Genome-Wide Identification and Analyses of Calmodulins and Calmodulin-like Proteins in Lotus japonicas

Abstract

L. japonicus, a model plant of legumes plants, is widely used in symbiotic nitrogen fixation. A large number of studies on it have been published based on the genetic, biochemical, structural studies. These results are secondhand reports that CaM is a key regulator during Rhizobial infection. In plants, there are multiple CaM genes encoding several CaM isoforms with only minor amino acid differences. Moreover, the regulation mechanism of this family of proteins during rhizobia infection is still unclear. In the current study, a family of genes encoding CaMs and CMLs that possess only the Ca2+-binding EF-hand motifs were analyzed. Using ML and BI tree based on amino acid sequence similarity, seven loci defined as CaMs and 19 CMLs, with at least 23% identity to CaM, were identified. The phylogenetics, gene structures, EF hand motif organization, and expression characteristics were evaluated. Seven CaM genes, encoding only 4 isoforms, were found in L. japonicus. According to qRT-PCR, four LjCaM isoforms are involved in different rhizobia infection stages. LjCaM1 might be involved in the early rhizobia infection epidermal cells stage. Furthermore, additional structural differences and expression behaviors indicated that LjCMLs may have different potential functions from LjCaMs.

Genome-Wide Analyses of Calcium Sensors Reveal Their Involvement in Drought Stress Response and Storage Roots Deterioration after Harvest in Cassava

“…Phylogenetic analyses showed that cassava CaMs, CMLs, and CBLs could be divided into two, four and four groups, respectively. together with those in Arabidopsis and rice ( Figure 1 ), which is consistent with previous phylogenetic classification of CaMs, CMLs, and CBLs in Arabidopsis , rice, strawberry, cotton, grapevine, and Lotus japonicus [ 22 , 23 , 25 , 50 ]. Moreover, this classification was also validated by conserved motif analysis, which indicated that all the identified CaMs, CMLs, and CBLs contained the typical EF-hand, and each subfamily shared similar motifs and exon-intron organizations ( Figure 2 and Figure 3 ).…”

“…Currently, based on genome-wide analysis, Ca 2+ sensors have been identified in various species [ 21 , 22 , 23 , 24 , 25 , 26 ]. There are 10 CBLs in Arabidopsis and 10 in rice, seven CaMs in Arabidopsis and five in rice, and 50 CMLs in Arabidopsis and 32 in rice.…”

Revealing the full-length transcriptome of caucasian clover rhizome development

“…These secondary metabolites are crucial for plant growth [ 44 ]. Similar to the rhizome of other plants ( Oryza longistaminata and Miscanthus lutarioriparius ) [ 12 , 19 ], some basal metabolism plays an important role in the rhizome of caucasian clover, for example, carbon metabolism (1389) and starch and sucrose metabolism (1189)(Fig. 2 c).…”

“…Growing evidence indicates that hormones affect tillering growth and the formation of storage organs [ 12 , 61 ]. Yi Kun’s research illustrated that 600 mg·L - 1 GA3 can promote the growth and development of caucasian clover rhizome and increase the contents of endogenous IAA, ZT and GA 3 [ 62 ].…”

“…In plants without reference genomes, high-throughput RNA sequencing (RNA-seq) technology has become a fast and effective way to master the molecular mechanisms of plants for research purposes [ 12 – 14 ]. This technology has been applied to the study of various rhizomatous species such as sorghum ( Sorghum halepense and Sorghum propinquum ) [ 15 , 16 ], bamboo ( Phyllostachys praecox ) [ 17 ], Oryza longistaminata [ 18 – 20 ], Equisetum hyemale [ 21 ], Panax ginseng [ 22 ], Phragmites australis [ 23 ], tropical lotus ( Nelumbo nucifera ) [ 24 ], CangZhu ( Atractylodes lacea ) [ 25 ], Ligusticum chuanxiong [ 26 ], ginger ( Zingiber officinale ) [ 27 ], and Miscanthus lutarioriparius [ 12 ]. Studies have shown that plant rhizomes are rich in growth regulators, which are related to the energy, metabolism, and hormones pathways of rhizome development.…”