[Re-sequencing and assembly of chicken T cell receptor gamma locus].

The genomic organization of the animal T cell receptor (TCR) loci is characterized by different gene families with high homology, and it is quite difficult to obtain accurate gene sequences and arrangements of these gene families. In this study, we identified the location of chicken TCR gamma chain (TCRγ or TRG) genes by comparing those TRG gene sequences with the chicken reference genome, and the corresponding bacterial artificial chromosome (BAC) clone, CH261-174P24, was chosen for further high-throughput DNA re-sequencing and assembly. As a result, a draft genome assembly containing ten scaffolds was obtained, which almost covered the chicken TRG gene locus and the flanking regions. Subsequently, the internal structure of these scaffolds was confirmed by PCR amplification and Sanger sequencing. Our analysis corrected two errors in the sequence-one near a TRG variable gene and one close to a gap, respectively, and several errors in the TRG variable genes in the chicken reference genome. In conclusion, our work has partially corrected the erroneously assembled sequences of the TRG gene locus in the chicken reference genome and thus provides a new method for genome sequence analysis of chicken TRA/D and TRB gene loci.

Identification of genes specifically or preferentially expressed in maize silk reveals similarity and diversity in transcript abundance of different dry stigmas.

BACKGROUND: In plants, pollination is a critical step in reproduction. During pollination, constant communication between male pollen and the female stigma is required for pollen adhesion, germination, and tube growth. The detailed mechanisms of stigma-mediated reproductive processes, however, remain largely unknown. Maize (Zea mays L.), one of the world's most important crops, has been extensively used as a model species to study molecular mechanisms of pollen and stigma interaction. A comprehensive analysis of maize silk transcriptome may provide valuable information for investigating stigma functionality. A comparative analysis of expression profiles between maize silk and dry stigmas of other species might reveal conserved and diverse mechanisms that underlie stigma-mediated reproductive processes in various plant species. RESULTS: Transcript abundance profiles of mature silk, mature pollen, mature ovary, and seedling were investigated using RNA-seq. By comparing the transcriptomes of these tissues, we identified 1,427 genes specifically or preferentially expressed in maize silk. Bioinformatic analyses of these genes revealed many genes with known functions in plant reproduction as well as novel candidate genes that encode amino acid transporters, peptide and oligopeptide transporters, and cysteine-rich receptor-like kinases. In addition, comparison of gene sets specifically or preferentially expressed in stigmas of maize, rice (Oryza sativa L.), and Arabidopsis (Arabidopsis thaliana [L.] Heynh.) identified a number of homologous genes involved either in pollen adhesion, hydration, and germination or in initial growth and penetration of pollen tubes into the stigma surface. The comparison also indicated that maize shares a more similar profile and larger number of conserved genes with rice than with Arabidopsis, and that amino acid and lipid transport-related genes are distinctively overrepresented in maize. CONCLUSIONS: Many of the novel genes uncovered in this study are potentially involved in stigma-mediated reproductive processes, including genes encoding amino acid transporters, peptide and oligopeptide transporters, and cysteine-rich receptor-like kinases. The data also suggest that dry stigmas share similar mechanisms at early stages of pollen-stigma interaction. Compared with Arabidopsis, maize and rice appear to have more conserved functional mechanisms. Genes involved in amino acid and lipid transport may be responsible for mechanisms in the reproductive process that are unique to maize silk.