Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes

Verma, Jitendra Kumar; Wardhan, Vijay; Singh, Deepali; Chakraborty, Subhra; Chakraborty, Niranjan

doi:10.3390/genes9040183

Cited by 23 publications

(60 citation statements)

References 78 publications

(101 reference statements)

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“…The exon/intron structure of GH3 genes was analyzed by comparing the coding DNA sequences (CDS) and the genomic sequences using the GSDS 2.0 (). The Multiple Expectation Maximization for motif Elicitation (MEME, ) tool was used to predict conserved motifs of GH3 proteins with these parameters: the number of motifs (20) and other parameters (default values) [27,29,30]. Gene structure and conserved motifs were visualized using TBtools [32].…”

Section: Methodsmentioning

confidence: 99%

Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Kong

Zhong

Deng

et al. 2019

Plants

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Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.

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Section: Methodsmentioning

confidence: 99%

Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Kong

Zhong

Deng

et al. 2019

Plants

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“…Multiple alignments with other plants species ( A. thaliana , S. tuberosum ) were conducted by Clustal W and phylogenetic dendrogram was generated by MEGA 6.0 using the Maximum Likelihood (ML) method with 1000 bootstrap replicates [ 67 , 68 , 69 ]. In order to obtain correct classification, the same Caryophyllales species Beta vulgaris L. also was used for phylogenetic analysis with carnation [ 6 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Aquaporins and Their Role in the Flower Opening Processes in Carnation (Dianthus caryophyllus)

Kong

Bendahmane

2018

Molecules

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Aquaporins (AQPs) are associated with the transport of water and other small solutes across biological membranes. Genome-wide identification and characterization will pave the way for further insights into the AQPs’ roles in the commercial carnation (Dianthus caryophyllus). This study focuses on the analysis of AQPs in carnation (DcaAQPs) involved in flower opening processes. Thirty DcaAQPs were identified and grouped to five subfamilies: nine PIPs, 11 TIPs, six NIPs, three SIPs, and one XIP. Subsequently, gene structure, protein motifs, and co-expression network of DcaAQPs were analyzed and substrate specificity of DcaAQPs was predicted. qRT-PCR, RNA-seq, and semi-qRTRCR were used for DcaAQP genes expression analysis. The analysis results indicated that DcaAQPs were relatively conserved in gene structure and protein motifs, that DcaAQPs had significant differences in substrate specificity among different subfamilies, and that DcaAQP genes’ expressions were significantly different in roots, stems, leaves and flowers. Five DcaAQP genes (DcaPIP1;3, DcaPIP2;2, DcaPIP2;5, DcaTIP1;4, and DcaTIP2;2) might play important roles in flower opening process. However, the roles they play are different in flower organs, namely, sepals, petals, stamens, and pistils. Overall, this study provides a theoretical basis for further functional analysis of DcaAQPs.

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“…Alba family proteins have been found to bind the DNA with no sequence specificity (Aravind et al, 2003; Kumar Verma et al, 2018). Moreover, the Alba proteins also do interact with diverse kinds of ribonucleic acid (RNA) and in addition to a number of ribonucleo-protein complexes, such as ribosomal ribonucleic acid (rRNA) and messenger ribonucleic acid (mRNA) (Xue et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

Knockdown of ghAlba_4 and ghAlba_5 Proteins in Cotton Inhibits Root Growth and Increases Sensitivity to Drought and Salt Stresses

Magwanga

Kirungu

et al. 2019

Front. Plant Sci.

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We found 33, 17, and 20 Alba genes in Gossypium hirsutum, Gossypium arboretum, and Gossypium raimondii, respectively. The Alba protein lengths ranged from 62 to 312 aa, the molecular weight (MW) from 7.003 to 34.55 kDa, grand average hydropathy values of −1.012 to 0.609 and isoelectric (pI) values of −3 to 11. Moreover, miRNAs such as gra-miR8770 targeted four genes, gra-miR8752 and gra-miR8666 targeted three genes, and each and gra-miR8657 a, b, c, d, e targeted 10 genes each, while the rests targeted 1 to 2 genes each. Similarly, various cis-regulatory elements were detected with significant roles in enhancing abiotic stress tolerance, such as CBFHV (RYCGAC) with a role in cold stress acclimation among others. Two genes, Gh_D01G0884 and Gh_D01G0922, were found to be highly induced under water deficit and salt stress conditions. Through virus-induced gene silencing (VIGS), the VIGS cotton plants were found to be highly susceptible to both water deficit and salt stresses; the VIGS plants exhibited a significant reduction in root growth, low cell membrane stability (CMS), saturated leaf weight (SLW), chlorophyll content levels, and higher excised leaf water loss (ELWL). Furthermore, the stress-responsive genes and ROS scavenging enzymes were significantly reduced in the VIGS plants compared to either the wild type (WT) and or the positively controlled plants. The VIGS plants registered higher concentration levels of hydrogen peroxide and malondialdehyde, with significantly lower levels of the various antioxidants evaluated an indication that the VIGS plants were highly affected by salt and drought stresses. This result provides a key foundation for future exploration of the Alba proteins in relation to abiotic stress.

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Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes

Cited by 23 publications

References 78 publications

Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Genome-Wide Identification and Characterization of Aquaporins and Their Role in the Flower Opening Processes in Carnation (Dianthus caryophyllus)

Knockdown of ghAlba_4 and ghAlba_5 Proteins in Cotton Inhibits Root Growth and Increases Sensitivity to Drought and Salt Stresses

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