA, transcriptome, and degradome sequencing of both of salt-tolerance (ST) and salt-sensitive (SS) wild emmer genotypes to identify the miRNA-mRNA modules associating with salt tolerance. Totally, 775 miRNAs, including 361 conserved known miRNAs and 414 novel miRNAs were detected. Differential expression analysis identified 93 salt-responsive miRNAs under salt stress. Combined with RNA-seq and degradome sequencing analysis, 224 miRNA-mRNA modules displayed the complete opposite expression trends between ST and SS genotypes, most of which functionally enriched into ROS homeostasis maintaining, osmotic pressure modulating, and root growth and development. Finally, the qRT-PCR and a large-scale yeast functional screening were also performed to initially validate the expression pattern and function of candidate genes. CONCLUSIONS: This study reported the key and specific miRNA-mRNA modules associated with salt tolerance in wild emmer, which lay the foundation for improving the salt tolerance in cultivated emmer and bread wheat through miRNA engineering approach.

BGFD: an integrated multi-omics database of barley gene families.

BACKGROUND: A gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and responses to environmental stimuli. Barley (Hordeum vulgare L.) is the fourth most cultivated cereal crop worldwide, and it is an important model species for genetic studies. Systematic identification and annotation of gene families are key for studies of molecular function and evolutionary history. RESULTS: We constructed a multi-omics database containing 5593 genes of 77 gene families called the Barley Gene Family Database (BGFD: http://barleygfdb.com ). BGFD is a free, user-friendly, and web-accessible platform that provides data on barley family genes. BGFD provides intuitive visual displays to facilitate studies of the physicochemical properties, gene structure, phylogenetic relationships, and motif organization of genes. Massive multi-omics datasets have been acquired and processed to generate an atlas of expression pattern profiles and genetic variation in BGFD. The platform offers several practical toolkits to conduct searches, browse, and employ BLAST functions, and the data are downloadable. CONCLUSIONS: BGFD will aid research on the domestication and adaptive evolution of barley; it will also facilitate the screening of candidate genes and exploration of important agronomic traits in barley.

Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.).

BACKGROUND: Long noncoding RNAs (lncRNAs) are emerging as the important regulators involving in growth and development as well as stress response in plants. However, current lncRNA studies were mainly performed at the individual level and the significance of it is not well understood in wheat. RESULTS: In this study, the lncRNA landscape of wheat spike was characterized through analysing a total of 186 spike RNA-seq datasets from 93 wheat genotypes. A total of 35,913 lncRNAs as well as 1,619 lncRNA-mRNA pairs comprised of 443 lncRNAs and 464 mRNAs were obtained. Compared to coding genes, these lncRNAs displayed rather low conservation among wheat and other gramineous species. Based on re-sequencing data, the genetic variations of these lncRNA were investigated and obvious genetic bottleneck were found on them during wheat domestication process. Furthermore, 122 lncRNAs were found to act as ceRNA to regulate endogenous competition. Finally, association and co-localization analysis of the candidate lncRNA-mRNA pairs identified 170 lncRNAs and 167 target mRNAs significantly associated with spike-related traits, including lncRNA.127690.1/TraesCS2A02G518500.1 (PMEI) and lncRNA.104854.1/TraesCS6A02G050300.1 (ATG5) associated with heading date and spike length, respectively. CONCLUSIONS: This study reported the lncRNA landscape of wheat spike through the population transcriptome analysis, which not only contribute to better understand the wheat evolution from the perspective of lncRNA, but also lay the foundation for revealing roles of lncRNA playing in spike development.

Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Fusarium graminearum Infection in Wheat.

RNA/DNA difference (RDD) is a post-transcriptional modification playing a crucial role in regulating diverse biological processes in eukaryotes. Although it has been extensively studied in plant chloroplast and mitochondria genomes, RDDs in plant nuclear genomes are not well studied at present. Here, we investigated the RDDs associated with fusarium head blight (FHB) through a novel method by comparing the RNA-seq data between Fusarium-infected and control samples of four wheat genotypes. A total of 187 high-confidence unique RDDs in 36 genes were identified, representing the first landscape of the FHB-responsive RDD in wheat. The majority (26) of these 36 RDD genes were correlated either positively or negatively with FHB levels. Effects of these RDDs on RNA and protein sequences have been identified, their editing frequency and the expression level of the corresponding genes provided, and the prediction of the effect on the minimum folding free energy of mRNA, miRNA binding, and colocation of RDDs with conserved domains presented. RDDs were predicted to induce modifications in the mRNA and protein structures of the corresponding genes. In two genes, TraesCS1B02G294300 and TraesCS3A02G263900, editing was predicted to enhance their affinity with tae-miR9661-5p and tae-miR9664-3p, respectively. To our knowledge, this study is the first report of the association between RDD and FHB in wheat; this will contribute to a better understanding of the molecular basis underlying FHB resistance, and potentially lead to novel strategies to improve wheat FHB resistance through epigenetic methods.

Genetic Diversity of Transcription Factor Genes in Triticum and Mining for Promising Haplotypes for Beneficial Agronomic Traits.

Transcription factor (TF) is a class of the sequence-specific DNA-binding proteins that modulate the transcription of target genes, and thus regulate their expressions. Variations in TF are the crucial determinants for phenotypic traits. Although much progress has been made in the functions of TF genes in wheat, one of the most important staple crops globally, the diversity of TF genes in wheat and its progenitors are not well understood, especially the agronomically promising haplotypes have not yet been characterized. Here, we identified a total of 6,023 TF genes from hexaploid wheat through a genome-search method and classified them into 59 gene families based on the conserved domain. The characteristics and dN/dS values of these genes showed evidently selective effects. Based on re-sequencing data, we found a strong genetic bottleneck among these TF genes on A and D subgenomes while no found in B subgenome during wheat domestication. Combined with selective signals and known QTLs on the whole genome, 21 TF genes were preliminarily found to be associated with yield-related traits. The haplotype frequency of these TF genes was further investigated in bread wheat and its progenitors and 13 major haplotypes were the casual loci related to key traits. Finally, the tissue-specific TF genes were also identified using RNA-seq analysis. This study provided insights into the diversity and evolution of TF genes and the identified TF genes and excellent haplotypes associating with traits will contribute to wheat genetic improvement.

Genomic insights into positive selection during barley domestication.

BACKGROUND: Cultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process. RESULTS: The rates of nonsynonymous substitution (Ka) to synonymous substitution (Ks) were calculated by comparing orthologous genes in different barley groups (wild vs. landrace and landrace vs. improved cultivar). The rates of evolution, properties, expression patterns, and diversity of positively selected genes (PSGs) and negatively selected genes (NSGs) were compared. PSGs evolved more rapidly, possessed fewer exons, and had lower GC content than NSGs; they were also shorter and had shorter intron, exon, and first exon lengths. Expression levels were lower, the tissue specificity of expression was higher, and codon usage bias was weaker for PSGs than for NSGs. Nucleotide diversity analysis revealed that PSGs have undergone a more severe genetic bottleneck than NSGs. Several candidate PSGs were involved in plant growth and development, which might make them as excellent targets for the molecular breeding of barley. CONCLUSIONS: Our comprehensive analysis of the evolutionary, structural, and functional divergence between PSGs and NSGs in barley provides new insight into the evolutionary trajectory of barley during domestication. Our findings also aid future functional studies of PSGs in barley.

The complete chloroplast genome and phylogenetic analysis of Astragalus sinicus Linne 1767.

Astragalus sinicus Linne 1767 is a traditional winter-growing green manure, that plays an important role in upgrading soil fertility and maintaining crop yield and quality for rice fields. This study reports the complete chloroplast genome of A. sinicus. The chloroplast genome contained 110 complete genes, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30 tRNA genes with 123,830 bp in length and a 34.66% GC content with IR loss. The evolutionary history, referred to as the maximum-likelihood (ML), showed that A. sinicus and Astragalus bhotanensis were most closely related. The chloroplast genome analysis of A. sinicus will serve as a reference for future studies on species evolution, plant conservation, and molecular phylogeny in Astragalus.

Genome-wide identification, expression analysis and evolutionary relationships of the IQ67-domain gene family in common wheat (Triticum aestivum L.) and its progenitors.

BACKGROUND: The plant-specific IQ67-domain (IQD) gene family plays an important role in plant development and stress responses. However, little is known about the IQD family in common wheat (Triticum aestivum L), an agriculturally important crop that provides more than 20% of the calories and protein consumed in the modern human diet. RESULTS: We identified 125 IQDs in the wheat genome and divided them into four subgroups by phylogenetic analysis. The IQDs belonging to the same subgroup had similar exon-intron structure and conserved motif composition. Polyploidization contributed significantly to the expansion of IQD genes in wheat. Characterization of the expression profile of these genes revealed that a few T. aestivum (Ta)IQDs showed high tissue-specificity. The stress-induced expression pattern also revealed a potential role of TaIQDs in environmental adaptation, as TaIQD-2A-2, TaIQD-3A-9 and TaIQD-1A-7 were significantly induced by cold, drought and heat stresses, and could be candidates for future functional characterization. In addition, IQD genes in the A, B and D subgenomes displayed an asymmetric evolutionary pattern, as evidenced by their different gain or loss of member genes, expression levels and nucleotide diversity. CONCLUSIONS: This study elucidated the potential biological functions and evolutionary relationships of the IQD gene family in wheat and revealed the divergent fates of IQD genes during polyploidization.