Research article

BMC Genomics

, 13:260

Open Access This content is freely available online to anyone, anywhere at any time.

Origin of a novel protein-coding gene family with similar signal sequence in Schistosoma japonicum

  • Evaristus Chibunna MbanefoAffiliated withDepartment of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki UniversityDepartment of Parasitology and Entomology, Faculty of Bioscience, Nnamdi Azikiwe University
  • , Yu ChuanxinAffiliated withLaboratory on Technology for Parasitic Disease Prevention and Control, Jiangsu Institute of Parasitic Diseases
  • , Mihoko KikuchiAffiliated withDepartment of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University
  • , Mohammed Nasir ShuaibuAffiliated withDepartment of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University
  • , Daniel BoamahAffiliated withDepartment of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University
  • , Masashi KirinokiAffiliated withLaboratory of Tropical Medicine and Parasitology, Dokkyo Medical University
  • , Naoko HayashiAffiliated withLaboratory of Tropical Medicine and Parasitology, Dokkyo Medical University
  • , Yuichi ChigusaAffiliated withLaboratory of Tropical Medicine and Parasitology, Dokkyo Medical University
  • , Yoshio OsadaAffiliated withDepartment of Immunology and Parasitology, The University of Occupational and Environmental Health
    • , Shinjiro HamanoAffiliated withDepartment of Parasitology, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University
    • , Kenji HirayamaAffiliated withDepartment of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University Email author 

Abstract

Background

Evolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal sequence trap (SST). To find the mechanism underlying the origination of these genes with similar core promoter regions and signal sequence, we adopted an integrated approach utilizing whole genome, transcriptome and proteome database BLAST queries, other bioinformatics tools, and molecular analyses.

Results

Our data, in combination with database analyses showed evidences of expression of these genes both at the mRNA and protein levels exclusively in all developmental stages of S. japonicum. The signal sequence motif was identified in 27 distinct S. japonicum UniGene entries with multiple mRNA transcripts, and in 34 genome contigs distributed within 18 scaffolds with evidence of genome-wide dispersion. No homolog of these genes or similar domain was found in deposited data from any other organism. We observed preponderance of flanking repetitive elements (REs), albeit partial copies, especially of the RTE-like and Perere class at either side of the duplication source locus. The role of REs as major mediators of DNA-level recombination leading to dispersive duplication is discussed with evidence from our analyses. We also identified a stepwise pathway towards functional selection in evolving genes by alternative splicing. Equally, the possible transcription models of some protein-coding representatives of the duplicons are presented with evidence of expression in vitro.

Conclusion

Our findings contribute to the accumulating evidence of the role of REs in the generation of evolutionary novelties in organisms’ genomes.

Keywords

Signal sequence trap Schistosoma japonicum Repetitive elements Gene duplication Secreted proteins Non-allelic homologous recombination