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For Selected: Download Citations EndNote Ris BibTeX Toggle Thumbnails Select The Complete Gene Sequencing of Bacilus subtilis Isolated from Rehmannia glutinosa and Study of Genes Related to Growth‑promoting Effects LA Guixiao, WANG Linlin, GUO Junqi, ZHAO Yulong, GUO Hongxia, JIA Hui, YANG Tiegang Journal of Henan Agricultural Sciences    2024, 53 (12): 75-85.   DOI: 10.15933/j.cnki.1004-3268.2024.12.008 Abstract （1064）      PDF （3510KB）（57）       Knowledge map    Save To investigate the genes associated with the growth‑promoting effects of Bacillus subtilis in Rehmannia glutinosa，whole genome sequencing was performed in this study and the genes associated with the growth‑promoting effects were discovered through functional annotation.The results showed that the genome size of Bacillus subtilis，an endophytic growth‑promoting bacterium of Rehmannia glutinosa，was 4 310 699 bp，with a GC content of 43.44%，and a total of 4 521 predicted coding genes.A total of 3 013，3 354，4 395，206，52，and 212 functional genes were annotated in the clusters of orthologous groups（COG） ，gene ontology（GO） ，kyoto encyclopedia of genes and genomes （KEGG） ，carbohydrate‑active enzymes（CAZyme），comprehensive antibiotic resistance database（CARD），and virulence factor database（VFDB），respectively.The annotation results indicated that there were 46 genes related to growth‑promoting function，with the majority of these genes involved in phosphorus solubilization，nitrogen fixation，and iron carrier processes.In the meantime，anti‑SMASH predicted that a total of 409 genes were enriched into 12 secondary metabolite synthesis gene clusters，with the majority encoding eight repressors，including fengycin，1‑carbapen‑2‑em‑3‑carboxylic acid，bacillaene，bacilysin，subtilosin A，surfactin，pulcherriminic acid，and bacillibactin.Among these，pulcherriminic acid and bacillibactin had been observed to facilitate the chelation of ferric ions in the surrounding environment. Reference | Related Articles | Metrics Select Identification of TCP Transcription Factors in Artemisia annua and Analysis of Their Expression Patterns under MeJA Treatment MA Qiyang, SONG Ge Journal of Henan Agricultural Sciences    2024, 53 (12): 62-74.   DOI: 10.15933/j.cnki.1004-3268.2024.12.007 Abstract （1481）      PDF （13374KB）（30）       Knowledge map    Save Based on the genome data of Artemisia annua，the TCP gene family members were identified，and their protein physicochemical properties，evolutionary relationships，and cis‑acting elements were analyzed. Transcriptome data were used to analyze the expression pattern of TCP transcription factors in Artemisia annua under different light treatments，and qRT‑PCR was used to detect their expression under methyl jasmonate（MeJA）treatment.The results showed that a total of 29 TCP genes（AaTCPs）were identified. AaTCPs differed greatly in protein physicochemical properties，in which the number of amino acids and protein molecular mass ranged from 132 to 443 and 14.60 to 47.86 ku，respectively，and the isoelectric points，instability indices，and fat coefficients were in the ranges of 5.67 to 9.99，33.28 to 69.77，and 51.70 to 77.40，respectively，and all of them were nuclear proteins.Phylogenetic relationships showed that AaTCPs could be classified into class Ⅰ（11）and class Ⅱ（18），unevenly distributed on eight chromosomes.The Motif number of AaTCPs ranged from 1 to 7，all of them contained one conserved TCP2 structural domain，and a large number of light‑，hormone‑，and stress‑responsive elements were present in their promoters.Protein interaction predictions revealed tight interactions among the protein members of AaTCPs except for AaTCP12 and AaTCP8.Transcriptome data showed that the expression levels of AaTCPs varied under different light treatments，and the expression of most genes was induced by light. qRT‑PCR analysis revealed that the expression of AaTCPs all increased to different degrees under MeJA treatment，showing dynamic changes with the extension of treatment time.In summary，the AaTCP gene family plays a significant role in light regulation and hormone response processes. Reference | Related Articles | Metrics Select Identification of HSF Gene Family in Eucommia ulmoides and Its Expression Analysis under Adverse Stresses WU Shujuan, XU Feng, WANG Guangan, WANG Chen Journal of Henan Agricultural Sciences    2024, 53 (9): 46-56.   DOI: 10.15933/j.cnki.1004-3268.2024.09.005 Abstract （1197）      PDF （6355KB）（141）       Knowledge map    Save Heat shock transcription factors（HSFs）play important roles in plant growth and development and in response to abiotic stresses.In order to understand the information of HSF gene family members in Eucommia ulmoides and reveal the structural characteristics and expression patterns of EuHSFs,this study analyzed the physicochemical properties,protein structure,phylogeny,gene structure,conserved domains,promoter cis‑acting elements,and the expression patterns of EuHSF genes in different developmental periods and abiotic stresses by bioinformatics methods and qRT‑PCR.The results showed that a total of 21 EuHSF genes were identified from Eucommia ulmoides,which differed in protein properties,with amino acid numbers,protein theoretical molecular masses,isoelectric points and instability coefficients ranging from 68—369,7.72—42.06 ku,4.31—9.22,and 7.05—67.28,respectively,and mainly consisted of acidic,hydrophilic,and unstable nuclear proteins.Phylogeneticanalysis showed that EuHSFs were divided into three subgroups,including ClassⅠ(1 EuHSF),ClassⅡ(7 EuHSFs)and ClassⅢ(13 EuHSFs),and promoter cis‑acting element analysis revealed that a large number of light‑responsive and hormone‑responsive elements in EuHSF genes.In addition,EuHSF genes were expressed at different developmental periods in Eucommia ulmoides leaves,but there were significant differences in the expression patterns. qRT‑PCR revealed that all EuHSFs responded to different abiotic stresses(high temperature,low temperature,high salinity,and drought),e.g.,most of the EuHSFs showed elevated expression under high‑temperature stress with the prolongation of the treatment time，and they were strongly responsive to both high and low temperatures.In summary,the EuHSF gene family has the function of regulating plant response to abiotic stresses. Reference | Related Articles | Metrics Select Identification and Expression Analysis of HD‑ZIP Family in Salvia miltiorrhiza LI Wan, CHENG Ruixing, DANG Xin Journal of Henan Agricultural Sciences    2024, 53 (7): 66-78.   DOI: 10.15933/j.cnki.1004-3268.2024.07.008 Abstract （1058）      PDF （6842KB）（139）       Knowledge map    Save To screen HD‑ZIP genes（SmHD‑ZIPs）in Salvia miltiorrhiza in response to high temperature stress，SmHD‑ZIPs were identified and analyzed by bioinformatics，and the expression pattern of SmHD‑ZIPs under high temperature stress was detected by qPCR. The results showed that there were 44 HD‑ZIP genes in S.miltiorrhiza，most of which were unevenly distributed on 8 chromosomes. SmHD‑ZIPs could be divided into four subfamilies：HD‑ZIP Ⅰ，HD‑ZIP Ⅱ，HD‑ZIP Ⅲ，HD‑ZIP Ⅳ. The sequence analysis results showed that the amino acid residues of these proteins ranged from 180 to 982，and the relative molecular weight of these proteins ranged from 20. 947 ku to 109. 620 ku. SmHD‑ZIPs were hydrophilic proteins without transmembrane domain，and most of them did not contain signal peptides.The isoelectric points of SmHD‑ZIPs were between 4. 48 and 10. 91，and they were almost expressed in the nucleus with the poor protein stability. Among the 44 SmHD‑ZIP genes，there were 10 gene duplication events，all of which were purified selection. The results of structure and motif analysis showed that the exon number of members of the same subfamily was basically the same，and the members of HD‑ZIP Ⅲ subfamily had the largest exon number and the largest motif number. Motifs 1 and 6 were conserved motifs of SmHD‑ZIP，motifs 10，11，12，13 and 15 was unique to the HD‑ZIP Ⅲ subfamily，while motif 5 were unique to the HD‑ZIP IV subfamily. By analyzing the expression patterns of SmHD‑ZIPs under high temperature（37℃）stress，it was found that the number of genes with increased and decreased expression was basically the same. Among the genes with up‑regulated expression，the expression levels of SmHD‑ZIP1.11，SmHD‑ZIP1.13，SmHD‑ZIP2.2，SmHD‑ZIP2.5，SmHD‑ZIP3.1，SmHD‑ZIP3.4，SmHD‑ZIP4.9，SmHD‑ZIP4.10 and SmHD‑ZIP4.12 were increased by more than 10 times，which could be used as candidate gene resources to improve the heat resistance of S.miltiorrhiza. Reference | Related Articles | Metrics Select Analysis on Chloroplast Genome of Paederia scandens WU Minhua, WU Zijian, YE Xiaoxia, TAN Jingyi, WANG Shen, HUANG Qionglin Journal of Henan Agricultural Sciences    2024, 53 (1): 70-77.   DOI: 10.15933/j.cnki.1004-3268.2024.01.008 Abstract （1552）      PDF （6478KB）（129）       Knowledge map    Save To elucidate the structure and sequence characteristics of chloroplast genome from Paederia scandens，the chloroplast genome sequencing was performed using high‑throughput sequencing technology，and then acquired sequence was assembled，annotated and analyzed via bioinformatics procedures.The results demonstrated that the chloroplast genome of P.scandens was a circular quadripartite molecule with a length of 153 456 bp and encoded 133 genes.Altogether 54 simple sequence repeats were detected in the plastome and the A/T mononucleotide was main type.A total of 26 983 codons were searched out and those with end of A/T were frequently used.Sequence alignment demonstrated more divergence in non‑coding region among five Rubiaceae species including P.scandens.Phylogenetic tree revealed close relationship of various chloroplast genome sequences of P.scandens and clearly displayed the evolutionary position of P.scandens in Rubiaceae. 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