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Çakır Ö, Arıkan B, Karpuz B, Turgut-Kara N. Expression analysis of miRNAs and their targets related to salt stress in Solanum lycopersicum H-2274. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2020.1870871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Özgür Çakır
- Department of Molecular Biology and Genetics, Science Faculty, İstanbul University, Istanbul, Turkey
| | - Burcu Arıkan
- Department of Molecular Biology and Genetics, Science Faculty, İstanbul University, Istanbul, Turkey
| | - Burcu Karpuz
- Programme of Molecular Biology and Genetics, Institute of Science, Istanbul University, Istanbul, Turkey
| | - Neslihan Turgut-Kara
- Department of Molecular Biology and Genetics, Science Faculty, İstanbul University, Istanbul, Turkey
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Cardoso TCDS, Alves TC, Caneschi CM, Santana DDRG, Fernandes-Brum CN, Reis GLD, Daude MM, Ribeiro THC, Gómez MMD, Lima AA, Gomes LAA, Gomes MDS, Gandolfi PE, Amaral LRD, Chalfun-Júnior A, Maluf WR, de Souza Gomes M. New insights into tomato microRNAs. Sci Rep 2018; 8:16069. [PMID: 30375421 PMCID: PMC6207730 DOI: 10.1038/s41598-018-34202-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.
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Affiliation(s)
- Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Tamires Caixeta Alves
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Carolina Milagres Caneschi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Douglas Dos Reis Gomes Santana
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | | | - Gabriel Lasmar Dos Reis
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus Martins Daude
- Laboratory of Molecular Analysis, Federal University of Tocantins (UFT), Gurupi, 77402-970, Brazil
| | | | - Miguel Maurício Díaz Gómez
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - André Almeida Lima
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | | | - Marcos de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Peterson Elizandro Gandolfi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Antonio Chalfun-Júnior
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | - Wilson Roberto Maluf
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil.
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Taneja M, Upadhyay SK. Molecular characterization and differential expression suggested diverse functions of P-type II Ca 2+ATPases in Triticum aestivum L. BMC Genomics 2018; 19:389. [PMID: 29792165 PMCID: PMC5966885 DOI: 10.1186/s12864-018-4792-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
Background Plant P-type II Ca2+ATPases are formed by two distinct groups of proteins (ACAs and ECAs) that perform pumping of Ca2+ outside the cytoplasm during homeostasis, and play vital functions during development and stress management. In the present study, we have performed identification and characterisation of P-type II Ca2+ATPase gene family in an important crop plant Triticum aestivum. Results Herein, a total of 33 TaACA and 9 TaECA proteins were identified from the various chromosomes and sub-genomes of Triticum aestivum. Phylogenetic analysis revealed clustering of the homoeologous TaACA and TaECA proteins into 11 and 3 distinct groups that exhibited high sequence homology and comparable structural organization as well. Both TaACA and TaECA group proteins consisted of eight to ten transmembrane regions, and their respective domains and motifs. Prediction of sub-cellular localization was found variable for most of the proteins; moreover, it was consistent with the evolutionarily related proteins from rice and Arabidopsis in certain cases. The occurrence of assorted sets of cis-regulatory elements indicated their diverse functions. The differential expression of various TaACA and TaECA genes during developmental stages suggested their roles in growth and development. The modulated expression during heat, drought, salt and biotic stresses along with the occurrence of various stress specific cis-regulatory elements suggested their association with stress response. Interaction of these genes with numerous development and stress related genes indicated their decisive role in various biological processes and signaling. Conclusion T. aestivum genome consisted of a maximum of 42 P-type II Ca2+ATPase genes, derived from each A, B and D sub-genome. These genes may play diverse functions during plant growth and development. They may also be involved in signalling during abiotic and biotic stresses. The present study provides a comprehensive insight into the role of P-type II Ca2+ATPase genes in T. aestivum. However, the specific function of each gene needs to be established, which could be utilized in future crop improvement programs. Electronic supplementary material The online version of this article (10.1186/s12864-018-4792-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mehak Taneja
- Department of Botany, Panjab University, Chandigarh, 160014, India
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