Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum

Baruah, Pooja Moni; Krishnatreya, Debasish B.; Bordoloi, Kuntala Sarma; Gill, Sarvajeet Singh; Agarwala, Niraj

doi:10.1016/j.plaphy.2021.02.031

Cited by 46 publications

(30 citation statements)

References 92 publications

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“…The accumulation of K + and its movement from soil to other plant parts are followed by the involvement of a complex potassium transport system, which consists of various transporters and channels [8]. Genome-wide identification and characterization studies have revolutionized our understanding of gene families in several plants [8][9][10][11][12][13]. Thirty-five genes previously reported in A. thaliana are now considered K + transporting proteins [9,10].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Genomic Organization, and Characterization of Potassium Transport-Related Genes in Cajanus cajan and Their Role in Abiotic Stress

Siddique

Babar

Zameer

et al. 2021

Plants

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Potassium is the most important and abundant inorganic cation in plants and it can comprise up to 10% of a plant’s dry weight. Plants possess complex systems of transporters and channels for the transport of K+ from soil to numerous parts of plants. Cajanus cajan is cultivated in different regions of the world as an economical source of carbohydrates, fiber, proteins, and fodder for animals. In the current study, 39 K+ transport genes were identified in C. cajan, including 25 K+ transporters (17 carrier-like K+ transporters (KUP/HAK/KTs), 2 high-affinity potassium transporters (HKTs), and 6 K+ efflux transporters (KEAs) and 14 K+ channels (9 shakers and 5 tandem-pore K+ channels (TPKs). Chromosomal mapping indicated that these genes were randomly distributed among 10 chromosomes. A comparative phylogenetic analysis including protein sequences from Glycine max, Arabidopsis thaliana, Oryza sativa, Medicago truncatula Cicer arietinum, and C. cajan suggested vital conservation of K+ transport genes. Gene structure analysis showed that the intron/exon organization of K+ transporter and channel genes is highly conserved in a family-specific manner. In the promoter region, many cis-regulatory elements were identified related to abiotic stress, suggesting their role in abiotic stress response. Abiotic stresses (salt, heat, and drought) adversely affect chlorophyll, carotenoids contents, and total soluble proteins. Furthermore, the activities of catalase, superoxide, and peroxidase were altered in C. cajan leaves under applied stresses. Expression analysis (RNA-seq data and quantitative real-time PCR) revealed that several K+ transport genes were expressed in abiotic stress-responsive manners. The present study provides an in-depth understanding of K+ transport system genes in C. cajan and serves as a basis for further characterization of these genes.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Genomic Organization, and Characterization of Potassium Transport-Related Genes in Cajanus cajan and Their Role in Abiotic Stress

Siddique

Babar

Zameer

et al. 2021

Plants

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“…The genome-wide identification of a gene family has been successfully applied to numerous gene families in plants. For example, the AT-Hook Motif Nuclear Localized gene family and β-Ketoacyl CoA synthetase gene family were identified in Glycine max L. [ 27 ] and Hordeum vulgare L. [ 28 ], respectively, from which the biochemical characteristics, gene structure, evolutionary relationships, and expression patterns of these gene families’ members could be deduced. Furthermore, the assignment of biological functions to each member of the gene family is attractive.…”

Section: Introductionmentioning

confidence: 99%

Genomic-Wide Identification and Characterization of the Uridine Diphosphate Glycosyltransferase Family in Eucommia ulmoides Oliver

Ouyang

Wang

Tang

et al. 2021

Plants

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Eucommia ulmoides Oliver is a woody plant with great economic and medicinal value. Its dried bark has a long history of use as a traditional medicinal material in East Asia, which led to many glycosides, such as aucubin, geniposide, hyperoside, astragalin, and pinoresinol diglucoside, being recognized as pharmacologically active ingredients. Uridine diphosphate glycosyltransferases (UGTs) catalyze a glycosyl-transferring reaction from the donor molecule uridine-5′-diphosphate-glucose (UDPG) to the substrate, which plays an important role in many biological processes, such as plant growth and development, secondary metabolism, and environmental adaptation. In order to explore the biosynthetic pathways of glycosides in E. ulmoides, 91 putative EuUGT genes were identified throughout the complete genome of E. ulmoides through function annotation and an UDPGT domain search. Phylogenetic analysis categorized them into 14 groups. We also performed GO annotations on all the EuUGTs to gain insights into their functions in E. ulmoides. In addition, transcriptomic analysis indicated that most EuUGTs showed different expression patterns across diverse organs and various growing seasons. By protein–protein interaction predication, a biosynthetic routine of flavonoids and their glycosides was also proposed. Undoubtedly, these results will help in future research into the biosynthetic pathways of glycoside compounds in E. ulmoides.

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“…According to the expression profile, 186 known lncRNAs, and 89 novel lncRNAs were found associated with pistil development in Prunus mume , which could provide new indications to elucidate how lncRNAs and their targets play role in pistil differentiation and flower development [ 36 ], highlighting the potential contributions of lncRNA in the flowering process. Although, for a better understanding of the functions lncRNAs and their target genes, several research works are carried out to identify abiotic stress responsive lncRNAs (In direct connection with flowering) under different conditions in many plants including Camellia sinensis [ 37 , 38 ], Capsicum annuum [ 39 ], Mangifera indica [ 40 ], Arachis hypogaea Linn [ 41 ], Zea mays [ 42 ], a substantial number of databases have been also developed to provide resources and broadly investigate lncRNAs in plants [ 20 , 43 – 45 ].…”

Section: Introductionmentioning

confidence: 99%

Global identification of long non-coding RNAs involved in the induction of spinach flowering

et al. 2021

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Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach.

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Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum

Cited by 46 publications

References 92 publications

Genome-Wide Identification, Genomic Organization, and Characterization of Potassium Transport-Related Genes in Cajanus cajan and Their Role in Abiotic Stress

Genome-Wide Identification, Genomic Organization, and Characterization of Potassium Transport-Related Genes in Cajanus cajan and Their Role in Abiotic Stress

Genomic-Wide Identification and Characterization of the Uridine Diphosphate Glycosyltransferase Family in Eucommia ulmoides Oliver

Global identification of long non-coding RNAs involved in the induction of spinach flowering

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