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Background  Duplications are very common in the evolution of plant genomes, explaining the high number of members in plant gene families. New genes born after duplication can undergo pseudogenization, neofunctionalization or subfunctionalization. Rice is a model for functional genomics research, an important crop for human nutrition and a target for biofortification. Increased zinc and iron content in the rice grain could be achieved by manipulation of metal transporters. Here, we describe the  ZINC-INDUCED FACILITATOR-LIKE (ZIFL)  gene family in plants, and characterize the genomic structure and expression of rice paralogs, which are highly affected by segmental duplication.    Results  Sequences of sixty-eight  ZIFL  genes, from nine plant species, were comparatively analyzed. Although related to MSF_1 proteins, ZIFL protein sequences consistently grouped separately. Specific ZIFL sequence signatures were identified. Monocots harbor a larger number of  ZIFL  genes in their genomes than dicots, probably a result of a lineage-specific expansion. The rice  ZIFL  paralogs were named  OsZIFL1  to  OsZIFL13  and characterized. The genomic organization of the rice  ZIFL  genes seems to be highly influenced by segmental and tandem duplications and concerted evolution, as rice genome contains five highly similar  ZIFL  gene pairs. Most rice  ZIFL  promoters are enriched for the core sequence of the Fe-deficiency-related box IDE1. Gene expression analyses of different plant organs, growth stages and treatments, both from our qPCR data and from microarray databases, revealed that the duplicated  ZIFL  gene pairs are mostly co-expressed. Transcripts of  OsZIFL4 ,  OsZIFL5 ,  OsZIFL7 , and  OsZIFL12  accumulate in response to Zn-excess and Fe-deficiency in roots, two stresses with partially overlapping responses.    Conclusions  We suggest that  ZIFL  genes have different evolutionary histories in monocot and dicot lineages. In rice, concerted evolution affected  ZIFL  duplicated genes, possibly maintaining similar expression patterns between pairs. The enrichment for IDE1 boxes in rice  ZIFL  gene promoters suggests a role in Zn-excess and Fe-deficiency up-regulation of  ZIFL  transcripts. Moreover, this is the first description of the  ZIFL  gene family in plants and the basis for functional studies on this family, which may play important roles in Zn and Fe homeostasis in plants.

bmc plant biology

ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa) paralogs