Beta-amylases (BAMs), key enzymes in starch hydrolysis, play an important role in plant growth, development, and resistance to abiotic stress. To mine the saline-alkali tolerance-related BAM genes in alfalfa (Medicago sativa L.), we identified MsBAM genes in the whole genome. The physicochemical properties, phylogeny, gene structures, conserved motifs, secondary structures, promoter cis-acting elements, chromosome localization, and gene replication relationships of BAM gene family members were analyzed. RNA-seq and quantitative real-time PCR (qRT-PCR) were employed to analyze the expression patterns of BAM family members under saline-alkali stress. The results showed that 54 BAM genes were identified in the genome, which were classified into 8 subgroups according to the phylogenetic tree. The members of the same subgroup had similar gene structures except that those of subgroups 1 and 7 had large differences. Conserved motif analysis showed that all MsBAM proteins had a typical glycohydrolysis domain. The chromosome localization analysis showed that MsBAM gene family members were unevenly distributed on 27 chromosomes. The duplication of gene segments led to the increase in BAM gene number in alfalfa. The promoters of BAM genes contained a large number of elements in response to plant hormones and stress. Transcriptome data and qRT-PCR results showed that the expression levels of most MsBAM genes were up-regulated in response to saline-alkali stress. Under the saline-alkali stress, the expression levels of 28 genes, including MsBAM6, were up-regulated on days 1 and 7, and those of 5 genes, including MsBAM9, were up-regulated by over 2 folds. In addition, under salt-alkali stress, BAM activity and soluble sugar content were significantly increased. These results indicate that BAM genes play a key role in alfalfa in response to saline-alkali stress, laying a foundation for further research in this field.
Medicago sativa/physiology* ; beta-Amylase/metabolism* ; Phylogeny ; Gene Expression Regulation, Plant ; Stress, Physiological/genetics* ; Multigene Family ; Alkalies ; Plant Proteins/genetics*

Lateral organ boundaries (LOB) domain (LBD) genes encode a family of transcription factors ubiquitous in higher plants, playing crucial roles in the growth, development, and stress responses. Hippophae rhamnoides, known for its drought, cold, and saline-alkali tolerance, offers significant economic benefits and ecological values. Utilizing the whole genome data and bioinformatics approaches, this study identified and analyzed the LBD gene family in H. rhamnoides. Additionally, we examined the expression pattern of HrLBD genes by integrating the transcriptome data from male and female flower buds in development. Eleven LBD genes were identified in H. rhamnoides, and these genes were distributed on five chromosomes. The HrLBD proteins showed the lengths ranging from 159 aa to 302 aa, the molecular weights between 18 249.91 Da and 33 202.01 Da, and the subcellular localization in the nucleus or chloroplasts. LBD protein domains and gene structures were highly conserved, featuring similar motifs. The phylogenetic analysis of HrLBD genes and the LBD genes in Arabidopsis thaliana and Hordeum vulgare revealed that HrLBD genes falled into two major categories: Class Ⅰ and Class Ⅱ. The transcriptome data and RT-qPCR showed that HrLBD genes were highly expressed in male flower buds, with up-regulated expression levels throughout bud development, indicating a role in the specific stage of male flower bud development. This study lays a theoretical foundation for exploring the roles of HrLBD genes in the growth, development, and sex differentiation of H. rhamnoides flower buds.
Flowers/genetics* ; Hippophae/metabolism* ; Phylogeny ; Gene Expression Regulation, Plant ; Plant Proteins/genetics* ; Transcription Factors/genetics* ; Multigene Family ; Genes, Plant

Docynia delavayi (Franch.) Schneid. is an economic fruit plant with high medicinal and edible values. The TCP gene family plays a vital role in plant growth and development. To explore the function of the TCP gene family in the growth and development of D. delavayi. In this study, the TCP gene family (DdeTCP) members were identified from the D. delavayi genome and their expression levels at different stages of seed germination and fruit development were analyzed. The results showed that a total of 18 DdeTCP genes were identified from the D. delavayi genome, with uneven location on 11 chromosomes. The phylogenetic tree showed that the 18 DdeTCPs could be classified into class Ⅱ (3) and class Ⅱ (15), suggesting that functional differentiation occurred among the DdeTCP family members. DdeTCP11 highly homologous to AtTCP14 was highly expressed in the early stage of seed germination, which suggested that this gene played a key role in seed germination. In addition, DdeTCP16 in class Ⅱ had a high expression level during the fruit ripening stage, which indicated that it might be related to fruit ripening. The findings lay a foundation for probing into the roles of the DdeTCP gene family in the growth and development of D. delavayi.
Phylogeny ; Gene Expression Regulation, Plant ; Multigene Family ; Genome, Plant/genetics* ; Plant Proteins/genetics* ; Transcription Factors/genetics* ; Germination/genetics* ; Fruit/growth & development* ; Genes, Plant

The plant AT-rich sequence and zinc-binding protein (PLATZ) family is composed of plant-specific zinc finger-like transcription factors, which play important roles in plant growth, development, and stress tolerance. In this study, to gain a better understanding of the PLATZ gene in C. sinensis and elucidate its response under drought and high temperature conditions, the PLATZ gene family of the C. sinensis cultivar 'Tieguanyin' was systematically identified, and a total of 12 CsPLATZ family members were identified. Expasy online and other bioinformatics tools were used to analyze the members of the PLATZ gene family in terms of protein physicochemical properties, phylogenetic relationships, cis-acting elements, gene structures, and intra- and inter-species collinearity. The results of phylogenetic analysis classified the CsPLATZ family members into 2 subfamilies. The conserved domains and gene structures of PLATZ family members within the same subfamily had a high degree of consistency, whereas a certain degree of diversity was observed among the subfamilies. Twelve PLATZ genes were unevenly distributed across 7 chromosomes of C. sinensis and the promoter regions of these genes had multiple cis-acting elements related to hormone and stress responses. The collinearity analysis showed that there were 4 pairs of duplication events in the CsPLATZ gene family, all of which were segmental duplications. Based on this gene family, C. sinensis had a closer evolutionary relationship with A. thaliana than with O. sativa. The transcriptome analysis showed that the expression levels of CsPLATZ family members varied in different tissue samples of C. sinensis. 6 genes (CsPLATZ-1, CsPLATZ-2, CsPLATZ-3, CsPLATZ-4, CsPLATZ-6, and CsPLATZ-8) with high expression in shoots, young leaves, and roots were selected for high temperature and drought stress treatments, and their expression was quantified by qRT-PCR. The results indicated that the six genes might play important roles in the response to drought stress. In addition, CsPLATZ-2 and CsPLATZ-8 might have important functions in the response to high temperature stress. The results of this study will contribute to a better understanding of the biological functions of PLATZ genes and their possible roles in the growth, development, and stress responses of C. sinensis.
Droughts ; Camellia sinensis/physiology* ; Phylogeny ; Gene Expression Regulation, Plant ; Plant Proteins/genetics* ; Stress, Physiological/genetics* ; Multigene Family ; Transcription Factors/genetics* ; Hot Temperature ; Genes, Plant

Sugarcane (Saccharum spp.) is an important sugar crop. Biotic and abiotic stresses such as diseases, cold, and drought are major factors limiting sugarcane production. β-1,3-glucanase (EC 3.2.1.39), a member of the pathogenesis-related protein family, plays an essential role not only in the plant defenses against pathogens but also in plant growth, development, and abiotic stress responses. To systematically investigate the sugarcane β-1,3-glucanase gene family, 132 glycoside hydrolase (GH) 17 family members were identified in the genomes of the sugarcane wild species Saccharum spontaneum 'Np-X', the tropical species S. officinarum 'LA-Purple', and the Saccharum spp. hybrid cultivar 'R570'. The results of the phylogenetic analysis categorized them into four subfamilies, of which subfamily Ⅳ had the largest proportion of members (102). The members of the sugarcane GH17 gene family contained five conserved motifs and 0-16 introns. The majority of the GH17 genes exhibited a genome-wide replication pattern, with 89.50% originating from S. spontaneum 'Np-X' and S. officinarum 'LA-Purple', while 58.10% of them in the Saccharum spp. hybrid cultivar 'R570' belonged to the discrete replication type. Four major classes of cis-acting elements were identified in the promoters, including the elements related to plant growth, development, and tissue-specific expression (14.21%), light-responsive elements (38.24%), biotic or abiotic stress-responsive elements (9.18%), and hormone-responsive elements (38.37%), which suggested that this gene family was involved in plant growth, development, hormone responses, and stress responses. Transcriptome and quantitative real-time PCR (RT-qPCR) analyses showed that the sugarcane GH17 genes exhibited tissue-specific expression and were differentially expressed under low temperature, drought, and hormone treatments, as well as during the interactions between different sugarcane genotypes and Sporisorium scitamineum, suggesting their potential roles in plant defenses. In addition, some SsGlu genes (SsGlu5, SsGlu20, SsGlu21, SsGlu25, SsGlu28, and SsGlu39) were expected to serve as candidate stress-related genes. This study lays a foundation for further revealing the molecular mechanisms of the stress resistance of sugarcane via β-1,3-glucanase genes.
Saccharum/physiology* ; Stress, Physiological/genetics* ; Glucan 1,3-beta-Glucosidase/metabolism* ; Multigene Family ; Phylogeny ; Gene Expression Regulation, Plant ; Plant Proteins/genetics*

Trihelix transcription factors play important roles in plant light responses, growth and development, and stress responses. However, Trihelix has not yet been reported in Eucommia ulmoides. In this study, bioinformatics methods were used to comprehensively identify and analyze the expression patterns of the Trihelix gene family in E. ulmoides, aiming to provide a basis for further functional studies of EuGTs genes. A total of 9 Trihelix gene family members were identified in E. ulmoides, encoding proteins with 339 to 883 amino acids, with isoelectric points ranging from 5.13 to 9.39 and relative molecular weights between 36 992.06 and 97 871.61. Subcellular localization results showed that only EuGT-2 was localized in chloroplasts, while the others were located in the nucleus. The Trihelix gene family was categorized into six subfamilies: GT-1, GT-2, SH4, SIP1, GTγ, and GTδ. EuGTs were distributed among three subfamilies: SH4, GT-1, and GT-2, containing 1, 6, and 2 Trihelix proteins, respectively, with 2 to 17 exons. The promoters of EuGTs contained various cis-acting elements related to hormones, stress, photoperiod, and growth and development. Collinearity analysis revealed 5 collinear gene pairs between E. ulmoides and Arabidopsis thaliana, and 14 collinear gene pairs between E. ulmoides and Populus. Expression pattern analysis showed that EuGTs exhibited tissue-specific expression: EuGT-1, EuGT-2 had the highest expression levels in leaves, EuGT-4, EuGT-6, EuGT-9 had the highest transcriptional levels in marginal peel, and EuGT-5、EuGT-8 were predominantly expressed in the xylem. As leaves developed, EuGTs showed a trend of asynchronous changes. No significant differences in EuGTs expression were observed between male and female flowers, with high expression levels mainly during the induction stage of flowering. The qRT-PCR analysis indicated that most EuGTs genes were most highly expressed in the leaves of E. ulmoides, while EuGT-5 was highly expressed in the stems. Under 200 mmol·L~(-1) NaCl treatment, most EuGTs genes exhibited an initial increase followed by a decrease in expression, significantly responding to salt stress. This study provides important genetic resources for further exploration of EuGTs gene functions and germplasm innovation in E. ulmoides.
Plant Proteins/metabolism* ; Gene Expression Regulation, Plant ; Eucommiaceae/chemistry* ; Phylogeny ; Multigene Family/genetics* ; Gene Expression Profiling ; Transcription Factors/metabolism* ; Genome, Plant/genetics*

Based on whole genome data, the identification and expression pattern analysis of the Atropa belladonna WRKY transcription factor family were conducted to provide a theoretical foundation for studying the biological functions and mechanisms of these transcription factors. In this study, bioinformatics methods were employed to identify members of the A. belladonna WRKY gene family and to predict their physicochemical properties, conserved motifs, promoter cis-acting elements, and chromosomal localization. Additionally, the expression patterns of the A. belladonna WRKY gene family under the regulation of environmental factors such as light quality and temperature were analyzed. The results revealed a total of 28 AbWRKY transcription factors, randomly distributed across 16 chromosomes, encoding 324-707 amino acids. Most AbWRKY proteins were acidic, unstable, and hydrophilic. Based on multiple sequence alignment and phylogenetic analysis, the WRKY gene family members were classified into two subfamilies. Conserved motif and domain analysis indicated that WRKY transcription factors in the same subfamily possessed conserved structural features. Promoter analysis predicted that the A. belladonna WRKY family contained light-responsive elements, hormone-responsive elements, and stress-responsive elements. Collinearity analysis showed that AbWRKY24 plays a crucial role in the expansion of the AbWRKY gene family. Then qRT-PCR results indicated that AbWRKY6, AbWRKY8, AbWRKY14, and AbWRKY24 responded to red light stress, while AbWRKY8, AbWRKY14, and AbWRKY24 responded to yellow light/low-temperature combined stress. AbWRKY6 and AbWRKY8 were significantly expressed in leaves and stems, AbWRKY27 and AbWRKY28 were significantly expressed in fibrous roots, and AbWRKY25 was significantly expressed in flowers. This study is the first to identify and analyze the WRKY gene family in A. belladonna and to examine its expression patterns under light and temperature regulation, laying a foundation for in-depth analysis and functional validation of the molecular mechanisms of A. belladonna WRKY transcription factors in responding to light quality and temperature environmental factors.
Transcription Factors/chemistry* ; Plant Proteins/metabolism* ; Phylogeny ; Gene Expression Regulation, Plant ; Light ; Temperature ; Atropa belladonna/metabolism* ; Multigene Family/genetics* ; Promoter Regions, Genetic/genetics* ; Sequence Alignment ; Amino Acid Sequence ; Genome, Plant/genetics*

Lysobacter harbors a plethora of cryptic biosynthetic gene clusters (BGCs), albeit only a limited number have been analyzed to date. In this study, we described the activation of a cryptic polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) gene cluster (lsh) in Lysobacter sp. DSM 3655 through promoter engineering and heterologous expression in Streptomyces sp. S001. As a result of this methodology, we were able to isolate two novel linear lipopeptides, lysohexaenetides A (1) and B (2), from the recombinant strain S001-lsh. Furthermore, we proposed the biosynthetic pathway for lysohexaenetides and identified LshA as another example of entirely iterative bacterial PKSs. This study highlights the potential of heterologous expression systems in uncovering cryptic biosynthetic pathways in Lysobacter genomes, particularly in the absence of genetic manipulation tools.
Lysobacter/metabolism* ; Streptomyces/metabolism* ; Lipopeptides/metabolism* ; Polyketide Synthases/genetics* ; Multigene Family

Xanthocillin is a unique natural product with an isonitrile group and shows remarkable antibacterial activity. In this study, the genome of an endophytic fungus Penicillium chrysogenum MT-40 isolated from Huperzia serrata was sequenced, and the gene clusters with the potential to synthesize xanthocillin analogues were mined by local BLAST and various bioinformatics analysis tools. As a result, a biosynthetic gene cluster (named for) responsible for the biosynthesis of xanthocillin analogues was identified by further heterologous expression of the key genes in Aspergillus oryzae NSAR1. Specifically, the ForB catalyzes the synthesis of 2-formamido-3-(4-hydroxyphenyl) acrylic acid, and the ForG catalyzes the dimerization of 2-formamido-3-(4-hydroxyphenyl) acrylic acid to produce the xanthocillin analogue N, N'-(1, 4-bis (4-hydroxyphenyl) buta-1, 3-diene-2, 3-diyl) diformamide. The results reported here provide a reference for further discovery of xanthocillin analogues from fungi.
Penicillium chrysogenum/genetics* ; Huperzia/microbiology* ; Acrylates ; Multigene Family

OBJECTIVE: To analyze the correlation between the mutational status of immunoglobulin heavy chain variable (IGHV) gene with the prognosis of patients with Waldenström macroglobulinemia (WM). METHODS: Immunoglobulin heavy chain gene (IGH) clonotypic sequence analysis was carried out to assess the mutational status of IGHV in the blood and/or bone marrow samples from 44 WM patients. The usage characteristics of IGHV-IGHD-IGHJ gene was explored. RESULTS: The most common IGHV subgroup was IGHV3, which was similar to the data from the Institute of Hematology of Chinese Academy of Medical Science. IGHV3-23 (20.45% vs. 15.44%) and IGHV3-74 (11.36% vs. 7.35%) were the main fragments used, which was followed by IGHV4 gene family (15.91% vs. 24.26%). However, no significant correlation was found between the IGHV4 usage and the prognosis of the patients. Should 98% be taken as the cut-off value for the IGHV mutation status, only 5 patients had no IGHV variant, and there was no correlation with the prognosis. Based on the X-tile analysis, 92.6% was re-selected as the cut-off value for the IGHV variant status in such patients. LDH was increased in 26 patients (59.1%) without IGHV variant (P < 0.05), whilst progression-free survival (P < 0.05) and overall survival (P < 0.05) were significantly shorter compared with those with IGHV variants. CONCLUSION The usage characteristics of IGHV-IGHD-IGHJ in our patients was similar to reported by the Institute of Hematology of Chinese Academy of Medical Science, albeit that no correlation was found between the IGHV4 usage and the prognosis of the patients. Furthermore, 98% may not be appropriate for distinguishing the IGHV variant status in WM patients.
Humans ; Immunoglobulin Heavy Chains/genetics* ; Multigene Family ; Mutation ; Waldenstrom Macroglobulinemia/genetics*