An overview of bioinformatics is presented with an emphasis on describing a set of tools, databases, and ontologies useful to the weed science community. These tools can be used to identify genes whose product may be the target site of a herbicide or in the degradation pathway of a xenobiotic. They may identify receptors responsible for pathogen recognition or enzymes in the metabolic pathway for allelopathic compounds. Whatever the gene of interest, bioinformatics allows researchers to assemble complete or partial genes from expressed sequence tags (ESTs), complete cDNAs, or complete genomes and then translate them into their corresponding amino acid sequences. Similarity searches can be used to find other proteins with homology to the gene of interest, which can provide clues to its function from the annotation of these database hits. The use of protein domain databases can also provide insight into the functional capabilities of the protein in question and delineate those portions essential for activity. Enzyme Commission (EZ) numbers or gene ontology (GO) descriptors allow placement of the protein within the larger network context of a biological system. These capabilities allow the scientist to probe deeper into the function of their protein of interest to gain a novel understanding of the biology.

A buffalo oocyte-specific subtracted cDNA library was constructed to identify exclusively or preferentially oocyte-expressed genes. The library represented an enriched population of transcripts obtained from oocytes of diverse ovarian follicular origin and at different stages of in vitro maturation. A total of 1173 high-quality sequences of oocyte-specific genes were clustered into 645 unique sequences, out of which 65.76% were represented as singlets and 34.26% as contig expressed sequence tags (ESTs; clusters). Analysis of sequences revealed that 498 of these sequences were identified as a known sequence in mammalian species including buffalo, 103 as uncharacterized ESTs and 44 unknown sequences including 1 novel EST, so far not reported in any species. Gene ontology annotation classified these sequences into functional categories of cellular events and biological processes associated with oocyte competence. Expression status of the isolated unknown ESTs confirmed that many of these are expressed in oocytes exclusively and in others preferentially, some in excess of 80-fold greater in comparison with a variety of somatic tissues. The isolated novel EST was detected to be expressed exclusively in oocytes and testicular cells only. To our knowledge, this is the first report giving a detailed transcriptome account of oocyte-expressed genes in buffalo. This study will provide important information on the physiological control of oocyte development, as well as many questions yet to be addressed on the reproductive process of buffalo.

The pacific white shrimp, Litopenaeus vannamei, is a popular species in aquaculture. Abdominal muscle accounts for 90% of shrimp flesh. Its growth and related genes, particularly the regulatory genes, is not well known. A cDNA library of shrimp juvenile abdominal muscle was established by PCR-based SMART™ cDNA technology. Library size was 5.0 × 106 pfu (plaque-forming unit) independent clones per microgram of starting RNA with the percentage of recombinant clones >95%. Sequence analysis of 311 randomly picked positive clones revealed 197 expressed sequence tags with average insert size of 745 nucleotides, 56% (110 of 197) clones having 5′-end sequence and 44% (87 of 197) clones having 3′-end sequence. Queries of the sequences by Blast identified 37 unknown sequences, and 160 unique clones, including 67 sequences of 100% identity matches, 28 high homologies (80% to 90% sequence match, >100 bits hit score in Blastn), 65 medium homologies (>100 bits hit score in Blastp) to the known EST sequences in the database. Among the high identity-matched ESTs, 12S ribosomal RNA, actin 1, actin 2, arginine kinase and beta-actin were the most abundant transcripts with 5 to 20 times of hit. Primary hit sequences originate from shrimp, insects, lobsters, crabs and crayfish. The EST sequences were categorized as muscle structural proteins (25%), rRNA and protein synthesis (25%), followed by mitochondrial functions (22%), exoskeleton (14%), enzymes (6%) and RNA splicing (2%), suggesting abundant and diverse transcripts present in the shrimp abdominal muscle cDNA library.

Chicken is one of the most important sources of animal protein for human consumption, and breeding programmes have been responsible for constant improvements in production efficiency and product quality. Furthermore, chicken has largely contributed to fundamental discoveries in biology for the last 100 years. In this article we review recent developments in poultry genomics and their contribution to adding functional information to the already existing structural genomics, including the availability of the complete genome sequence, a comprehensive collection of mRNA sequences (ESTs), microarray platforms, and their use to complement QTL mapping strategies in the identification of genes that underlie complex traits. Efforts of the Brazilian Poultry Genomics Programme in this area resulted in generation of a resource population, which was used for identification of Quantitative Trait Loci (QTL) regions, generation of ESTs and candidate gene studies that contributed to furthering our understanding of the complex biological processes involved in growth and muscular development in chicken.

The risk posed by food borne pathogens in eggs has taken on a high priority for government and consumer. In Europe there has been concern that plans to move from battery cages may increase the risk from eggs. For this reason there is some pressure to demonstrate progress in reducing risk from eggs. At the level of the egg the approach has been to improve resistance of the eggshell to breakage using selection for quasi-static compression or specific gravity. The review will consider phenotypic measurement and developments in genetics and genomics that can place new tools in the hands of poultry breeders, should they want to use them.

New phenotypic measurements that better describe the physical and antibacterial properties of the egg and eggshell need to be developed which accurately measure the egg's natural defence characteristics to complement the developments in chicken genomics. Acoustic resonance analysis to measure the stiffness of the eggshell and ultra-structural measurements using electron microscopy in pedigree populations are methods which have been examined. Also organic matrix measurements, antimicrobial properties and bacterial penetration measurements that have only been of academic interest may be used in test populations. Genetics and genomics can be used with these phenotypic measurements to identify genetic markers that can be used in selection programmes, rather than the measurements themselves, using whole genome scans for quantitative trait loci and association analysis with candidate genes. The availability of the chicken genome sequence and EST resources has made carrying out these analyses easier in pedigree breeding flocks.

The parasitic protozoan Toxoplasma gondii and its relatives (e.g. Plasmodium spp., which cause malaria) constitute a major global health problem. In recent years, the elucidation of biological processes in these parasites has accelerated with the application of genetic and genomic methodologies. Genetic analyses in T. gondii have revealed a remarkably stable 87 Mb (megabase) nuclear genome consisting of 11 chromosomes showing little variation across strains. Population studies demonstrate that the small amount of variation defines three clonal lineages where phenotypes such as virulence are associated with a single lineage. The random generation of cDNA (complementary DNA) sequences derived from different strains and developmental stages has highlighted the genetic differences underlying observed phenotypic variation. T. gondii also contains an extrachromosomal 35 kb (kilobase) circular DNA within an organelle with plastid-like properties. The limited coding capacity of the 35 kb organellar genome suggests that proteins responsible for organelle function(s) must be encoded by the nucleus. Scrutiny of T. gondii nuclear cDNA sequences has uncovered a number of proteins thought to carry out essential roles in the organelle (e.g. fatty acid biosynthesis). The synergism between these seemingly unrelated genomic studies has provided a greater understanding of parasite pathogenesis and has identified several new targets for chemotherapy.

Sarcoptes scabiei is an important parasitic mite in both man and animals. Little is known about the molecular interactions between this pathogen and its host. This is in part explained by the paucity of mite-derived material, including antigens. To extend the knowledge of the molecular repertoire in S. scabiei, we have performed a gene survey by an expressed sequence tag (EST) analysis. A total of 1020 ESTs were generated from an S. scabiei cDNA library. The average sequence read was 510 bp after editing and the overall sequencing success was 89%. Clustering of the sequences resulted in 76 clusters, comprising 36% of the ESTs. Sequence similarity searches showed that almost half of the S. scabiei ESTs could be assigned a putative identity. Many of these transcripts shared similarity with genes involved in basic metabolism and cellular organization. In the data set we also identified several proteases and other types of potential allergens implicated in various disease mechanisms. A relatively large fraction of the ESTs coded for different proteins carrying protease inhibitor-like domains. The clones with no similarity to previously identified genes constituted 11% of our transcripts. The EST data generated in this study will be a valuable resource in further studies of the biology of S. scabiei and in the identification of genes that can serve as potential targets in the control of the parasite.

Genome projects for the parasitic helminths Brugia malayi (a representative filarial nematode) and Schistosoma were initiated in 1995 by the World Health Organization with the ultimate objectives of identifying new vaccine candidates and drug targets and of developing low resolution genome maps. Because no genetic maps are available, and very few genes have been characterized from either parasite group, the first goal of both Initiatives has been to catalogue new genes for future placement on chromosome and physical maps. These genes have been identified by the expressed sequence tag (EST) approach, utilising cDNA libraries constructed from diverse life cycle stages. To date, the Initiatives have deposited over 16000 Brugia ESTs and nearly 8000 Schistosoma ESTs in Genbank's dbEST database, corresponding to 6000 and over 3600 genes respectively (33% of Brugia's estimated gene compliment, 18–24% of that of Schistosoma). Large fragment, genomic libraries have been constructed in BAC and YAC vectors for studies of genomic organization and for physical and chromosome mapping, and public, hypertext genomic databases have been established to facilitate data access. We present a summary of progress within the helminth genome initiatives and give several examples of important gene discoveries and future applications of these data.

The genetic differences between praziquantel-resistant (R) and susceptible (S) strains of Schistosoma mansoni (Fallon & Doenhoff, 1994) were explored using RAPD and by cloning differentially expressed mRNAs by subtractive PCR. No differences between the 2 strains were detectable by RAPD using 41 different primers indicating that no major genomic rearrangements were present. Subtractive PCR generated a number of fragments, 1 of which was shown to correspond to an over-expressed mRNA in the R strain and to encode a fragment of the subunit 1 of cytochrome-c oxidase (SCOX1). In the absence of a complete sequence for this gene, we used EST sequences to compile a consensus sequence for the 904 bp at the 3′ end that enabled us to choose primers for semi-quantitative RT–PCR. This technique showed that SCOX1 was indeed over-expressed about 5 to 10-fold in the R strain whereas the genes encoding the 28 kDa glutathione S-transferase, glutathione peroxidase, NADH dehydrogenase subunit 5 and the ATP-binding cassette family protein SMDR2 were not. In contrast, cytochrome-c oxidase enzyme activity was 4-fold lower in the R strain than in the S strain.