Article
Plant Sciences
Yilin Liu, Fuquan Ce, Huan Tang, Guifu Tian, Lei Yang, Wei Qian, Hongli Dong
Summary: In this study, a total of 117 putative SCPL genes were identified in Brassica napus, and their distribution, evolution and functions were investigated. The results showed that the SCPL gene family was amplified during polyploidization, and the genes in the same group displayed high conservation. Furthermore, the study suggested the important role of the BnSCPL52 gene in seed yield and silique length in rapeseed.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Plant Sciences
Zhi-Qi Wang, Tai-Fei Yu, Guo-Zhong Sun, Jia-Cheng Zheng, Jun Chen, Yong-Bin Zhou, Ming Chen, You-Zhi Ma, Wen-Liang Wei, Zhao-Shi Xu
Summary: The study identified 38 CrRLK1L genes in soybean genome and found that GmCrRLK1L20 plays a vital role in defending against drought and salinity stresses. The gene structure, phylogenetic analysis, and subcellular localization provided insights into the potential mechanisms of these genes in soybean growth and development.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Shaofei Rao, Xinyang Wu, Hongying Zheng, Yuwen Lu, Jiejun Peng, Guanwei Wu, Jianping Chen, Fei Yan
Summary: This study identified 31 CrRLK1L members in the Nicotiana benthamiana genome, divided into 6 phylogenetic groups with similar structures and motifs. The NbCrRLK1Ls were predicted to be regulated by cis-acting elements and by transcription factors. Expression profiles showed diverse patterns across tissues, and responses to pathogens indicated potential involvement in plant immunity.
Article
Biochemistry & Molecular Biology
Lei Gu, Yongyan Cao, Xuanxuan Chen, Hongcheng Wang, Bin Zhu, Xuye Du, Yiyue Sun
Summary: This study systematically identified and analyzed the SSL genes in maize, revealing their important roles in maize growth, development, and response to stresses. The evolutionary relationships and potential functions of these genes were also investigated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Chen Qiu, Jinhui Chen, Weihuang Wu, Bojun Liao, Xueyan Zheng, Yong Li, Jing Huang, Jisen Shi, Zhaodong Hao
Summary: The COBRA gene in the rare and endangered woody plant Liriodendron chinense was found to encode a plant-specific glycosylphosphatidylinositol (GPI)-anchored protein (GAP) that plays a crucial role in cellulose deposition in the cell wall. The study identified 7 COBRA-like (COBL) genes in the plant's genome, which were divided into two subfamilies, SF I and SF II. The expression patterns of these genes showed tissue-specific expression, with LcCOBL5 highly expressed in the phloem and xylem, indicating its potential role in cellulose biosynthesis. Furthermore, three LcCOBL genes (LcCOBL3, LcCOBL4, and LcCOBL5) were found to respond to abiotic stresses such as cold, drought, and heat stress, suggesting their involvement in stress responses.
Article
Virology
Fuqing Wu, Jeremiah Oghuan, Anna Gitter, Kristina D. Mena, Eric L. Brown
Summary: Rapid and accurate diagnosis of infections is crucial for disease control. We analyzed the specificity of the primers and probes in the CDC recommended MPV real-time diagnostic assay and found significant sequence mismatches. Mismatch-corrected primers showed improved detection sensitivity of MPV. Our study also identified two real-time PCR assays with high specificity for MPV detection.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Yunfen Liu, Feilong Yin, Lingyan Liao, Liang Shuai
Summary: In this study, the CsCML gene family in cucumber was identified and characterized using bioinformatic analysis. Forty-four CsCML gene members were identified and analyzed for gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny. Spatiotemporal expression analysis revealed distinct expression patterns for CsCML genes in different tissues and environmental conditions, and cis-acting element analysis showed the presence of hormone, stress, and plant growth and development-related elements in the promoter regions. These findings provide a foundation for further investigation of the physiological functions of CsCMLs.
Article
Biochemistry & Molecular Biology
Konstantin Zaytsev, Alexey Fedorov, Eugene Korotkov
Summary: We have developed a new method for classifying promoter sequences using a genetic algorithm and the MAHDS sequence alignment method. Four classes of human promoters were created, using 17,310 sequences from the EPD database. A search for potential promoter sequences (PPSs) in the human genome was conducted, resulting in 3,065,317 PPSs, with only 1,241,206 located in unannotated regions. Intersections were found between PPSs and true promoters, transposable elements, and interspersed repeats.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek
Summary: TRTools is a Python library and suite of command line tools developed for filtering, merging and quality control of TR genotype files, utilizing an internal harmonization module to make it compatible with outputs from a wide range of TR genotypers.
Article
Biochemistry & Molecular Biology
Yuan Zhang, Xiaoyan Wang, Fei Han, Tianxiang Gao
Summary: This study used bioinformatics methods to identify and analyze the Toll-like receptor (TLR) gene family members in the marbled rockfish (Sebastiscus marmoratus). It found that there are 11 TLR gene family members in Sebastiscus marmoratus, which can be divided into five different subfamilies. The study also revealed the expression patterns and upregulation of certain TLRs in different tissues after a poly(I:C) challenge. The results provide insights into the structure, function, and expression of TLRs in marbled rockfish.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Gunjan Baid, Daniel E. Cook, Kishwar Shafin, Taedong Yun, Felipe Llinares-Lopez, Quentin Berthet, Anastasiya Belyaeva, Armin Topfer, Aaron M. Wenger, William J. Rowell, Howard Yang, Alexey Kolesnikov, Waleed Ammar, Jean-Philippe Vert, Ashish Vaswani, Cory Y. McLean, Maria Nattestad, Pi-Chuan Chang, Andrew Carroll
Summary: DeepConsensus improves the accuracy and quality of PacBio HiFi reads by significantly reducing read errors through sequence correction.
NATURE BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Jing Zhang, Tianzhen Cui, Yachun Su, Shoujian Zang, Zhennan Zhao, Chang Zhang, Wenhui Zou, Yanling Chen, Yue Cao, Yao Chen, Youxiong Que, Niandong Chen, Jun Luo
Summary: The GLR gene plays a crucial role in the development, signaling pathways, and response to environmental stress in sugarcane. The study identified and characterized 43 GLR genes in sugarcane, which could be divided into three clades. The findings suggest that the sugarcane GLRs may be involved in growth and development, hormone synthesis, and response to biotic and abiotic stresses.
Article
Plant Sciences
Gen Pan, Zheng Li, Ming Yin, Siqi Huang, Jie Tao, Anguo Chen, Jianjun Li, Huijuan Tang, Li Chang, Yong Deng, Defang Li, Lining Zhao
Summary: This study identified 13 CsCOL genes in the cannabis genome, which were divided into three subgroups with conserved structures. Chromosome distribution analysis revealed uneven distribution of CsCOL genes on 7 chromosomes. Tissue-specific expression analysis showed most CsCOL genes were preferentially expressed in leaves.
Article
Multidisciplinary Sciences
Brianna Chrisman, Chloe He, Jae-Yoon Jung, Nate Stockham, Kelley Paskov, Peter Washington, Dennis P. Wall
Summary: The unmapped readspace of whole genome sequencing data is often overlooked but contains valuable signals of human infection and contamination. By analyzing unmapped and poorly aligned reads from over 1000 families and nearly 5000 individuals, this study reveals insights into common viral, bacterial, and computational contamination in whole genome sequencing studies. It also highlights the need for standard protocols to identify and remove contamination in order to ensure the accuracy of sequencing-based research results.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Xiaomin Xu, Lili Zhang, Wan Zhao, Liang Fu, Yuxuan Han, Keke Wang, Luyu Yan, Ye Li, Xiao-Hong Zhang, Dong-Hong Min
Summary: In this study, a total of 210 candidate genes encoding SCPL proteins were identified in wheat, which were classified into three subfamilies based on structural characteristics. Among these genes, 209 were unevenly distributed across 21 wheat chromosomes, with a significant proportion derived from duplication events. The analysis revealed the potential roles of TaSCPL genes in abiotic stress response, providing valuable resources for enhancing the resistance of wheat to adverse environments.