Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily of Gossypium raimondii

He, Daohua; Zhongping, Lei; Xing, Hongyi; Tang, Baoshan

doi:10.1016/j.gene.2014.07.054

Cited by 25 publications

(19 citation statements)

References 35 publications

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“…Meanwhile, our results have complemented the earlier study of ALDH superfamily in G . raimondii [15] by the comparative genomics approach. Furthermore, it’s worth noting that families 5, 7, 12, 22 were represented by only one gene number in all the surveyed diploid species, and one or two counterparts in allotetraploids cottons.…”

Section: Discussionmentioning

confidence: 99%

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Comparative genomic study of ALDH gene superfamily in Gossypium: A focus on Gossypium hirsutum under salt stress

et al. 2017

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Aldehyde dehydrogenases (ALDHs) are a superfamily of enzymes which play important role in the scavenging of active aldehydes molecules. In present work, a comprehensive whole-genomic study of ALDH gene superfamily was carried out for an allotetraploid cultivated cotton species, G. hirsutum, as well as in parallel relative to their diploid progenitors, G. arboreum and G. raimondii. Totally, 30 and 58 ALDH gene sequences belong to 10 families were identified from diploid and allotetraploid cotton species, respectively. The gene structures among the members from same families were highly conserved. Whole-genome duplication and segmental duplication might be the major driver for the expansion of ALDH gene superfamily in G. hirsutum. In addition, the expression patterns of GhALDH genes were diverse across tissues. Most GhALDH genes were induced or repressed by salt stress in upland cotton. Our observation shed lights on the molecular evolutionary properties of ALDH genes in diploid cottons and their alloallotetraploid derivatives. It may be useful to mine key genes for improvement of cotton response to salt stress.

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Section: Discussionmentioning

confidence: 99%

“…Though ALDH gene superfamily has been reported in G . raimondii [15], little is known about their detail information in other cotton species, especially the potential role under salt stress in upland cotton.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic study of ALDH gene superfamily in Gossypium: A focus on Gossypium hirsutum under salt stress

et al. 2017

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“…The number of sequenced plant genomes is greatly increasing. Therefore, the occurrence and composition of ALDHs have been extensively studied in several plant species, including Physcomitrella patens [15], Chlamydomonas reinhardtii [15], Arabidopsis thaliana [14], Oryza sativa [18, 19], Zea mays [20], Gossypium raimondii [21], Sorghum bicolor [15], and Foxtail Millet [22]. …”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization of the aldehyde dehydrogenase gene superfamily in soybean and its potential role in drought stress response

Wang¹,

Liu²,

Li³

et al. 2017

BMC Genomics

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BackgroundAldehyde dehydrogenases (ALDHs) represent a group of enzymes that detoxify aldehydes by facilitating their oxidation to carboxylic acids, and have been shown to play roles in plant response to abiotic stresses. However, the comprehensive analysis of ALDH superfamily in soybean (Glycine max) has been limited.ResultsIn present study, a total of 53 GmALDHs were identified in soybean, and grouped into 10 ALDH families according to the ALDH Gene Nomenclature Committee and phylogenetic analysis. These groupings were supported by their gene structures and conserved motifs. Soybean ALDH superfamily expanded mainly by whole genome duplication/segmental duplications. Gene network analysis identified 1146 putative co-functional genes of 51 GmALDHs. Gene Ontology (GO) enrichment analysis suggested the co-functional genes of these 51 GmALDHs were enriched (FDR < 1e-3) in the process of lipid metabolism, photosynthesis, proline catabolism, and small molecule catabolism. In addition, 22 co-functional genes of GmALDHs are related to plant response to water deprivation/water transport. GmALDHs exhibited various expression patterns in different soybean tissues. The expression levels of 13 GmALDHs were significantly up-regulated and 14 down-regulated in response to water deficit. The occurrence frequencies of three drought-responsive cis-elements (ABRE, CRT/DRE, and GTGCnTGC/G) were compared in GmALDH genes that were up-, down-, or non-regulated by water deficit. Higher frequency of these three cis-elements was observed for the group of up-regulated GmALDH genes as compared to the group of down- or non- regulated GmALDHs by drought stress, implying their potential roles in the regulation of soybean response to drought stress.ConclusionsA total of 53 ALDH genes were identified in soybean genome and their phylogenetic relationships and duplication patterns were analyzed. The potential functions of GmALDHs were predicted by analyses of their co-functional gene networks, gene expression profiles, and cis-regulatory elements. Three GmALDH genes, including GmALDH3H2, GmALDH12A2 and GmALDH18B3, were highly induced by drought stress in soybean leaves. Our study provides a foundation for future investigations of GmALDH gene function in soybean.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3908-y) contains supplementary material, which is available to authorized users.

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“…Besides the effect of speciation, they appear to evolve through gene duplication as shown in diverse species [31,36,37,39]. Although the driving forces of the duplication events are unclear, it is remarkable that the ALDH genes often do not have the same expression patterns and a number of isoforms per family.…”

Section: Discussionmentioning

confidence: 99%

“…thaliana [31], Eutrema salsugineum [35], Gossypium raimondii [36], Glycine max [37], Populus trichocarpa [2], O . sativa [38], Sorghum bicolor [2], Setaria italica [39], and Z .…”

Section: Methodsmentioning

confidence: 99%

Active Sites of Reduced Epidermal Fluorescence1 (REF1) Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots

2016

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Plant aldehyde dehydrogenases (ALDHs) play important roles in cell wall biosynthesis, growth, development, and tolerance to biotic and abiotic stresses. The Reduced Epidermal Fluorescence1 is encoded by the subfamily 2C of ALDHs and was shown to oxidise coniferaldehyde and sinapaldehyde to ferulic acid and sinapic acid in the phenylpropanoid pathway, respectively. This knowledge has been gained from works in the dicotyledon model species Arabidopsis thaliana then used to functionally annotate ALDH2C isoforms in other species, based on the orthology principle. However, the extent to which the ALDH isoforms differ between monocotyledons and dicotyledons has rarely been accessed side-by-side. In this study, we used a phylogenetic approach to address this question. We have analysed the ALDH genes in Brachypodium distachyon, alongside those of other sequenced monocotyledon and dicotyledon species to examine traits supporting either a convergent or divergent evolution of the ALDH2C/REF1-type proteins. We found that B. distachyon, like other grasses, contains more ALDH2C/REF1 isoforms than A. thaliana and other dicotyledon species. Some amino acid residues in ALDH2C/REF1 isoforms were found as being conserved in dicotyledons but substituted by non-equivalent residues in monocotyledons. One example of those substitutions concerns a conserved phenylalanine and a conserved tyrosine in monocotyledons and dicotyledons, respectively. Protein structure modelling suggests that the presence of tyrosine would widen the substrate-binding pocket in the dicotyledons, and thereby influence substrate specificity. We discussed the importance of these findings as new hints to investigate why ferulic acid contents and cell wall digestibility differ between the dicotyledon and monocotyledon species.

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Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily of Gossypium raimondii

Cited by 25 publications

References 35 publications

Comparative genomic study of ALDH gene superfamily in Gossypium: A focus on Gossypium hirsutum under salt stress

Comparative genomic study of ALDH gene superfamily in Gossypium: A focus on Gossypium hirsutum under salt stress

Genome-wide characterization of the aldehyde dehydrogenase gene superfamily in soybean and its potential role in drought stress response

Active Sites of Reduced Epidermal Fluorescence1 (REF1) Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots

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