Huaqin Xu

University of California, Davis, Davis, California, United States

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Publications (12)14.53 Total impact

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    ABSTRACT: The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.
    RNA 10/2014; 20(12). DOI:10.1261/rna.046532.114 · 4.62 Impact Factor
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    ABSTRACT: We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3,696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines (RILs) that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultra-dense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.
    G3-Genes Genomes Genetics 03/2013; DOI:10.1534/g3.112.004929 · 2.51 Impact Factor
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    ABSTRACT: Bacterial plant pathogens manipulate their hosts by injection of numerous effector proteins into host cells via type III secretion systems. Recognition of these effectors by the host plant leads to the induction of a defense reaction that often culminates in a hypersensitive response manifested as cell death. Genes encoding effector proteins can be exchanged between different strains of bacteria via horizontal transfer, and often individual strains are capable of infecting multiple hosts. Host plant species express diverse repertoires of resistance proteins that mediate direct or indirect recognition of bacterial effectors. As a result, plants and their bacterial pathogens should be considered as two extensive coevolving groups rather than as individual host species coevolving with single pathovars. To dissect the complexity of this coevolution, we cloned 171 effector-encoding genes from several pathovars of Pseudomonas and Ralstonia. We used Agrobacterium tumefaciens-mediated transient assays to test the ability of each effector to induce a necrotic phenotype on 59 plant genotypes belonging to four plant families, including numerous diverse accessions of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum). Known defense-inducing effectors (avirulence factors) and their homologs commonly induced extensive necrosis in many different plant species. Nonhost species reacted to multiple effector proteins from an individual pathovar more frequently and more intensely than host species. Both homologous and sequence-unrelated effectors could elicit necrosis in a similar spectrum of plants, suggesting common effector targets or targeting of the same pathways in the plant cell.
    Plant physiology 08/2009; 150(4):1733-49. DOI:10.1104/pp.109.140251 · 7.39 Impact Factor
  • Huaqin Xu, Ying Jin
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    ABSTRACT: Biological database management is complicated due to the complex structure and semantics of biological data. Constraint management is important to ensure the accuracy of the data. Existing relational databases may not fully support constraint enforcement, although they may be easy to operate by biologists. We propose an active rule-based approach to enforce constraints on an existing database without changing the original system structure or the underlying database. This paper presents the framework of our BioRule project to support constraint management using our XML-based active rule language, named BioRL. The syntax of BioRL is based on the XQuery standard, while biological semantics are represented declaratively in rules by using XQuery expressions and functions. When events such as data updates occur in a database, rules can be triggered to check user-defined constraints automatically. This paper describes the rule language, the architectural components, and the rule execution environment of the BioRule system. Rule examples and an application scenario are also provided in the paper to illustrate the use of active rules for constraint management.
    01/2008; 3(1).
  • Huaqin Xu, Ying Jin
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    ABSTRACT: High throughput biological experiments produce a large amount of biological data that can be updated by time. Inconsistent data stored in the same or different databases may lead to serious biological research problems. Constraint management is important to ensure biological data integrity. Some existing databases were built for the easy use for biologists; however the database management system (DBMS) may not have a sufficient constraint management system. In this paper, we propose an XML-based active rule language, named BioRL, to enforce constraints on existing databases without changing the original system structures or the underlying databases. In BioRL language, biological semantics are represented declaratively in active rules by using XQuery expressions and functions. This paper presents the syntax of the BioRL language, with examples that illustrate the use of BioRL in an application environment. This paper also presents the BioRule system to support the specification and execution of BioRL, focusing on the architectural components of the BioRL parser and the BioRL repository.
    Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics, BMEI 2008, May 28-30, 2008, Sanya, Hainan, China - Volume 1; 01/2008
  • D. Jones, Ying Jin, Huaqin Xu
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    ABSTRACT: XML is becoming one of the most common means to exchange data throughout the internet. Biological research is advancing at very high rates as a result of the large amounts of information that can be passed to researchers throughout the world, thereby increasing collaboration and reducing redundancy. There are limitations to the use of this data if there is no ability to verify it. This paper presents our BioRule system that uses active rules to verify the integrity of XML data. This system consists of a language named BioRL and an execution environment that supports event detection and rule processing. The paper discusses the language, architecture, and implementation to enforce constraints over XML documents being manipulated within a native XML database.
    Bioinformatics and Biomedicine, 2007. BIBM 2007. IEEE International Conference on; 12/2007
  • Ying Jin, M.L. Tescher, Huaqin Xu
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    ABSTRACT: Constraints are important to ensure consistency and validity of biological data to computerize biological findings. Incorrect data could lead to serious scientific problems when conducting further biology research and experiments. We propose an XML-based active rule system named BioRule to enforce constraints on top of existing data sources. The BioRule system serves as a middleware to filter inconsistent data before populating or updating data sources. Biological semantics are specified in active rules, while the validation can be enforced by the BioRule system automatically according to the defined rules. To facilitate and simplify the specification of active rules, we developed a web-based user-friendly tool to guide end-users. Rule examples, over an existing biology application, are also provided in this paper to illustrate the specification of active rules though web-based interfaces for constraint validation.
    Information Reuse and Integration, 2007. IRI 2007. IEEE International Conference on; 09/2007
  • Denise Jones, Ying Jin, Huaqin Xu
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    ABSTRACT: XML is becoming one of the most common means to exchange data throughout the internet. Biological research is advancing at very high rates as a result of the large amounts of information that can be passed to researchers throughout the world, thereby increasing collaboration and reducing redundancy. There are limitations to the use of this data if there is no ability to verify it. This paper presents our BioRule system that uses active rules to verify the integrity of XML data. This system consists of a language named BioRL and an execution environment that supports event detection and rule processing. The paper discusses the language, architecture, and implementation to enforce constraints over XML documents being manipulated within a native XML database.
    Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007, Silicon Valley, CA, USA, November 2-4, 2007; 01/2007
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    ABSTRACT: Next Generation Sequencing (NGS)-based assemblies of moderately large genomes [1-3 Gb] often consist of thousands of scaffolds. The combination of NGS and segregation analysis allows the generation of saturated, ultra-high density genetic maps, which can be employed to improve the contiguity of genome assemblies. The genome of the cultivated lettuce, Lactuca sativa, cv. Salinas has been sequenced in collaboration with the BGI supported by a consortium of ten breeding companies. The SOAPdenovo assembly of the L. sativa genome (2.7 Gb) consisted of 21,500 scaffolds covering 2.38 Gb [http://lgr.genomecenter.ucdavis.edu/]. We also sequenced L. serriola, a close relative of L. sativa and its likely progenitor. In addition, 99 Recombinant Inbred Lines (RILs) from a cross between L. sativa x L. serriola genotypes was sequenced at 1x coverage. We then used Genotyping by Shotgun Sequencing (GBSS) to generate a comprehensive map of the Lactuca genome. Comparison of the sequences from L. sativa, L. serriola and the RILs using CLC Genomics Workbench revealed more than 11 million reliable high-quality SNPs. Custom scripts were used to assign haplotypes to scaffolds and to identify chimeric misassemblies. The latter were corrected by breakage at the junction point. GBSS and segregation analysis of the RILs allowed the chromosomal assignment of more than ten thousand scaffolds and their ordering into genetic bins, covering 2.3 Gb of the lettuce genome. The resulting comprehensive chromosome assemblies are facilitating the identification and functional analysis of candidate genes for a broad spectrum of domestication and agriculturally-important phenotypes.
    International Plant and Animal Genome Conference XXII 2014;
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    ABSTRACT: The genome of cultivated lettuce (L. sativa) has been sequenced in collaboration with BGI and a consortium of ten breeding companies. The assembly currently consists of 21,500 scaffolds for a total of 2.38 Gb representing 88% of the 2.7 Gb lettuce genome. Lettuce’s wild relative L. serriola has also been sequenced. The L. serriola assembly currently contains 45,020 scaffolds combined into 1.99 Gb (74% of lettuce genome). Comparison between L. sativa and L. serriola assemblies has identified conserved and highly divergent genomic regions between the two genomes. More than 11 million high quality SNPs have also been identified. Using these SNPs a genetic map was constructed on a RIL population between L. sativa and L. serriola. Segregation of scaffold haplotypes on the RIL families has been used to validate the assembly and to identify chimeric scaffolds as well as locate over 90% of the assembled genome into chromosomal linkage groups. Genome annotation of the assembled genome using three prediction pipelines postulated a set of 94,556 non-redundant gene models. From those, 41,000 high confidence gene models were identified using an overlapping weighted evidence gene model scoring method (OWEG score) that combines transcriptomic and prediction evidence. This set represents 94% of all NCBI ESTs from lettuce aligned to the genome. The genome is now being characterized for genes of agricultural importance.
    International Plant and Animal Genome Conference XXII 2014;

Publication Stats

43 Citations
14.53 Total Impact Points

Institutions

  • 2007–2014
    • University of California, Davis
      • • Department of Plant Sciences
      • • Seed Biotechnology Center
      Davis, California, United States
    • California State University, Sacramento
      Sacramento, California, United States