Genome-wide identification of aquaporin encoding genes in Brassica oleracea and their phylogenetic sequence comparison to Brassica crops and Arabidopsis.

Till A Diehn,Nadine Bernhardt,Gerd P Bienert,Benjamin Pommerrenig,Anja Hartmann

doi:10.3389/fpls.2015.00166

Till A Diehn, Nadine Bernhardt + Show 3 more

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https://doi.org/10.3389/fpls.2015.00166

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Abstract

Aquaporins (AQPs) are essential channel proteins that regulate plant water homeostasis and the uptake and distribution of uncharged solutes such as metalloids, urea, ammonia, and carbon dioxide. Despite their importance as crop plants, little is known about AQP gene and protein function in cabbage (Brassica oleracea) and other Brassica species. The recent releases of the genome sequences of B. oleracea and Brassica rapa allow comparative genomic studies in these species to investigate the evolution and features of Brassica genes and proteins. In this study, we identified all AQP genes in B. oleracea by a genome-wide survey. In total, 67 genes of four plant AQP subfamilies were identified. Their full-length gene sequences and locations on chromosomes and scaffolds were manually curated. The identification of six additional full-length AQP sequences in the B. rapa genome added to the recently published AQP protein family of this species. A phylogenetic analysis of AQPs of Arabidopsis thaliana, B. oleracea, B. rapa allowed us to follow AQP evolution in closely related species and to systematically classify and (re-) name these isoforms. Thirty-three groups of AQP-orthologous genes were identified between B. oleracea and Arabidopsis and their expression was analyzed in different organs. The two selectivity filters, gene structure and coding sequences were highly conserved within each AQP subfamily while sequence variations in some introns and untranslated regions were frequent. These data suggest a similar substrate selectivity and function of Brassica AQPs compared to Arabidopsis orthologs. The comparative analyses of all AQP subfamilies in three Brassicaceae species give initial insights into AQP evolution in these taxa. Based on the genome-wide AQP identification in B. oleracea and the sequence analysis and reprocessing of Brassica AQP information, our dataset provides a sequence resource for further investigations of the physiological and molecular functions of Brassica crop AQPs.

Highlights

Arabidopsis thaliana serves frequently as a reference for comparative genomics and gene functions in plants despite its genomic, phylogenetic, and physiological distance to most of the analyzed species
Data Resource Arabidopsis thaliana, B. oleracea, and B. rapa genomic and annotation data were downloaded from the TAIR10 database2, the Bolbase database3, and the BRAD database4, respectively
The highly conserved intron located in the sequence encoding loop D is missing in all NIP3 isoforms and the otherwise conserved intron separating the exons encoding TMH3 is missing in all NIP2 and NIP5 isoforms. These results show that NIP1, NIP4, NIP6, and NIP7 genes are more similar with respect to their gene structure

Summary

Introduction

Arabidopsis thaliana serves frequently as a reference for comparative genomics and gene functions in plants despite its genomic, phylogenetic, and physiological distance to most of the analyzed species. Brassica crops are used worldwide for animal and human nutrition, as catch and cover crops and for biofuel production This genus includes important vegetables [Brassica rapa ssp. The three diploid species B. rapa (A genome), B. nigra (B genome), and B. oleracea (C genome) formed the amphidiploid species B. juncea (A and B genomes), B. napus (A and C genomes), and B. carinata (B and C genomes) probably by independent hybridizations. This interspecific cytogenetic relationship was already described by the ‘U’s triangle theory of Nagaharu (Nagaharu, 1935) stating that the genomes of three ancestral species of Brassica combined to generate three modern vegetables and oilseed crop species. The A. thaliana genome has undergone duplications, deletions, rearrangements, and a reduction in chromosome number even since the divergence from its close relative Arabidopsis lyrata 5 MYA (Hu et al, 2011)

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