Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure

Identification and Bioinformatic Analysis of CAMTA Genes in Olive (Olea europaea L.)

“…Özbilen / Uluslararası Fen Araştırmalarında Yenilikçi Yaklaşımlar Dergisi / International Journal of Innovative Approaches in Science Research, 2021, Vol. 6 (2), 64-78 74 Linum usitatissimum (Ali et al, 2020), 18 for Oryza sativa (Gain et al, 2022) and 7 for Solanum lycopersicum (Fang et al, 2022).…”

“…In some genome-wide identification studies, CAMTA genes are grouped due to their existence on specific chromosomes (Shangguan et al, 2014;Yuan et al, 2021;Gain et al, 2022) however in olive they all are located at different chromosomes. While in A. thaliana CAMTA genes from 1 to 6 have 12, 13, 14, 13, 13 and 10 exons in their number one splice variant, respectively, olive OeCAMTA1a has 10, OeCAMTA2a has 10, OeCAMTA2 has 12, OeCAMTA3 has 13, OeCAMTA4a has 4, OeCAMTA4b has 18 and OeCAMTA5 has 13 exons.…”

“…To understand the phylogenetic relationship of olive CAMTAs, an unrooted phylogenetic tree is drawn and it is noticed that CAMTA proteins are grouped in 4 main branches and every branch contained A. thaliana CAMTA1 is present predominantly in the nuclei (Bouche et al, 2002). Also, in Fragaria × ananassa (Leng et al, 2015), P. trichocarpa (Wei et al, 2017), Gossypium species (Pant et al, 2018), in Triticum aestivum (Yang et al, 2020), in Linum usitatissimum (Ali et al, 2020), Oryza sativa (Gain et al, 2022) it was bioinformatically shown that CAMTAs are mostly localized in the nucleus.…”

“…Thanks to genome sequencing and bioinformatic tools, many CAMTAs were identified in various plant species. For the phylogenetic analysis, CAMTA protein sequences of A. thaliana (Yang and Poovaiah, 2002), Citrus species (Zhang et al, 2019), Glycine max (Wang et al, 2015), Linum usitatissimum (Ali et al, 2020), Nicotiana tabacum (Kakar et al,2018), Oryza sativa (Gain et al, 2022), Phaseolus vulgaris (Büyük et al, 2019), Populus trichocarpa (Wei et al, 2017), Solanum lycopersicum (Fang et al, 2022) and Vitis vinifera (Shangguan et al, 2014) were downloaded from NCBI (National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/) and from Phytozome v13 (https://phytozome-next.jgi.doe.gov/) databases. These sequences were aligned with olive sequences using MUSCLE algorithm (Edgar, 2004) in Geneious software with default parameters.…”

“…Since CAMTAs are first discovered in tobacco (Yang and Poovaiah, 2000), this gene family is studied widely in numerous plant species such as: Arabidopsis thaliana (Yang and Poovaiah, 2002), Vitis vinifera (Shangguan et al, 2014), Glycine max (Wang et al, 2015), Populus trichocarpa (Wei et al, 2017), Citrus species (Zhang et al, 2019), Phaseolus vulgaris (Büyük et al, 2019), Linum usitatissimum (Ali et al, 2020), Oryza sativa (Gain et al, 2022) and Solanum lycopersicum (Fang et al, 2022). CAMTAs are found to be involved in lots of biological process like drought (Pandey et al, 2013;Kakar et al, 2018;Zhang et al, 2019), cold (Doherty et al, 2009;Kim et al, 2013;Wei et al, 2017;Kakar et al, 2018;Primo-Capella et al, 2021), salt stress (Wei et al, 2017;Büyük et al, 2019;Zhang et al, 2019;Yuan et al, 2021), wounding or pathogenic invasions (Nie et al, 2012;Wei et al, 2017;Kakar et al, 2018), hormone signaling (Wei et al, 2017;Zhang et al, 2019), ethylene signaling and fruit ripening (Yang et al, 2012).…”