Genome-wide Identification and Expression Analysis of CaM/CML Gene Family in Sacred Lotus (Nelumbo nucifera)

Gao, Li; Damaris, Rebecca Njeri; Yu, Feng; Yang, Pingfang

doi:10.1007/s11105-021-01330-6

Cited by 5 publications

(4 citation statements)

References 66 publications

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“…Our study indicated that a few CML genes ( CsCML3 , 15 , 16 , 17 , 19 , 21 , 28 , 30 , 32 , and 34 ) contained myristoylation and/or palmitoylation sites, which may cause CML conformation changes and promote protein–membrane and protein–protein interactions. CMLs were reported localized in various parts; in this study, the CsCML proteins were mainly localized in the nucleus and cytoplasmic, which was in consonance with lotus ( Gao et al, 2022 ). CMLs mediate Ca 2+ signal transduction by binding with Ca 2+ to form CML/Ca 2+ complex compounds.…”

Section: Discussionsupporting

confidence: 77%

Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber

Liu

Yin

Liao

et al. 2023

PeerJ

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Background The calmodulin-like (CML) protein is a crucial Ca2+-binding protein that can sense and conduct the Ca2+ signal in response to extracellular stimuli. The CML protein families have been identified and characterized in many species. Nevertheless, scarce information on cucumber CML is retrievable. Methods In this study, bioinformatic analyses, including gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny, were comprehensively performed to identify and characterize CsCML gene members. Spatiotemporal expression analysis in different organs and environment conditions were assayed with real-time quantitative polymerase chain reaction (qRT-PCR). Results Forty-four CsCMLs family members were well characterized, and the results showed that the 44 CsCML proteins contained one to four EF-hand domains without other functional domains. Most of the CsCML proteins were intron-less and unevenly distributed on seven chromosomes; two tandemly duplicated gene pairs and three segmentally duplicated gene pairs were identified in the cucumber genome. Cis-acting element analysis showed that the hormone, stress, and plant growth and development-related elements were in the promotor regions. In addition, spatiotemporal expression analysis revealed distinctive expression patterns for CsCML genes in different tissues and environmental conditions, and a putative protein interaction network also confirmed their potential role in responding to various stimuli. These results provide a foundation for understanding CsCMLs and provide a theoretical basis for further study of the physiological functions of CsCMLs.

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Section: Discussionsupporting

confidence: 77%

Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber

Liu

Yin

Liao

et al. 2023

PeerJ

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“…The predicted number of EF-hands were four in PbCaM s and two–four in PbCML s, which is consistent with those in apple [ 40 ]. Based on phylogenetic relationships, PbCaM/CML proteins were clustered into 11 subgroups ( Figure 1 ), which was the same as that of B. napus [ 17 ], less than Nelumbo nucifera (twelve subgroups) [ 41 ], and more than wheat (seven subgroups) [ 38 ]. All PbCaM genes were clustered in a unique subgroup.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of Calmodulin and Calmodulin-like Genes, Revealing CaM3 and CML13 Participating in Drought Stress in Phoebe bournei

Fu,

Wang,

Han

et al. 2023

IJMS

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Calmodulin (CaM) and calmodulin-like (CML) proteins are major Ca2+ sensors involved in the regulation of plant development and stress responses by converting Ca2+ signals into appropriate cellular responses. However, characterization and expression analyses of CaM/CML genes in the precious species, Phoebe bournei, remain limited. In this study, five PbCaM and sixty PbCML genes were identified that only had EF-hand motifs with no other functional domains. The phylogenetic tree was clustered into 11 subgroups, including a unique clade of PbCaMs. The PbCaMs were intron-rich with four EF-hand motifs, whereas PbCMLs had two to four EF-hands and were mostly intronless. PbCaMs/CMLs were unevenly distributed across the 12 chromosomes of P. bournei and underwent purifying selection. Fragment duplication was the main driving force for the evolution of the PbCaM/CML gene family. Cis-acting element analysis indicated that PbCaMs/CMLs might be related to hormones, growth and development, and stress response. Expression analysis showed that PbCaMs were generally highly expressed in five different tissues and under drought stress, whereas PbCMLs showed specific expression patterns. The expression levels of 11 candidate PbCaMs/CMLs were responsive to ABA and MeJA, suggesting that these genes might act through multiple signaling pathways. The overexpression of PbCaM3/CML13 genes significantly increased the tolerance of yeast cells to drought stress. The identification and characterization of the CaM/CML gene family in P. bournei laid the foundation for future functional studies of these genes.

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“…Among the various calcium sensor proteins reported, CaM and CMLs are the most conserved and the major calcium receptor proteins in plants. Although the analyses of CaM/CML gene family in several plant species have been conducted by genome-wide survey, including Arabidopsis [10], rice [12], tomato [13,47], lotus [18], cabbage [48], apple [14], and wheat [40], there has been no systematic study of CaM/CML genes in C. sinensis. In Ma's report, only 5 CsCMLs were identified in the tea plant, although the details of these genes are unclear [19].…”

Section: Discussionmentioning

confidence: 99%

“…As a result of genome sequencing in several plant species, the CaM/CML gene family has been characterized at the genome-wide level. A total of 7 AtCaM and 50 AtCML have been identified in Arabidopsis [10], 5 OsCaM and 32 OsCML in rice (Oryza sativa) [12], 6 SpCaM and 45 SpCML in wild tomato (Solanum pennellii) [13], 4 MdCaM and 58 MdCML in apple (Malus x domestica) [14], 3 VviCaM and 62 VviCML in grapevine (Vitis vinifera) [15], 25 BnaCaM and 168 BnaCML in Brassica napus [16], 8 MeCaM and 48 MeCML in cassava (Manihot esculenta) [17], and 34 CaM/CML genes in lotus (Nelumbo nucifera) [18]. However, the bioinformatics of the CaM and CML families in Camellia sinensis have not yet been thoroughly investigated.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Calmodulin and Calmodulin-like Genes Family in Tea Plant and Their Roles under Abiotic Stress

Kang

Zhao

Wang

et al. 2022

Forests

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As an important Ca2+ sensor, calmodulin (CaM) and calmodulin-like protein (CML) play core roles in plant growth, development, and response to environmental stimuli. The CaM/CML gene family has been well characterized in various plant species, such as Arabidopsis thaliana, rice, and tomato; however, in the tea plant, the CaM/CML gene family has not been systematically and comprehensively characterized. In the present study, a total of 5 CsCaM and 60 CsCML proteins were identified from the tea plant genome, which were unevenly distributed on the 14 chromosomes of the tea plant. All the proteins contained two to four EF-hand domains. Meanwhile, an integrated analysis of physicochemical properties, sequence structure, motif identification, phylogeny, gene duplication, promoter cis-elements, and RNA-seq expression profiles in the CsCaM/CML gene family was performed. Transcriptome analysis revealed that CsCaM/CMLs were differentially expressed in different tissues of the tea plant, suggesting their potential roles in plant growth and development. The expression profiles associated with various stress treatments revealed that CsCaM/CML genes were involved in a wide range of abiotic factors, including cold and drought stress. Quantitative real-time PCR (qRT-PCR) was also used to validate the differences in expression under abiotic stress. Overall, these findings enhanced our understanding of CsCaM/CML genes and provided useful information for further research into their molecular functions in abiotic stress response, and in multiple physiological processes in the tea plant.

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Genome-wide Identification and Expression Analysis of CaM/CML Gene Family in Sacred Lotus (Nelumbo nucifera)

Cited by 5 publications

References 66 publications

Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber

Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber

Genome-Wide Identification and Expression Analysis of Calmodulin and Calmodulin-like Genes, Revealing CaM3 and CML13 Participating in Drought Stress in Phoebe bournei

Genome-Wide Identification and Characterization of Calmodulin and Calmodulin-like Genes Family in Tea Plant and Their Roles under Abiotic Stress

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