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As the key transcription factors regulating auxin responsive genes expression, auxin response factors (ARFs) play critical roles in diverse aspects of plant growth and development. Betula pendula is a valuable ornamental tree, and the information on ARF gene family of B. pendula is needed for better understanding. The publication of the genome sequence of B. pendula enable to analyze the bioinformatics information and expression pattern of BpeARF gene family on the genome-wide basis. In this study, physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, conserved domain, motif composition, and cis-acting element of BpeARF gene family were analyzed, and expression patterns of BpeARF genes were investigated using completely random design in different tissues and under exogenous NAA and drought treatments. A total of 17 BpeARF genes was identified from B. pendula genome, which were unevenly distributed on 13 chromosomes and encoded adequate proteins ranging from 613 to 1135 amino acids in length. Three BpeARF gene pairs were formed by segmental duplication, and the Ka/Ks values of these BpeARF gene pairs were less than 1. According to the phylogenetic relationship among B. pendula, Betula platyphylla, Populus trichocarpa, and Arabidopsis thaliana, the BpeARF genes were divided into four classes, and the intron/exon structure, conserved domain, and motif composition showed high similarity among the BpeARF genes within the same class. The cis-acting elements in the promoter regions of BpeARF genes were related to tissue development, hormone response, and stress resistance. Quantitative real-time PCR exhibited diverse expression patterns of BpeARF genes in different tissues and in response to exogenous auxin treatment and drought stress. The expressions of one, ten, seven, and three BpeARF genes were the high levels in buds, young leaves, stems, and roots, respectively. Under exogenous NAA treatment, six BpeARF genes in stems and roots were upregulated expression at all timepoints. Under drought stress, BpeARF7 and BpeARF15 were upregulated in stems and roots, and BpeARF5 and BpeARF6 were downregulated in leaves, stems, and roots. Our results provided valuable information for the classification and putative functions of BpeARF gene family, which may be helpful for selecting candidate genes and verifying gene function in the genetic engineering of birch trees in further research. [ABSTRACT FROM AUTHOR]

Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits. [ABSTRACT FROM AUTHOR]

Background: MIKC type MADS-box transcription factors are one of the largest gene families and play a pivotal role in flowering time and flower development. Chimonanthus salicifolius belongs to the family Calycanthaceae and has a unique flowering time and flowering morphology compared to other Chimonanthus species, but the research on MIKC type MADS-box gene family of C. salicifolius has not been reported. Objective: Identification, comprehensive bioinformatic analysis, the expression pattern of MIKC-type MADS-box gene family from different tissues of C. salicifolius. Methods: Genome-wide investigation and expression pattern under different tissues of the MIKC-type MADS-box gene family in C. salicifolius, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, promoter cis-acting element were performed. Results: A total of 29 MIKC-type MADS-box genes were identified from the whole genome sequencing. Interspecies synteny analysis revealed more significant collinearity between C. salicifolius and the magnoliids species compared to eudicots and monocots. MIKC-type MADS-box genes from the same subfamily share similar distribution patterns, gene structure, and expression patterns. Compared with Arabidopsis thaliana, Nymphaea colorata, and Chimonanthus praecox, the FLC genes were absent in C. salicifolius, while the AGL6 subfamily was expanded in C. salicifolius. The selectively expanded promoter (AGL6) and lack of repressor (FLC) genes may explain the earlier flowering in C. salicifolius. The loss of the AP3 homologous gene in C. salicifolius is probably the primary cause of the morphological distinction between C. salicifolius and C. praecox. The csAGL6a gene is specifically expressed in the flowering process and indicates the potential function of promoting flowering. Conclusion: This study offers a genome-wide identification and expression profiling of the MIKC-types MADS-box genes in the C. salicifolius, and establishes the foundation for screening flowering development genes and understanding the potential function of the MIKC-types MADS-box genes in the C. salicifolius. [ABSTRACT FROM AUTHOR]

Response regulator (RR) is the core component of cytokinin (CK) signaling, and it regulates the expression of numerous downstream CK-responsive genes. However, the knowledge regarding the pecan RR (CiRR) gene family is still limited. In this study, we first monitored trans-zeatin riboside (tZR) content in the graft union 0, 7, 14, and 32 days after grafting and then conducted genome-wide analysis and expression profiling of the CiRR gene family using an available genome sequence and RNA-seq dataset, aiming to better understand the roles of CK during pecan grafting. The dynamic contents of tZR showed an increased trend during the specific period for both the scion and rootstock. There were 20 CiRRs in the pecan genome, including 12 type A CiRRs, 5 type B members, and 3 type C genes. All members contained a receiver domain and type B CiRRs possessed an additional Myb-like DNA-binding domain. Promoter analysis showed that the CiRR gene family contained cis-elements associated with growth and development, hormones, and stress. A total of 10 genes, including CiRR18/9/4a/14a/12c/5/12b/14b/2b/2a, were abundantly expressed in the samples of different tissues, drought stress, and kernel development. There were 12 genes (CiRR5/18/4a/12b/2b/12c/14b/2a/14a/4b/9/11a) showing active expressions during grafting, and weighted gene co-expression network analysis (WGCNA) grouped them into six modules. Among them, CiRR14a and CiRR12b were the hub genes for the turquoise and brown modules, respectively. Functional annotation indicated that the turquoise module was associated with gene transcription and translation, while the brown module was related to cell proliferation. Our results suggest that the CiRR gene family central to CK signaling is probably involved in callus formation during pecan grafting.

The jasmonate ZIM domain (JAZ) protein belongs to the TIFY ((TIF[F/Y]XG) domain protein) family, which is composed of several plant-specific proteins that play important roles in plant growth, development, and defense responses. However, the mechanism of the sorghum JAZ family in response to abiotic stress remains unclear. In the present study, a total of 17 JAZ genes were identified in sorghum using a Hidden Markov Model search. In addition, real-time quantification polymerase chain reaction (RT-qPCR) was used to analyze the gene expression patterns under abiotic stress. Based on phylogenetic tree analysis, the sorghum JAZ proteins were mainly divided into nine subfamilies. A promoter analysis revealed that the SbJAZ family contains diverse types of promoter cis-acting elements, indicating that JAZ proteins function in multiple pathways upon stress stimulation in plants. According to RT-qPCR, SbJAZ gene expression is tissue-specific. Additionally, under cold, hot, polyethylene glycol, jasmonic acid, abscisic acid, and gibberellin treatments, the expression patterns of SbJAZ genes were distinctly different, indicating that the expression of SbJAZ genes may be coordinated with different stresses. Furthermore, the overexpression of SbJAZ1 in Escherichia coli was found to promote the growth of recombinant cells under abiotic stresses, such as PEG 6000, NaCl, and 40°C treatments. Altogether, our findings help us to better understand the potential molecular mechanisms of the SbJAZ family in sorghum in response to abiotic stresses.

As the key transcription factors regulating auxin responsive genes expression, auxin response factors (ARFs) play critical roles in diverse aspects of plant growth and development. Betula pendula is a valuable ornamental tree, and the information on ARF gene family of B. pendula is needed for better understanding. The publication of the genome sequence of B. pendula enable to analyze the bioinformatics information and expression pattern of BpeARF gene family on the genome-wide basis. In this study, physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, conserved domain, motif composition, and cis-acting element of BpeARF gene family were analyzed, and expression patterns of BpeARF genes were investigated using completely random design in different tissues and under exogenous NAA and drought treatments. A total of 17 BpeARF genes was identified from B. pendula genome, which were unevenly distributed on 13 chromosomes and encoded adequate proteins ranging from 613 to 1135 amino acids in length. Three BpeARF gene pairs were formed by segmental duplication, and the Ka/Ks values of these BpeARF gene pairs were less than 1. According to the phylogenetic relationship among B. pendula, Betula platyphylla, Populus trichocarpa, and Arabidopsis thaliana, the BpeARF genes were divided into four classes, and the intron/exon structure, conserved domain, and motif composition showed high similarity among the BpeARF genes within the same class. The cis-acting elements in the promoter regions of BpeARF genes were related to tissue development, hormone response, and stress resistance. Quantitative real-time PCR exhibited diverse expression patterns of BpeARF genes in different tissues and in response to exogenous auxin treatment and drought stress. The expressions of one, ten, seven, and three BpeARF genes were the high levels in buds, young leaves, stems, and roots, respectively. Under exogenous NAA treatment, six BpeARF genes in stems and roots were upregulated expression at all timepoints. Under drought stress, BpeARF7 and BpeARF15 were upregulated in stems and roots, and BpeARF5 and BpeARF6 were downregulated in leaves, stems, and roots. Our results provided valuable information for the classification and putative functions of BpeARF gene family, which may be helpful for selecting candidate genes and verifying gene function in the genetic engineering of birch trees in further research.

The GDSL esterase/lipase family contains many functional genes that perform important biological functions in growth and development, morphogenesis, seed oil synthesis, and defense responses in plants. The expression of GDSL esterase/lipase genes can respond to biotic and abiotic stresses. Although GDSL esterase/lipase family genes have been identified and studied in other plants, they have not been identified and their functions remain unclear in tomato. This study is the first to identify 80 GDSL esterase/lipase family genes in tomato, which were named SlGELP1–80. These genes were mapped to their positions on the chromosomes and their physical and chemical properties, gene structure, phylogenetic relationships, collinear relationships, and cis-acting elements were analyzed. The spatiotemporal expression characteristics of the SlGELP genes in tomato were diverse. In addition, RNA-seq analysis indicated that the expression patterns of the SlGELP genes in tomato differed before and after inoculation with Stemphylium lycopersici. qRT-PCR was used to analyze the expression of five SlGELP genes after treatments with S. lycopersici, salicylic acid and jasmonic acid. Finally, this study was the first to identify and analyze GDSL esterase/lipase family genes in tomato via bioinformatics approaches, and these findings provide new insights for improving the study of plant disease resistance.

In higher plants, light capture of chlorophyll a/b binding protein (Lhc) plays a crucial role in the plant's response to adverse environment. So far, the family has not been systematically identified in grapes. In this study, 20 VvLhcs were identified in the grape genome, which were distributed in 13 of 19 grape chromosomes and divided into 7 developing branches. The results of gene duplication analysis showed that 6 VvLhcs formed fragment duplication events, while there was no tandem duplication in VvLhcs. Exon–intron structure analysis showed that they had a wide number of exons. Protein conserved motif analysis showed that VvLhcs contained more similar motif structures in the same phylogenetic branch. The cis-acting elements in the VvLhcs promoter region mainly respond to light, plant hormones and abiotic stresses. In addition, qRT-PCR results showed that different proportions of salt stress and red-blue light affected the expression of VvLhcs and the expression patterns of genes in different grape varieties were different. The results for further study on different grape varieties in different combinations of red and blue light of the Lhc provide a theoretical basis. [ABSTRACT FROM AUTHOR]

Insect cuticle is critical for the environmental adaptability and insecticide resistance of insects. However, there is no clear understanding of the structure and protein components of the cuticle during each developmental stage of holometabolous insects, and knowledge about the protein components within each layer is vague. We conducted serial sectioning, cuticular structure analysis, and transcriptome sequencing of the larval, pupal, and adult cuticles of Bombyx mori. The deposition processes of epicuticle, exocuticle, and endocuticle during larval, pupal, and adult cuticle formation were similar. Transcriptome analysis showed that these cuticle formations share 74% of the expressed cuticular protein (CP) genes and 20 other structural protein genes, such as larval serum protein and prisilkin. There are seven, six, and eleven stage-specific expressed CP genes in larval, pupal, and adult cuticles, respectively. The types and levels of CP genes may be the key determinants of the properties of each cuticular layer. For example, the CPs of the RR-2 protein family with high contents of histidine (His) are more essential for the exocuticle. Functional analysis suggested that BmorCPAP1-H is involved in cuticle formation. This study not only offers an in-depth understanding of cuticle morphology and protein components but also facilitates the elucidation of molecular mechanisms underlying cuticle formation in future studies. [ABSTRACT FROM AUTHOR]

Insect cuticle is critical for the environmental adaptability and insecticide resistance of insects. However, there is no clear understanding of the structure and protein components of the cuticle during each developmental stage of holometabolous insects, and knowledge about the protein components within each layer is vague. We conducted serial sectioning, cuticular structure analysis, and transcriptome sequencing of the larval, pupal, and adult cuticles of Bombyx mori. The deposition processes of epicuticle, exocuticle, and endocuticle during larval, pupal, and adult cuticle formation were similar. Transcriptome analysis showed that these cuticle formations share 74% of the expressed cuticular protein (CP) genes and 20 other structural protein genes, such as larval serum protein and prisilkin. There are seven, six, and eleven stage-specific expressed CP genes in larval, pupal, and adult cuticles, respectively. The types and levels of CP genes may be the key determinants of the properties of each cuticular layer. For example, the CPs of the RR-2 protein family with high contents of histidine (His) are more essential for the exocuticle. Functional analysis suggested that BmorCPAP1-H is involved in cuticle formation. This study not only offers an in-depth understanding of cuticle morphology and protein components but also facilitates the elucidation of molecular mechanisms underlying cuticle formation in future studies.

MADS-box is a critical transcription factor regulating the development of floral organs and plays essential roles in the growth and development of floral transformation, flower meristem determination, the development of male and female gametophytes, and fruit development. In this study, 36 MIKC-type MADS-box genes were identified in the ‘Taishanhong’ pomegranate genome. By utilizing phylogenetic analysis, 36 genes were divided into 14 subfamilies. Bioinformatics methods were used to analyze the gene structure, conserved motifs, cis-acting elements, and the protein interaction networks of the MIKC-type MADS-box family members in pomegranate, and their expressions pattern in different tissues of pomegranate were analyzed. Tissue-specific expression analysis revealed that the E-class genes (PgMADS03, PgMADS21, and PgMADS27) were highly expressed in floral tissues, while PgMADS29 was not expressed in all tissues, indicating that the functions of the E-class genes were differentiated. PgMADS15 of the C/D-class was the key gene in the development network of pomegranate flower organs, suggesting that PgMADS15 might play an essential role in the peel and inner seed coat development of pomegranate. The results in this study will provide a reference for the classification, cloning, and functional research of pomegranate MADS-box genes.

NLR (NOD-like receptor) is a large class of cytoplasmic family protein that belonging to the pattern recognition receptors (PRRs), which exerts autoimmune activities by detecting pathogen-associated molecular patterns (PAMPs) and regulating immune related pathways. Black rockfish (Sebastes schelgelii) is an important economic fish widely located in coastal areas of East Asia. With the enlargement of its cultivation scale, various pathogens threaten its production, which resulted in dramatic economic losses. However, little information is available about the NLR genes in S. schlegelii. In this study, 23 NLR genes were identified and classified in S. schlegelii based on the whole genome database. Phylogenetic analysis showed that these NLR genes was clearly divided into five subfamilies. Comparison of copy numbers in vertebrates showed NLRC3 or NLRC3-like genes expanded in teleost fish about ~5–50 million years ago. The Ka/Ks ratios of most NLR genes were less than one, indicating they underwent purifying selection except for APAF1. Protein-protein interaction analysis showed that NLR proteins interacted with immune molecules such as caspase, ripk2 and TRAF. Besides, the expression patterns of NLR genes in mucosal tissues after Edwardsiella tarda infection were investigated by qRT-PCR. These results provided valuable evidence for understanding of the immune regulation mechanism and function of NLR genes in S. schlegelii. • Totally, 23 NLR genes were identified in S. schelgelii. • The characteristics and expression patters to E. tarda of NLRs were analyzed. • The expansion time of fish-specific NLRC3 or NLRC3-like family were estimated. [ABSTRACT FROM AUTHOR]

MADS-box is a critical transcription factor regulating the development of floral organs and plays essential roles in the growth and development of floral transformation, flower meristem determination, the development of male and female gametophytes, and fruit development. In this study, 36 MIKC-type MADS-box genes were identified in the 'Taishanhong' pomegranate genome. By utilizing phylogenetic analysis, 36 genes were divided into 14 subfamilies. Bioinformatics methods were used to analyze the gene structure, conserved motifs, cis-acting elements, and the protein interaction networks of the MIKC-type MADS-box family members in pomegranate, and their expressions pattern in different tissues of pomegranate were analyzed. Tissue-specific expression analysis revealed that the E-class genes (PgMADS03, PgMADS21, and PgMADS27) were highly expressed in floral tissues, while PgMADS29 was not expressed in all tissues, indicating that the functions of the E-class genes were differentiated. PgMADS15 of the C/D-class was the key gene in the development network of pomegranate flower organs, suggesting that PgMADS15 might play an essential role in the peel and inner seed coat development of pomegranate. The results in this study will provide a reference for the classification, cloning, and functional research of pomegranate MADS-box genes. [ABSTRACT FROM AUTHOR]

Gibberellin (GAs) plays the important role in the regulation of grape developmental and growth processes. The bioinformatics analysis confirmed the differential expression of GA2, GA3, and GA20 gibberellin oxidase genes (VvGA2oxs, VvGA3oxs, and VvGA20oxs) in the grape genome, and laid a theoretical basis for exploring its role in grape. Based on the Arabidopsis GA2oxs, GA3oxs, and GA20oxs genes already reported, the VvGA2oxs, VvGA3oxs, and VvGA20oxs genes in the grape genome were identified using the BLAST software in the grape genome database. Bioinformatics analysis was performed using software such as DNAMAN v.5.0, Clustalx, MapGene2Chrom, MEME, GSDS v.2.0, ExPASy, DNAsp v.5.0, and MEGA v.7.0. Chip expression profiles were generated using grape Affymetrix GeneChip 16K and Grape eFP Browser gene chip data in PLEXdb. The expression of VvGA2oxs, VvGA3oxs, and VvGA20oxs gene families in stress was examined by qRT-PCR (Quantitative real-time-PCR). There are 24 GAoxs genes identified with the grape genome that can be classified into seven subgroups based on a phylogenetic tree, gene structures, and conserved Motifs in our research. The gene family has higher codon preference, while selectivity is negative selection of codon bias and selective stress was analyzed. The expression profiles indicated that the most of VvGAox genes were highly expressed under different time lengths of ABA (Abscisic Acid) treatment, NaCl, PEG and 5 °C. Tissue expression analysis showed that the expression levels of VvGA2oxs and VvGA20oxs in different tissues at different developmental stages of grapes were relatively higher than that of VvGA3oxs. Last but not least, qRT-PCR (Real-time fluorescent quantitative PCR) was used to determine the relative expression of the GAoxs gene family under the treatment of GA3 (gibberellin 3) and uniconazole, which can find that some VvGA2oxs was upregulated under GA3 treatment. Simultaneously, some VvGA3oxs and VvGA20oxs were upregulated under uniconazole treatment. In a nutshell, the GA2ox gene mainly functions to inactivate biologically active GAs, while GA20ox mainly degrades C20 gibberellins, and GA3ox is mainly composed of biologically active GAs. The comprehensive analysis of the three classes of VvGAoxs would provide a basis for understanding the evolution and function of the VvGAox gene family in a grape plant. [ABSTRACT FROM AUTHOR]