Chickens (Gallus gallus) were the first avian species selected for whole genome sequencing because of their economic value, use as a food source, livelihood security and research importance. Any living organism contains a galaxy of genes which express all the phenotypes or characters by encoding proteins and peptides, and playing regulatory roles in the biological system. Functional genomics in turn, is a multidisciplinary approach to identify and demonstrate the functional roles of genes and other regulatory molecules such as microRNA and CpG methylation in biological pathways. In the last two decades, the chicken genome database has made significant advancements in accruing large amounts of genomic information through employing advanced bio-informatic tools. Several techniques such as cDNA microarray, serial analysis of gene expression, massively parallel signature sequencing, cDNA subtractive hybridisation and next generation sequencing have been utilised to investigate the genome-wide expression profile instead of revealing expression pattern of one or a few genes in various avian species. Expressed sequence tag or cDNA sequences are the key factors for identification of novel genes and understanding the complex molecular cascades of ontology. A large-scale cDNA library has been constructed from embryonic and adult tissues and consequently identified the presence of about 19,000 functional genes in chickens. The micro RNAs play crucial role in gene expression and to date, approximately 496 micro RNAs have been characterised. The non-coding RNA alters gene expression involved in cellular process, by modulating the chromatin architecture, transcription, RNA splicing, editing, translation and turnover. Functional genomics studies have been extensively used to identify genes associated with several production traits, immuno-genetic mechanism, host-pathogen interaction, pathogen biology etc. Nutrigenomics have determined the genomic mechanism involved in feed utilisation, metabolism and cholesterol synthesis etc., which ultimately reveal potential applications for improving the nutritional efficiency of birds. This review discusses the tools and utility of functional genomics approaches in chicken.

The study of bovine mammary gland functional genomics requires appropriate cDNA library collections to access gene expression patterns from different developmental and physiological stages. The present study was undertaken with the objective to identify candidate genes involved in the process of increased milk synthesis following 0, 48 and 96 h of recombinant bovine somatotropin (rbST) treatment to Surti buffalo (Bubalus bubalis) through differential display reverse transcriptase PCR (DDRT-PCR). Of a total 50 sequenced DD bands, 64% of ESTs were differentially expressed (appeared only in post-treatment samples, i.e. 48 h and 96 h) and 36% were up-regulated after rbST treatment. Of the ESTs 32%were found to be located on Bos taurus chromosome 24 (equivalent to buffalo chromosome 22), whereas 16% of ESTs could not be mapped, indicating that they are specific to buffalo. Quantitative real time PCR assay of 15 ESTs revealed transcript level surge in 13 ESTs, and decline in one EST, while one showed up-regulation in expression level at 48 h while down-regulation at 96 h. This study indicates more than 30 novel transcripts, with unknown function, involved in increased milk synthesis and also the involvement of many more genes in the physiology of milk production than once thought.

Domestic yak (Bos grunniens) metallothionein-I (MT-I) and metallothionein-III (MT-III) cDNA 3′-end full-length sequences (331 and 378 bp; GenBank accession MT-I no. AY758557, MT-III no. DQ492300) from the total RNA of liver and brain tissues were amplified and cloned by reverse transcription polymerase chain reaction (RT-PCR) and 3′-rapid amplification of cDNA ends (RACE) using the primers YMT-I SP and M13 primers M4, and YMT-III SP and M13 primers M4, respectively, which included the MT-I (183 bp) coding sequence, MT-III (207 bp) cDNA coding sequences, and also the tailing signal AATAAA and Poly(A) at the 3′-ends of the MT-I and MT-III, respectively. The analyses showed that the yak cDNA sequence coding for MT-I protein was composed of 61 amino acids, including 20 cysteines having a conserved tripeptide structure, for example C–X–C, C–C–X–C–C, C–X–X–C and so on. The yak cDNA sequence coding for MT-III protein was composed of 68 amino acids, including 19 cysteines having both MT-III-specific conserved tripeptides and the same conserved tripeptides as MT-I, including T, CPCP, GEGAEA and so on. They were all comparatively conservative in molecular evolution. These structures indicated that MT-III had the same physiological functions regarding heavy metals (detoxification and so on) as MT-I, and also different specific functions from MT-I, including inhibition of neuron growth.

The c-fos and c-jun proto-oncogenes are involved in the regulation of gene expression, cell proliferation, differentiation and tumorigenesis. Embryogenesis, like tumorigenesis, involves dramatic cell growth, cleavage and differentiation processes. Activation of the c-fos and c-jun proto-oncogenes in sheep conceptuses during the period of rapid growth and elongation was examined using reverse transcription and polymerase chain reaction (RT-PCR). The specificity of PCR products was determined by Southern blot hybridisation analysis with a non-radioactive DNA probe. A band corresponding to a 507 bp fragment (predicted amplified c-fos gene cDNA product) was observed in 3 of 9 day-13, 1 of 4 day-14 and 1 of 2 day-16 embryos. Meanwhile, a 400 bp c-jun transcript was aslo detected in 1 or 2 day-12, 3 of 9 day-13 and 2 of 2 day-16 embroyos. These results suggest that mRNA transcripts of c-fos and c-jun proto-oncogenes were specifically expressed during the period of ovine embryonic elongation and may have a possible role in preimplantation embryonic development of sheep.

cDNAs for the major cysteine endopeptidase (CEpase) of mung bean (Vigna radiata [L.] Wilczek) seedling cotyledons have been cloned using gene-specific primers with the polymerase chain reaction (PCR) in a 3'-RACE system. A cDNA clone for CEpase, pKL042, that is 1221 bp long excluding the poly A tail was isolated. It appears to contain the entire coding sequence for a 362-residue-long polypeptide. The N-terminal sequence for the mature CEpase begins at position 128 of the putative translation product, suggesting removal of an N-terminal hydrophobic signal peptide and additional sequences to produce the mature protease. Northern blot hybridization with CEpase cDNA pKL042 as probe indicates that CEpase transcript is not detectable in the cotyledons or the embryonic axis of dry seeds, but is first detectable in the day 1 cotyledons and in the day 3 axis. The level of CEpase mRNA in both cotyledons and axis increases as growth proceeds. A decline of protease activity, however, is observed after day 3 in the cotyledons, even though the level of protease transcripts continues to increase until day 8. Detachment of the axis from the cotyledons before day 3 results in the prevention of the normal increase in both protease activity and CEpase mRNA.

A partial amino acid sequence of a vigour-related protein, V-1, from cauliflower (Brassica oleracea L.) seeds was obtained, after isolation by two-dimensional gel electrophoresis and gas-phase micro-sequencing. The sequence was found to have high homology to soybean seed maturation proteins. However, the position of the sequence in the V-1 polypeptide suggests that the V-1 and soybean proteins have different polypeptide structures. An osmoprimed seeds cDNA library was constructed and has been screened by a cDNA probe derived from the V-1 sequence. Two cDNA clones with high homology to aspartic protease (EC 3.4.23) from barley grain were isolated. The expression of putative aspartic protease mRNA was found to be enhanced by osmopriming, however the clones were found to have no significant sequence homology to the V-1.

We produced a mAb against the Babesia caballi extracellular merozoite termed mAb 2H2 and used it to screen a cDNA expression library prepared from B. caballi merozoite mRNA for highly expressed proteins. The complete nucleotide sequence of the cloned gene had 1547 nucleotides and contained a 36-nucleotide intron. The 1398 nucleotide open reading frame predicts a 51 kDa protein showing similarity to protein disulfide isomerase (PDI) from other species. The PDI gene had a predicted N-terminal signal sequence of 19 amino acids and a C-terminal tetrapeptide sequence (His-Thr-Glu-Leu; HTEL) for retention in lumen of the endoplasmic reticulum (ER). The recombinant protein expressed in baculovirus showed an apparent mass of 51 kDa, identical to that the native B. caballi protein. Moreover, the ER retention signal site (HTEL) of the recombinant protein retained its function in ER of insect cells. This 51 kDa protein was strongly expressed by extracelluar B. caballi merozoites in indirect immunofluorescence antibody tests, and was not expressed in the early phase of trophozoite development. Interestingly, detailed observation showed that the reaction of anti-P51 antibody and mAb 2H2 against pear-shaped forms was very erratic, some displaying one or two brightly fluorescent patterns.

A pollen cDNA library of Japanese pear (Pyrus pyrifolia) from the family Rosaceae was constructed and a cDNA (bgn-1) of 1408 bp, which encodes a protein (BGN-1) secreted from growing pollen tubes, was cloned and sequenced. bgn-1 cDNA is composed of a 5′-untranslated region of 47 bp, an open reading frame of 1194 bp encoding 397 amino acid residues and a complete 3′-untranslated region of 167 bp. Alignment of the deduced amino acid sequence of bgn-1 with that of barley (Hordeum vulgare) β-1,3-glucanase (GII) showed 39.7% amino acid identity. Several residues that were critical for the function of GII were conserved in the deduced BGN-1 polypeptide. Moreover, hydrophobic cluster analysis (HCA) showed an overall HCA homology score of 87.1% and analysis of BGN-1 with the 3D-PSSM program predicted a three-dimensional structure of BGN-1 highly homologous to that of barley GII with ≥95% certainty. These results suggest that the cloned bgn-1 cDNA encodes a β-1,3-glucanase-like protein in Japanese pear. The predicted mature protein (375 amino acids) has a theoretical molecular mass of 40 723 Da, a basic pI of 9.59 and a diagnostic amino acid residue mode of D, L, S and L, which is very similar to that of growth-related subfamily D (D, L, S and Q) in cereals. A ProXXPro repeat is also found between positions 352 and 367 in the C-extension region.

A copper/zinc superoxide dismutase (Cu/ZnSOD) gene and a manganese superoxide dismutase (MnSOD) gene of the human parasite Clonorchis sinensis have been cloned and their gene products functionally characterized. Genes Cu/ZnSOD and MnSOD encode proteins of 16 kDa and 25·4 kDa, respectively. The deduced amino acid sequences of the two genes contained highly conserved residues required for activity and secondary structure formation of Cu/ZnSOD and MnSOD, respectively, and show up to 73·7% and 75·4% identities with their counterparts in other animals. The genomic DNA sequence analysis of Cu/ZnSOD gene revealed this as an intronless gene. Inhibitor studies with purified recombinant Cu/ZnSOD and MnSOD, both of which were functionally expressed in Escherichia coli, confirmed that they are copper/zinc and manganese-containing SOD, respectively. Immunoblots showed that both C. sinensis Cu/ZnSOD and MnSOD should be antigenic for humans, and both, especially the C. sinensis MnSOD, exhibit extensive cross-reactions with sera of patients infected by other trematodes or cestodes. RT-PCR and SOD activity staining of parasite lysates indicate that there are no significant differences in mRNA level or SOD activity for both species of SOD, indicating cytosolic Cu/ZnSOD and MnSOD might play a comparatively important role in the C. sinensis antioxidant system.

Ectomycorrhiza formation is a complex developmental process that is still not well understood. To study this process, we identified genetic markers for mycorrhiza development by differential screening of a cDNA library obtained from fully developed Picea abies–Amanita muscaria mycorrhizas. Twenty-three cDNA clones were identified that showed significantly altered gene expression during the ectomycorrhizal interaction. A detailed analysis was performed for two fungal cDNA clones, SC13 and SC25, exhibiting the most pronounced differences. SC13 encodes a protein of 184 amino acid residues that shows no homology with any sequence in databases. It was highly expressed in non-mycorrhizal hyphae, whereas its expression was decreased at least 50-fold in mycorrhizas and fruit bodies. SC25 encodes a protein of 198 residues that shows weak sequence homology with extensin-like plant proteins. The expression of this gene was weak in non-mycorrhizal hyphae but approx. 30-fold higher in mycorrhizas and fruit bodies. Because the expression of both developmentally regulated fungal genes was identical for mycorrhizas and fruit bodies, a common regulation mechanism for both developmental processes is proposed.

A gene encoding a protein of 646 amino acid residues with a molecular mass of 71·3 kDa showing homology to the cytoplasmic form of the 70 kDa heat shock protein was cloned and sequenced from the nematode parasite Trichinella britovi (Tb). The gene was expressed in vitro as a protein of 71 kDa that was immunoprecipitated by a Trichinella-infected rabbit serum. Monospecific polyclonal antibodies raised against the recombinant Tb Hsp70 expressed in Escherichia coli, recognized a protein of 70 kDa by Western blot analysis of Tb soluble antigen (muscular stage). Tb Hsp70 was located in the nuclei of the muscle larvae as determined by the indirect immunofluorescent pattern on cross-sections of the worm. The expression of this protein was not detected in adult worm nuclei suggesting a differential expression of Hsp70 between the 2 stages of Trichinella.

Scolexin is a coagulation-provoking plasma protein induced in response to bacterial or viral infection of larval Manduca sexta, a large lepidopterous insect. Here we report the isolation and sequencing of two cDNA clones that code for scolexin isoforms sharing 80% sequence identity. The scolexin sequences have low but recognizable sequence similarity to members of the chymotrypsin family and represent a new subfamily of chymotrypsin-like serine proteinases. Comparison with known structures reveals the conservation of key catalytic residues and a possible specificity for small nonpolar residues. Most remarkable is the absence of a canonical activation peptide cleavage site. This suggests that the regulation of scolexin activity will involve a novel activation mechanism.

Tapeworms absorb and consume large quantities of glucose through their syncytial tegument, storing the excess as glycogen. Although some studies on the metabolism of glucose in several tapeworms are available, the proteins that mediate its uptake and distribution in their tissue have not been identified. We describe the isolation and characterization of cDNA clones encoding 2 facilitated diffusion glucose transporters (TGTP1 and TGTP2) from Taenia solium, the causal agent of human and porcine cysticercosis. Radio-isotope labelled hexose uptake mediated by TGTP1 expressed in Xenopus oocytes is inhibited by the natural stereoisomers d-glucose and d-mannose but not by l-glucose. Transport by TGTP1 is sensitive to classical inhibitors of facilitated diffusion such as phloretin and cytochalasin B, and insensitive to ouabain. TGTP2 did not function in Xenopus oocytes. Localization studies using specific anti-TGTP1 and anti-TGTP2 antibodies show that TGTP1 is abundant in a number of structures underlying the tegument in adult parasites and larvae, whereas TGTP2 appears to be localized only on the tegumentary surface of the larvae and is not detected in adults.

Neospora caninum is an apicomplexan parasite of veterinary importance which invades many different cell types and tissues. N. caninum tachyzoites proliferate intracellularly by endodyogeny. Eventually the massive proliferation of tachyzoites leads to host cell lysis and the newly formed parasites are released and invade neighbouring cells. Tachyzoite cell surface molecules could serve as ligands, mediating host cell adhesion and invasion. Nc-p43 is a recently identified N. caninum tachyzoite surface protein which is functionally involved in the processes leading to host cell invasion in vitro. Affinity-purified antibodies directed against Nc-p43 were used to screen a lambda gt22A-cDNA expression library constructed from N. caninum tachyzoites. The cDNA insert of one immunoreactive clone was subcloned and expressed in E. coli as a poly-histidine fusion protein. The identity of the resulting recombinant antigen termed recNc-p43 was confirmed by immunoblotting, immunofluorescence and electron microscopy using affinity-purified antibodies. The sequence of the cDNA insert encoding recNc-p43 was determined. Analysis of the deduced amino acid sequence revealed that Nc-p43 exhibited similarity to SAG1 (p30) and SAG3 (p43), 2 major surface antigens of Toxoplasma gondii tachyzoites. These similarities were not reflected on the immunochemical level, since no cross-antigenicity between SAG1, SAG3 and Nc-p43 was observed.

A mutation of a gene (discovered in Festuca pratensis Huds. and designated sid ) confers indefinite greenness on senescing leaves. Via intergeneric hybrids with Lolium multiflorum L. and Lolium perenne L., the mutant gene (sidy) has been introgressed into a range of Lolium backgrounds. Using genomic in situ hybridization we have identified segments carrying sidy in recombinant chromosomes of Lolium–Festuca introgression lines. We also used L. perenne lines segregating 1[ratio ]1 for the staygreen character to tag the gene with molecular markers. In two mapping populations a total of 84 genotypes were screened with isoenzymes, RAPD primers, RFLP probes and AFLP primer pairs. Over 180 polymorphic loci were identified, representing 10 linkage groups spanning 600 cM. Two AFLP markers are linked to sid at 4·6 and 14·9 cM, close enough to be usable for marker-assisted selection. Introgression of sidy into Lolium temulentum L. resulted in the production of near-isogenic inbreeding lines suitable for comparative studies of gene expression. Using a variation of the method of representational difference analysis a very small number of cDNAs have been identified as promising candidates for sid, or genes directly regulated by sid.

Two cDNAs encoding cysteine proteinases were isolated from a cDNA library constructed from feeding females of Heterodera glycines. The library was screened with a cysteine proteinase gene fragment originally amplified from cDNA of H. glycines. Database searches predict that 1 cDNA (hgcp-I) encodes a cathepsin L-like proteinase, while the second (hgcp-II) encodes a cathepsin S-like enzyme. Both predicted proteins contain a short secretion signal sequence, a long pro-peptide and a mature protein of 219 amino acids. Southern blot analysis suggests that the cathepsin S-like enzyme, HGCP-II, is encoded by a single-copy gene in contrast to the cathepsin L-like proteinase, HGCP-I which may have 2 homologues. The regions encoding the mature proteinases were cloned into an expression vector and recombinant protein produced in E. coli. HGCP-I was shown, after refolding, to cleave the synthetic peptide Z-Phe-Arg-AMC, and this activity could be inhibited by the engineered rice cystatin Oc-IΔD86. HGCP-II showed no activity against the synthetic substrates tested. The knowledge gained from these studies will improve our understanding of plant nematode proteinases and aid the development of a rational proteinase inhibitor-based approach to plant nematode resistance.