Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

Abstract

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.

Peer Review #1 of "Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum) (v0.1)"

“…All EsSIP subfamily genes displayed three exons with similar lengths. This description of exonintron structure provides additional evidence to support the classification results (Kong et al, 2017).…”

Next generation sequencing to investigate genomic diversity in Caryophyllales

“…In addition, to their fascinating trait evolution, the Caryophyllales are well known for important crops and horticultural species like sugar beet, quinoa and spinach. Most prominent is the genome sequence of Beta vulgaris [7] which was often used as a reference for studies within Caryophyllales [7–10]. In addition, genomes of Spinacia oleracea [7,11], Dianthus caryophyllus [12], Amaranthus hypochondriacus [13], Chenopodium quinoa [14] were sequenced.…”

The Tonoplast Intrinsic Protein Gene KvTIP3 is Responsive to Different Abiotic Stresses in Kosteletzkya virginica

“…35 and 36 AQPs were identified in Arabidopsis and maize, respectively [5,6]. In addition, the number of AQPs isolated was 28 in Vitis vinifera L. [7], 28 in Beta vulgaris [8], 55 in Populus trichocarpa [9], 41 in Solanum lycopersicum [10], 63 in bamboo [11], 66 in Glycine max [12], and 71 in cotton [13].…”