Yingqin Luo

South China Agricultural University

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i-10 index

Research Trends

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Roy Curtiss

University of Florida

Jinyan Huang

Zhejiang University

Greg Golden

Arizona State University

Suhong Bu

South China Agricultural University

Yijun Wang

Yangzhou University

Jiseon Yang

Arizona State University

Xiaoya Liang

South China Agricultural University

Hongyuan Zhao

Henan Institute of Science and Technology

Yuan‐Ming Zhang

Huazhong Agricultural University

Weifeng Yang

South China Agricultural University

Cooperative Institutions

South China Agricultural University

Key Laboratory of Guangdong Province

Arizona State University

State Key Laboratory For Conservation and Utilization of Subtropical Agro-Bioresources

Zhejiang University

Tongji University

Southwest University

University of California, San Diego

East China University of Science and Technology

Nanjing Agricultural University

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GS6.1 controls kernel size and plant architecture in rice

Planta (2023)

Hongyuan Zhao Yu Fu Yuan‐Ming Zhang Yingqin Luo Weifeng Yang

Panicle

Kernel (algebra)

Rice plant

10.1007/s00425-023-04201-4

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Citations (1)

GS6.1 controls kernel size and plant architecture in rice

Research Square (Research Square) (2023)

Hongyuan Zhao Yu Fu Yuan‐Ming Zhang Yingqin Luo Weifeng Yang

Abstract Kernel size and plant architecture are critical agronomic traits that greatly influence kernel yield in rice. We identified a novel quantitative trait locus (QTL), named GS6.1 , which regulates kernel size and plant architecture in rice. Near isogenic line- GS6.1 (NIL- GS6.1 ) produces long and narrow kernels by regulating cell length and width in the hull, thus increasing the 1000-kernel weight. Compared with the control, the plant height, panicles per plant, panicle length, kernels per plant, and secondary branches per panicle of NIL- GS6.1 are increased. In addition, GS6.1 regulates the kernel filling rate. GS6.1 controls kernel size at least in part through regulating the transcription levels of EXPA13 , EXPA19 , EXPB14 , GS2 , GS3 , GL3 , GL6 , OML4 , GL7 , and GL10 . These results indicate that GS6.1 might be beneficial for improving kernel yield and plant architecture in rice breeding by molecular design.

Panicle

Kernel (algebra)

10.21203/rs.3.rs-2616757/v1

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Citations (0)

BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes

BMC Bioinformatics (2007)

Yingqin Luo Cong Fu Da‐Yong Zhang Kui Lin

Abstract Background Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest. Description BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ) and Unweighted Pair-Group Method using Arithmetic averages (UPGMA). Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint. Conclusion BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by annotations make BPhyOG a powerful web server for genomic and genetic studies. It is freely available at http://cmb.bnu.edu.cn/BPhyOG .

Bacterial genome size

Tree (set theory)

Comparative Genomics

10.1186/1471-2105-8-266

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Citations (20)

Exploring Effects of Network Spatial Characteristics on Macroscopic Fundamental Diagram

Procedia - Social and Behavioral Sciences (2013)

Dabin Liao Wanjing Ma Yingqin Luo Zongqi Shi

Macroscopic Fundamental Diagram (MFD) builds a relationship between the outflow and accumulation of the network in variant of demands and appears frequently in urban transportation networks under certain conditions. However, MFD is not expected if the network is heterogeneous. This paper studies the impact of network spatial characteristics on the existence and characteristics of a MFD based on simulation. Firstly, the paper analysis the network spatial influence factors, including the size and the critical link of the neighborhood that may influence the existence of a MFD and its shape respectively. Then, how this factors influences the property of MFD is explored.

10.1016/j.sbspro.2013.08.175

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Citations (2)

Complete Genome Sequence of the Universal Killer Salmonella enterica Serovar Typhimurium UK-1 (ATCC 68169)

Journal of Bacteriology (2011)

Yingqin Luo Qingke Kong Jiseon Yang Greg Golden Soo-Young Wanda

The Salmonella enterica serovar Typhimurium strain UK-1 exhibits the highest invasion and virulence attributes among the most frequently studied strains. S. Typhimurium UK-1 has been used as the foundation for developing recombinant vaccines and has been used extensively on virulence and colonization studies in chickens and mice. We describe here the complete genome sequence of S. Typhimurium UK-1. Comparative genomics of Salmonella Typhimurium will provide insight into factors that determine virulence and invasion.

Salmonella enterica

Strain (injury)

Comparative Genomics

10.1128/jb.05224-11

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Citations (37)

The Molecular Ecology Analysis of Microbial Communities in Waste Water–based Mud

Petroleum Science and Technology (2013)

Zaisan Yang Yanbo Zhou Xunchao Xiang Zeping Zhu Ling Pen

The molecular ecology analysis of microorganisms is important for the development of biological treatment of waste water–based mud. The bacterial 16S rRNA gene clone library was constructed to detect the community diversity in waste drilling fluid in this study. The phylogenetic analysis indicated that most of clones were clustered in β, γ-proteobacteria with the phylotypes belonging to γ-proteobacteria accounting for 78.6% of the clone library. Halomonas sp. and Chromohalobacter sp. as moderately halophilic bacteria were the main bacteria in waste water–based mud, accounting for 47.8% of the total of clones. This study provides the certainty of chance of the improvement of biological treatment by the selection of dominant strain.

Halomonas

Phylotype

Library

Microcosm

10.1080/10916466.2011.608401

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Citations (3)

Detection and differentiation of wild-type and vaccine strains of canine distemper virus by a duplex reverse transcription polymerase chain reaction.

PubMed (2015)

Xiaolin Dong Wen‐Hsiung Li Jun Zhu W. J. Liu Mingqiu Zhao

Canine distemper virus (CDV) is the cause of canine distemper (CD) which is a severe and highly contagious disease in dogs. In the present study, a duplex reverse transcription polymerase chain reaction (RT-PCR) method was developed for the detection and differentiation of wild-type and vaccine strains of CDV. Four primers were designed to detect and discriminate the two viruses by generating 638- and 781-bp cDNA products, respectively. Furthermore, the duplex RT-PCR method was used to detect 67 field samples suspected of CD from Guangdong province in China. Results showed that, 33 samples were to be wild-type-like. The duplex RT-PCR method exhibited high specificity and sensitivity which could be used to effectively detect and differentiate wild-type and vaccine CDV, indicating its use for clinical detection and epidemiological surveillance.

Canine distemper

Duplex (building)

Source

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Citations (4)

Export of Extracellular Polysaccharides Modulates Adherence of the Cyanobacterium Synechocystis

PLoS ONE (2013)

Michael L. Fisher Rebecca Allen Yingqin Luo Roy Curtiss

The field of cyanobacterial biofuel production is advancing rapidly, yet we know little of the basic biology of these organisms outside of their photosynthetic pathways. We aimed to gain a greater understanding of how the cyanobacterium Synechocystis PCC 6803 (Synechocystis, hereafter) modulates its cell surface. Such understanding will allow for the creation of mutants that autoflocculate in a regulated way, thus avoiding energy intensive centrifugation in the creation of biofuels. We constructed mutant strains lacking genes predicted to function in carbohydrate transport or synthesis. Strains with gene deletions of slr0977 (predicted to encode a permease component of an ABC transporter), slr0982 (predicted to encode an ATP binding component of an ABC transporter) and slr1610 (predicted to encode a methyltransferase) demonstrated flocculent phenotypes and increased adherence to glass. Upon bioinformatic inspection, the gene products of slr0977, slr0982, and slr1610 appear to function in O-antigen (OAg) transport and synthesis. However, the analysis provided here demonstrated no differences between OAg purified from wild-type and mutants. However, exopolysaccharides (EPS) purified from mutants were altered in composition when compared to wild-type. Our data suggest that there are multiple means to modulate the cell surface of Synechocystis by disrupting different combinations of ABC transporters and/or glycosyl transferases. Further understanding of these mechanisms may allow for the development of industrially and ecologically useful strains of cyanobacteria. Additionally, these data imply that many cyanobacterial gene products may possess as-yet undiscovered functions, and are meritorious of further study.

Synechocystis

ENCODE

10.1371/journal.pone.0074514

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Citations (75)

Comparative Genome Analysis of the High Pathogenicity Salmonella Typhimurium Strain UK-1

PLoS ONE (2012)

Yingqin Luo Qingke Kong Jiseon Yang Arindam Mitra Greg Golden

Salmonella enterica serovar Typhimurium, a gram-negative facultative rod-shaped bacterium causing salmonellosis and foodborne disease, is one of the most common isolated Salmonella serovars in both developed and developing nations. Several S. Typhimurium genomes have been completed and many more genome-sequencing projects are underway. Comparative genome analysis of the multiple strains leads to a better understanding of the evolution of S. Typhimurium and its pathogenesis. S. Typhimurium strain UK-1 (belongs to phage type 1) is highly virulent when orally administered to mice and chickens and efficiently colonizes lymphoid tissues of these species. These characteristics make this strain a good choice for use in vaccine development. In fact, UK-1 has been used as the parent strain for a number of nonrecombinant and recombinant vaccine strains, including several commercial vaccines for poultry. In this study, we conducted a thorough comparative genome analysis of the UK-1 strain with other S. Typhimurium strains and examined the phenotypic impact of several genomic differences. Whole genomic comparison highlights an extremely close relationship between the UK-1 strain and other S. Typhimurium strains; however, many interesting genetic and genomic variations specific to UK-1 were explored. In particular, the deletion of a UK-1-specific gene that is highly similar to the gene encoding the T3SS effector protein NleC exhibited a significant decrease in oral virulence in BALB/c mice. The complete genetic complements in UK-1, especially those elements that contribute to virulence or aid in determining the diversity within bacterial species, provide key information in evaluating the functional characterization of important genetic determinants and for development of vaccines.

Salmonella enterica

Pathogenicity island

Genomic island

Comparative Genomics

Strain (injury)

10.1371/journal.pone.0040645

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Citations (30)

Evolutionary Dynamics of Overlapped Genes in Salmonella

PLoS ONE (2013)

Yingqin Luo Fabia U. Battistuzzi Kui Lin

Presence of overlapping genes (OGs) is a common phenomenon in bacterial genomes. Most frequently, overlapping genes share coding regions with as few as one nucleotide to as many as thousands of nucleotides. Overlapping genes are often co-regulated, transcriptionally and translationally. Overlapping genes are also subject to the whims of evolution, as the gene overlap is known to be disrupted in some species/strains and participating genes are sometimes lost in independent lineages. Therefore, a better understanding of evolutionary patterns and rates of the disruption of overlapping genes is an important component of genome structure and evolution of gene function. In this study, we investigate the fate of ancestrally overlapping genes in complete genomes from 15 contemporary strains of Salmonella species. We find that the fates of overlapping genes inside and outside operons are distinctly different. A larger fraction of overlapping genes inside operons conserves their overlap as compared to gene pairs outside of the operons (average 0.89 vs. 0.83 per genome). However, when overlapping genes in the operons separate, one partner is lost more frequently than in those separated genes outside of operons (average 0.02 vs. 0.01 per genome). We also investigate the fate of a pan set of overlapping genes at the present and ancestral nodes over a phylogenetic tree based on genome sequence data, respectively. We propose that co-regulation plays important roles on the fates of genes. Furthermore, a vast majority of disruptions occurred prior to the common ancestor of all 15 Salmonella strains, which enables us to obtain an estimate of disruptions between Salmonella and E. coli.

Bacterial genome size

10.1371/journal.pone.0081016

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Citations (2)