Genome-wide identification and characterization of aquaporin genes (AQPs) in Chinese cabbage (Brassica rapa ssp. pekinensis)

Peng, Tao; Zhong, Xinmin; Li, Biyuan; Wang, Wuhong; Yue, Zhichen; Lei, Juanli; Guo, Weiling; Huang, Xiaoyun

doi:10.1007/s00438-014-0874-9

Cited by 55 publications

(66 citation statements)

References 79 publications

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“…These results are possible evidence of biased gene loss in the sHSP family of Chinese cabbage, with a whole-genome triplication of two-step origin. Similar results have been observed in other gene families, e.g., AQP (Tao et al, 2014). However, Br18.0B I, Br20.1 ER, and Br16.2 had no syntenic orthologs in A. thaliana, while no syntenic orthologs of At17.6A I, At17.6C I, or At17.8 I were found in Chinese cabbage (Table 2).…”

Section: Discussionsupporting

confidence: 86%

Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis)

Peng

Guo²,

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Small heat shock proteins (sHSPs) are essential for the plant's normal development and stress responses, especially the heat stress response. The information regarding sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis) is sparse, hence we performed a genome-wide analysis to identify sHSP genes in this species. We identified 26 non-redundant sHSP genes distributed on all chromosomes, except chromosome A7, with one additional sHSP gene identified from an expressed sequence tag library. Chinese cabbage was found to contain more sHSP genes than Arabidopsis. The 27 sHSP genes were classified into 11 subfamilies. We identified 22 groups of sHSP syntenic orthologous genes between Chinese cabbage and Arabidopsis. In addition, eight groups of paralogous genes were uncovered in Chinese cabbage. Protein structures of the 27 Chinese cabbage sHSPs were modeled using Phyre2, which revealed that all of them contain several conserved β strands across different subfamilies. In general, gene structure was conserved within each subfamily between P. Tao et al.

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Section: Discussionsupporting

confidence: 86%

Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis)

Peng

Guo²,

et al. 2015

Genet. Mol. Res.

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“…Based on these findings, we concluded that there are 59 functional AQP genes in B. rapa , which we named based on nomenclature used in other plants and guided by sequence similarity and phylogenetic analysis. Tao et al [23] previously reported 53 AQP genes in B. rapa , and our analysis found these, along with six more AQP genes. Additional file 1: Table S1 lists the chromosomal position, ORF length and orthologous genes, as well as predicted protein length, iso-electric point and molecular weight for each of these 59 B. rapa AQP genes.…”

Section: Resultssupporting

confidence: 72%

Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa

et al. 2017

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BackgroundPlants contain a range of aquaporin (AQP) proteins, which act as transporter of water and nutrient molecules through living membranes. AQPs also participate in water uptake through the roots and contribute to water homeostasis in leaves.ResultsIn this study, we identified 59 AQP genes in the B. rapa database and Br135K microarray dataset. Phylogenetic analysis revealed four distinct subfamilies of AQP genes: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs). Microarray analysis showed that the majority of PIP subfamily genes had differential transcript abundance between two B. rapa inbred lines Chiifu and Kenshin that differ in their susceptibility to cold. In addition, all BrPIP genes showed organ-specific expression. Out of 22 genes, 12, 7 and 17 were up-regulated in response to cold, drought and salt stresses, respectively. In addition, 18 BrPIP genes were up-regulated under ABA treatment and 4 BrPIP genes were up-regulated upon F. oxysporum f. sp. conglutinans infection. Moreover, all BrPIP genes showed down-regulation under waterlogging stress, reflecting likely the inactivation of AQPs controlling symplastic water movement.ConclusionsThis study provides a comprehensive analysis of AQPs in B. rapa and details the expression of 22 members of the BrPIP subfamily. These results provide insight into stress-related biological functions of each PIP gene of the AQP family, which will promote B. rapa breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-0979-5) contains supplementary material, which is available to authorized users.

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“…In addition, the ar/R selectivity filter is highly conserved and typical of watertransporting aquaporins (F/H/T/R). The same ar/R selectivity filter sequence is shared by the PIP sub-family in different plant species such as Z. mays, A. thaliana, P. trichocarpa, S. lycopersicum, G. max and B. rapa (Chaumont et al 2001;Johanson et al 2001;Gupta and Sankararamakrishnan 2009;Reuscher et al 2013;Zhang et al 2013;Tao et al 2014). SIn plants,everal researchers hypothesize PIP aquaporins have a central role in roots water absorption in rootsfor plant PIP aquaporins, suggesting thatand this proteins could also actively regulate root and leaf hydraulics (Maurel et al 2008;Li et al 2014).…”

Section: ; Magadum Et Al 2013) Duplicated Genes Could Undergo Pmentioning

confidence: 99%

“…This differential expression could be plant-, aquaporin-, or stress-specific. Differential expression of aquaporins in response to different environmental stresses has been comprehensively evaluated in several plant species such as Arabidopsis, maize, poplar and B. rapa in the past years (Alexandersson et al 2005;Zhu et al 2005;Cohen et al 2013;Tao et al 2014). Regarding common bean, few aquaporins have been characterized to date.…”

Section: ; Magadum Et Al 2013) Duplicated Genes Could Undergo Pmentioning

confidence: 99%

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

Ariani

Gepts

2015

Mol Genet Genomics

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Plant Aaquaporins are a large and diverse family of water channel proteins that are essential for several physiological processes in living organisms. in all living organisms. In plants, this family has the highest diversity of protein isoforms and substrate specificities compared to animals and bacteria. Numerous studies have linked plant aquaporins with a plethora of processes, such as nutrient acquisition, CO 2 transport, plant growth and development, and response to abiotic stresses.However, little is knowns about this protein family in common bean. Here, we present a genomewide identification of the aquaporin gene family in common bean (Phaseolus vulgaris L.), a legume crop essential for human nutrition. We identified 41 full-length coding aquaporin sequences in the common bean genome, divided by phylogenetic analysis into five sub-families (PIPs, TIPs, NIPs, SIPs and XIPs). Residues determining substrate specificity of aquaporins (i.e., NPA motifs and ar/R selectivity filter) seem conserved between common bean and other plant species, allowing inference of substrate specificity for these proteins. Thanks to the availability of RNA-sequencing datasets, expression levels in different organs and in leaves of wild and domesticated bean accessions were evaluated. Three aquaporins (PvTIP1;1, PvPIP2;4 and PvPIP1;2) have the overall highest mean expressions, with PvTIP1;1 having the highest expression among all aquaporins. We performed an EST database mining to identify drought responsive aquaporins in common bean. This analysis showed a significant increase in expression for PvTIP1;1 in drought stress conditions compared to well-watered environments. The pivotal role suggested for PvTIP1;1 in regulating water homeostasis and drought stress response in the common bean, should be verified by further field experimentation under drought stress.

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Genome-wide identification and characterization of aquaporin genes (AQPs) in Chinese cabbage (Brassica rapa ssp. pekinensis)

Cited by 55 publications

References 79 publications

Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis)

Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis)

Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

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