Genome-Wide Identification and Characterization of the LRR-RLK Gene Family in Two Vernicia Species by Huiping Zhu, Yangdong Wang, Hengfu Yin, Ming Gao, Qiyan Zhang, Yicun Chen

“…Here, we identified 236 and 230 LRR-RLKs in two industrial oil-producing trees: Vernicia fordii and Vernicia montana, respectively. Sequence alignment analyses showed that the homology of the RLK domain (23.81%) was greater than that of the LRR domain (9.51%) among the Vf/VmLRR-RLKs. …”
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Detection of Mycoplasma spp. from snakes from five different families by Marline M. Faulhaber, Florence Tardy, Franziska Saul, Elisabeth Müller, Michael Pees, Rachel E. Marschang

“…The detected bacteria can be divided into at least 6 genetically diverse clusters representing different genera and species based on multiple sequence alignment and phylogenetic analysis. Conclusions These results show that diverse mycoplasmas are found in pythons and other snakes. …”
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Analysis of expression and transport activity of sugar transporter gene HpSWEET7 from red pitaya by ZHENG Qianming, YAN Shuang, XIE Pu, WANG Honglin, MA Yuhua

“…[Methods] HpSWEET7 gene was isolated from ‘Zihonglong’, and sequence alignment and phylogenetic relationship were analyzed. …”
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Genome-Wide Identification of miRNAs in Oily Persimmon (<i>Diospyros oleifera</i> Cheng) and Their Functional Targets Associated with Proanthocyanidin Metabolism by Meng Zhang, Rong Wu, Xinlong Hu, Zhengrong Luo, Qinglin Zhang, Sichao Yang

“…In our study, we identified genome-wide microRNAs (miRNAs) and their precursor sequence based on the chromosome-scale genome of oily persimmon and the miRNA database of “Eshi 1” according to the sequence alignment and secondary structure accession. The targets were predicted on the psRNATarget software based on the genome CDS database. …”
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Complete Genome Sequence and Comparative Genome Analysis of Variovorax sp. Strains PAMC28711, PAMC26660, and PAMC28562 and Trehalose Metabolic Pathways in Antarctica Isolates by Prasansah Shrestha, Jayram Karmacharya, So-Ra Han, Jun Hyuck Lee, Hyun Park, Tae-Jin Oh

“…The trehalose metabolic pathway was analyzed via bioinformatics tools, such as the dbCAN2 Meta server, Prokka annotation, Multiple Sequence Alignment, ANI calculator, and PATRIC database, which helped to predict trehalose biosynthesis and degradation genes’ involvement in the complete genome of Variovorax strains. …”
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A survey of the Sli gene in wild and cultivated potato by Mercedes Ames, Andy Hamernik, William Behling, David S. Douches, Dennis A. Halterman, Paul C. Bethke

“…To learn more about Sli diversity and function in wild species relatives of cultivated potato, we obtained Sli gene sequences that extended from the 5′UTR to the 3′UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. …”
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Detection of Dengue Virus-Specific IgM and IgG Antibodies through Peptide Sequences of Envelope and NS1 Proteins for Serological Identification by Pradeep Kumar Nagar, Deepali Savargaonkar, Anupkumar R. Anvikar

“…Sequence homologies of peptides with other Flavivirus were checked by Multiple Sequence Alignment Tool ClustalX2. Peptide sequences were synthesized chemically by solid-phase peptide synthesis technique. …”
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Surveillance of SARS-CoV-2 variants in Henan, China from 2023 to 2024 by Yun Song, Bicong Wu, Hongxia Ma, Yafei Li, Su Yan, Jingjing Pan, Haifeng Wang, Ying Ye, Xueyong Huang, Wanshen Guo

“…Genome sequence analysis was performed with CLC Genomics Workbench, and genotyping and sequence alignment were carried out using the Nextclade platform. …”
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Prevalence and Molecular Characterization of Cysticercus tenuicollis Isolated from Some Intermediate Host in Kurdistan-Iraq by Abdullah Ahmed Hama, Rostam Hama Zorab, Fatima Mohammed Ali, Awaz M. Salih, Amer Abdullah Hassan

“…The nucleotide sequence alignment of cytochrome oxidase subunit 1 (CO 1) gene revealed that the amplified DNA fragment is belong to Taenia hydatigena and Echinococcus granulosus and the nucleotide sequences of T. hydatigena deposited in GenBank under accession number (MH638348). …”
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The Chloroplastic Small Heat Shock Protein Gene KvHSP26 Is Induced by Various Abiotic Stresses in Kosteletzkya virginica by Xiaohua Liu, Lizi Zhao, Jianzhao Li, Lijun Duan, Kai Zhang, Xuqiang Qiao, Weihuan Li, Chengchao Zheng, Xiaoli Tang, Hongxia Zhang

“…Bioinformatics analyses revealed that KvHSP26 encoded a chloroplastic protein with the typical features of sHSPs. Amino acid sequence alignment and phylogenetic analysis demonstrated that KvHSP26 shared 30%-77% homology with other sHSPs from Arabidopsis, cotton, durian, salvia, and soybean. …”
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The Association between Deoxyribonucleic Acid Hypermethylation in Intron VII and Human Leukocyte Antigen-C∗07 Expression in Patients with Endometriosis by Wenrong Zhao, Lei Lei, Rui Chen, Yanmin Zhang, Linlin Chang, Jingxin Cheng

“…The test screened methylation-differentiated 5′–C–phosphate–G–3′ (CpG) sites and then located the target genes affected by these sites following sequence alignment. Then, an additional 22 patients and 26 healthy controls were enrolled to further verify the difference in the selected genes between endometriosis patients and healthy women. …”
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Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.) by Huijie Zhai, Kunpeng Xu, Meng Wang, Zhenchuang Wang, Ziyang Cai, Ao Li, Anxin He, Xiaoming Xie, Lingling Chai, Mingjiu Liu, Xingqi Ou, Zhongfu Ni

“…These primer pairs are believed to be unique and polymorphic in the wheat genome; as gathered from the evidence, (i) 76.18 to 99.34% of the 11,016 primer pairs yielded a single hit during sequence alignment with 18 sequenced genomes, (ii) 83.59 to 90.98% of 1042 synthesized primer pairs amplified a single band in 16 wheat accessions, and (iii) 59.69 to 99.81% of the tested 1042 primer pairs were polymorphic between E6015-3S and 15 individual wheat accessions. …”
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High Antennal Expression of <i>CYP6K1</i> and <i>CYP4V2</i> Participate in the Recognition of Alarm Pheromones by <i>Solenopsis invicta</i> Buren by Xinyi Jiang, Jiacheng Shen, Peng Lin, Youming Hou

“…To understand whether the highly expressed CYPs in the antennae play an olfactory function in <i>Solenopsis invicta</i> worker, in this study, we find six highly expressed antennal CYPs from the transcriptome of <i>S. invicta</i>. Multiple sequence alignment and phylogenetic analysis divided them into two families: the CYP3 family (<i>SinvCYP6K1</i>, <i>SinvCYP6K1-1</i>) and the CYP4 family (<i>SinvCYP4C1</i>, <i>SinvCYP4C1-1</i>, <i>SinvCYP4C1-2</i>, <i>SinvCYP4V2</i>). …”
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Development of a 50K SNP array for whole-genome analysis and its application in the genetic localization of eggplant (Solanum melongena L.) fruit shape by Chuying Yu, Qihong Yang, Weiliu Li, Yaqin Jiang, Guiyun Gan, Liangyu Cai, Xinchun Li, Zhiqiang Li, Wenjia Li, Min Zou, Yang Yang, Yikui Wang

“…The BSA-seq data were located in the 78444173−84449348 interval on chromosome 3, with a size of 6 Mb, which was narrowed to 712.6 kb through fine mapping. Further sequence alignment and expression analysis revealed SmIQD14 as a candidate gene controlling eggplant fruit shape. …”
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Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching ho... by Pengyu Zhang, Jingchen Hao, Yafen Zhang, Junfeng Su, Guozhuang Sun, Jun Xie, Jian Hu, Guocai Li

“…Acquired antimicrobial resistance genes and virulence factors carried in the isolated group genome were analyzed by ResFinder, PubMLST and VFDB. Sequence alignment was used to analyze genetic environment around bla OXA−23. …”
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Diversity in mitotic DNA repair efficiencies between commercial inbred maize lines and native Central American purple landraces by Carlos Víquez-Zamora, Sergio Castro-Pacheco, María Viñas, Pablo Bolaños-Villegas

“…The kinase gene ZeaATM1 was amplified and sequenced in B73, Mo17, P1 and P2. Multiple sequence alignment of DNA and aminoacid sequences was performed using ClustalW. …”
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Detection of 5 Kinds of Genes Related to Plasmid-Mediated Quinolone Resistance in Four Species of Nonfermenting Bacteria with 2 Drug Resistant Phenotypes by De-Song Ming, Qing-Qing Chen, Xiao-Ting Chen

“…The amplified products were analyzed by 1% agarose gel electrophoresis and sequenced. Sequence alignment was carried out using the bioinformatics technique. …”
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Transcriptome Analysis of <i>Stephania yunnanensis</i> and Functional Validation of CYP80s Involved in Benzylisoquinoline Alkaloid Biosynthesis by Wenlong Shi, Qishuang Li, Xinyi Li, Linglong Luo, Jingyi Gan, Ying Ma, Jian Wang, Tong Chen, Yifeng Zhang, Ping Su, Xiaohui Ma, Juan Guo, Luqi Huang

“…We then identified candidate genes through functional annotation and sequence alignment and further analyzed them in combination with the genome. …”
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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? by Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Hiran A. Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Laszlo Irinyi, Rajesh Jeewon, Peter R. Johnston, Paul M. Kirk, Elaine Malosso, Tom W. May, Wieland Meyer, Maarja Öpik, Vincent Robert, Marc Stadler, Marco Thines, Duong Vu, Andrey M. Yurkov, Ning Zhang, Conrad L. Schoch

“…Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. …”
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Identification and expression analysis of the heat shock proteins Hsp70, Hsp90, and Hsp90b in Litopenaeus vannamei under low-temperature stress by Min Peng, Hui Wang, Shuiping Wen, Zheng Liang, Zheng Huang, Bin Zhang, Tianchong Chen, Qingyun Liu, Qiangyong Li, Yuan Meng, Yuliu Huang, Chunling Yang, Digang Zeng, Manyuan Li, Weilin Zhu, Yongzhen Zhao

“…Additionally, the survival rate of L. vannamei significantly decreased following hsp90 knockdown. DNA sequence alignment identified 12 single nucleotide polymorphisms (SNPs) in the hsp70 gene and 17 SNPs in the hsp90 gene. …”
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