Why lncRNAs were not conserved? Is it for adaptation?

Karlık, Elif

doi:10.51753/flsrt.1027595

Cited by 2 publications

(2 citation statements)

References 81 publications

(89 reference statements)

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“…To date, 7970 among 19,908 lncRNAs have been annotated by CANTATAdb [15,16]. Annotation and sequencing studies revealed that CNT0018772 had two exon and one intron, while sequencing data of cDNA did not contain any intron part, indicating that this lncRNA may undergo the excision of introns or alternative splicing [17]. According to our previous studies, expression analysis of CNT0018772 and CNT0031477 demonstrated that these two lncRNAs were affected by salt stress.…”

Section: Introductionmentioning

confidence: 90%

Dilemmas between barley cultivars under salinity stress

Karlık¹

2022

Sigma J Eng Nat Sci - Sigma Müh Fen Bil Derg

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Salinity is one of reasons causing the greatest yield-reducing factors leads various physiological and biochemical effects. Recently, long non-coding RNAs (lncRNAs) became prominent as crucial regulators in various biological processes, including developmental processes and stress responses such as salinity. In this study, physiological responses of four Hordeum vulgare L. cvs genotypes (Beyşehir 99, Hasat, Konevi 98 and Tarm 92) were assessed for 150 mM salinity treatment for 3 days germination period, maize (CNT0018772) and rice (CNT0031477) lncRNAs localizations in barley chromosomes via fluorescence in situ hybridization (FISH). Physiological responses of barley varieties, including root and shoot heights, fresh and dry weights, water content (WC) and protein content were affected differently by 150 mM salinity stress. The germination percentage of Beyşehir 99 and Tarm 92 reduced while Konevi 98 was slightly increased. However, proline content changed only in Beyşehir 99. According to FISH results, the localizations of CNT0018772 and CNT0031477 were revealed up 6 and 8 signals, respectively. This study may contribute new insight into lncRNAs functions underlying the salinity tolerance mechanisms in different barley varieties.

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Section: Introductionmentioning

confidence: 90%

Dilemmas between barley cultivars under salinity stress

Karlık¹

2022

Sigma J Eng Nat Sci - Sigma Müh Fen Bil Derg

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“…The multi-exon homologs were probed for intron-exon size variation and such pairs were selected for identification of splice site and SRP protein site mutations (Kharabian, 2010;Karlik, 2021) through ESEfinder2.0 (http://krainer01.cshl.edu/tools/ ESE2/). The cut-off for splice donor and splice acceptor sites was kept at 6.9 and for branch site was 2.0.…”

Section: Alternative Splicing and Proteinprotein Interactionmentioning

confidence: 99%

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

Parakkunnel¹,

K²,

Girimalla³

et al. 2022

Front. Plant Sci.

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Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.

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Why lncRNAs were not conserved? Is it for adaptation?

Cited by 2 publications

References 81 publications

Dilemmas between barley cultivars under salinity stress

Dilemmas between barley cultivars under salinity stress

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

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