Gerard Lazo - Academia.edu (original) (raw)

Papers by Gerard Lazo

F1000Research, Apr 12, 2017

PLOS ONE, May 12, 2014

Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of... more Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings.

The Royal Society of Chemistry eBooks, May 19, 2004

Journal of Agricultural and Food Chemistry, Mar 4, 2013

Starch granule surface-associated proteins were separated by HPLC and identified by direct protei... more Starch granule surface-associated proteins were separated by HPLC and identified by direct protein sequencing. Among the proteins identified was one that consisted of two polypeptide chains of 11 and 19 kDa linked by disulfide bonds. Sequencing of tryptic peptides from each of the polypeptides revealed similarities between some of the peptides and avenin-like b proteins encoded by partial cDNAs in NCBI. To identify a contiguous sequence that matched all of the peptides, contigs encoding three avenin-like b proteins were constructed from ESTs of the cultivar Butte 86. All peptide sequences were found in a protein encoded by one of these contigs that had not been identified previously. Protein and DNA sequences indicated that the two polypeptide chains were derived from a parent protein that had been cleaved at the C-terminal position of an asparagine residue. The name farinin is suggested for this protein and other avenin-like b proteins. Evolutionary relationships of the protein are discussed and a simple computer molecular model was constructed. On the basis of its sequence, the new protein was likely to be allergenic but unlikely to be active in celiac disease.

International journal of systematic bacteriology, Jul 1, 1987

Cloned deoxyribonucleic acid (DNA) fragments, derived from a cosmid library of a Florida isolate ... more Cloned deoxyribonucleic acid (DNA) fragments, derived from a cosmid library of a Florida isolate of Xanthomonas campestris pv. citri 3041 were used to detect restriction fragment-length polymorphism among 93 strains of X. campestris, which make up 26 pathovars. DNA clones were radiolabeled and hybridized against

Proceedings of the National Academy of Sciences of the United States of America, Sep 1, 1986

Gene-for-gene interactions of five cloned avirulence genes from Xanthomonas campestris pv. malvac... more Gene-for-gene interactions of five cloned avirulence genes from Xanthomonas campestris pv. malvacearum with specific resistance genes in cotton

Database, 2022

As one of the US Department of Agriculture-Agricultural Research Service flagship databases, Grai... more As one of the US Department of Agriculture-Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves the data and community needs of globally distributed small grains researchers for the genetic improvement of the Triticeae family and Avena species that include wheat, barley, rye and oat. GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the findable, accessible, interoperable and reusable principles, enhancing and maintaining an intuitive web interface, creating tools to enable easy data access and establishing data connections within and between GrainGenes and other biological databases to facilitate knowledge discovery. GrainGenes operates within the biological database community, collaborates with curators and genome sequencing groups and contributes to the AgBioData Consortium and the International Wheat Initiative through the Wheat Information System (WheatIS). Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue (WGC). There are >4.8 million gene models in 51 genome browser assemblies, 6273 quantitative trait loci and >1.4 million genetic loci on 4756 genetic and physical maps contained within 443 mapping sets, complete with standardized metadata. Most notably, 50 new genome browsers that include outputs from the Wheat and Barley PanGenome projects have been created. We provide an example of an expression quantitative trait loci track on the International Wheat Genome Sequencing Consortium Chinese Spring wheat browser to demonstrate how genome browser tracks can be adapted for different data types. To help users benefit more from its data, GrainGenes created four tutorials available on YouTube. GrainGenes is executing its vision of service by continuously responding to the needs of the global small grains community by creating a centralized, long-term, interconnected data repository.

Phytochemistry, Jul 1, 2012

Theoretical and Applied Genetics, Sep 14, 2011

Allotetraploid (2n = 4x = 28) Leymus triticoides and Leymus cinereus are divergent perennial gras... more Allotetraploid (2n = 4x = 28) Leymus triticoides and Leymus cinereus are divergent perennial grasses, which form fertile hybrids. Genetic maps with n = 14 linkage groups (LG) comprised with 1,583 AFLP and 67 heterologous anchor markers were previously used for mapping quantitative trait loci (QTLs) in these Communicated by T. Komatsuda.

Genome, Dec 1, 2003

D hordein, a prolamin storage protein of barley endosperms, is highly homologous to the high mole... more D hordein, a prolamin storage protein of barley endosperms, is highly homologous to the high molecular weight (HWM) glutenin subunits, which are the major determinants of bread-making quality in wheat flour. In hexaploid wheat (AABBDD), each genome contains two paralogous copies of HMW-glutenin genes that encode the xand y-type HMW-glutenin subunits. Previously, we reported the sequence analysis of a 102-kb genomic region that contains the HMW-glutenin locus of the D genome from Aegilops tauschii, the donor of the D genome of hexaploid wheat. Here, we present the sequence analysis of a 120-kb D-hordein region of the barley genome, a more distantly related member of the Triticeae grass tribe. Comparative sequence analysis revealed that gene content and order are generally conserved. Genes included in both of these orthologous regions are arranged in the following order: a Xa21-like receptor kinase, an endosperm globulin, an HMW prolamin, and a serine (threonine) protein kinase. However, in the wheat D genome, a region containing both the globulin and HMW-glutenin gene was duplicated, indicating that this duplication event occurred after the separation of the wheat and barley genomes. The intergenic regions are divergent with regard to the sequence and structural organization. It was found that different types of retroelements are responsible for the intergenic structure divergence in the wheat and barley genomes. In the barley region, we identified 16 long terminal repeat (LTR) retrotransposons in three distinct nested clusters. These retroelements account for 63% of the contig sequence. In addition, barley D hordein was compared with wheat HMW glutenins in terms of cysteine residue conservation and repeat domain organization.

Methods in molecular biology, 2009

Databases have become an integral part of all aspects of biological research, including basic and... more Databases have become an integral part of all aspects of biological research, including basic and applied plant biology. The importance of databases continues to increase as the volume of data from direct and indirect genomics approaches expands. What is not always obvious to users of databases is the range of available database resources, their access points, or some basic elements of database querying. This chapter briefly summarizes the history of data access via the Internet and reviews some basic terms and considerations in dealing with plant and crop databases. The reader is directed to some of the major publicly available Internet-accessible relevant databases with summaries of the major focuses of those databases, and several examples are given to illustrate how to access plant genomics data. Finally, an outline is given of some of the issues facing the future of plant and crop databases.

Frontiers in Plant Science, Jul 13, 2023

Wheat is one of the most important cereal crops for the global food security. Due to its narrow g... more Wheat is one of the most important cereal crops for the global food security. Due to its narrow genetic base, modern bread wheat cultivars face challenges from increasing abiotic and biotic stresses. Since genetic improvement is the most sustainable approach, finding novel genes and alleles is critical for enhancing the genetic diversity of wheat. The tertiary gene pool of wheat is considered a gold mine for genetic diversity as novel genes and alleles can be identified and transferred to wheat cultivars. Aegilops geniculata and Ae. umbellulata are the key members of the tertiary gene pool of wheat and harbor important genes against abiotic and biotic stresses. Homoeologous-group five chromosomes (5U u and 5M g) have been extensively studied from Ae. geniculata and Ae. umbellulata as they harbor several important genes including Lr57, Lr76, Yr40, Yr70, Sr53 and chromosomal pairing loci. In the present study, using chromosome DNA sequencing and RNAseq datasets, we performed comparative analysis to study homoeologous gene evolution in 5M g , 5U u, and group 5 wheat chromosomes. Our findings highlight the diversity of transcription factors and resistance genes, resulting from the differential expansion of the gene families. Both the chromosomes were found to be enriched with the "response to stimulus" category of genes providing resistance against biotic and abiotic stress. Phylogenetic study positioned the M genome closer to the D genome, with higher proximity to the A genome than the B genome. Over 4000 genes were impacted by SNPs on 5D, with 4-5% of those genes displaying nondisruptive variations that affect gene function.

In contrast to the recent advancements made in meiotic gene discovery for plants such as Arabidop... more In contrast to the recent advancements made in meiotic gene discovery for plants such as Arabidopsis, the progress for wheat has been difficult, hampered principally by a large, polyploid genome. We report here on genomics approaches to identify and characterise genes involved in meiosis in wheat. The first approach used comparative genetics to define the genic content of the 3DS region deleted in the pairing homoeologous mutant ph2a (a deletion mutant at the Ph2 locus). More than 200 genes linked to Ph2 have been identified, several as candidates for the Ph2 gene(s). The degree of synteny at the gene level in wheat and rice across the region analysed has been established in detail and the extent of the deleted segment in ph2a clarified. Furthermore, the spatial transcriptional characteristics of genes linked to Ph2 have been analysed using data from wheat expressed sequence tag (EST) databases in combination with recently developed analysis software. The second approach used a cDNA microarray derived from an anther library to examine gene expression in a temporal series experiment from pre-meiosis to the tetrad stage of meiotic development. We report on these results and their relevance to meiotic and anther developmental processes.http://www.intl-pag.org/12/abstracts/W31_PAG12_143.htm

Kluwer Academic Publishers eBooks, Jan 19, 2006

Although it is frequently stated that due to the size of the Triticeae genomes (for size of cerea... more Although it is frequently stated that due to the size of the Triticeae genomes (for size of cereal genomes, see Gupta and Varshney, Chapter 1) they will not be completely sequenced in the near future, the advance in technologies, the growing evidence of the value of whole ...

F1000Research, 2019

In March 2019, 45 scientists and software engineers from around the world converged at the Univer... more In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.