Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: Novel insights into synteny, structures, and transcript profiles

- Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea.
- The BoCNGC genes were differentially expressed in seven B.
- Full list of author information is available at the end of the article.
- 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0.
- Localized in the plasma membrane [6, 7], vacuole membrane [8], or nuclear envelope [9], CNGCs are controlled from inside the cell by secondary messen- gers such as Ca 2+ /calmodulin (CaM) and cyclic nucleotide monophosphates (cNMPs.
- A latest study of the A.
- We applied multiple tools and programs to complete in-depth ana- lyses of each CNGC gene family member, including an analysis of the physiological and biochemical properties of the encoded proteins.
- Our objective was to elucidate the diversification, expansion, and evolution of the CNGC gene family.
- For a complete overview of the B.
- thaliana CNGC genes as queries in BLAST searches of the Ensembl Plants database.
- Out of the 34 non-redundant putative gene sequences retrieved, eight gene accessions with truncated sequences or lacking CNGC -specific domains (CNBD and transmembrane) were eliminated from analyses (Additional file 1).
- Finally, 26 CNGC genes containing both essential domains (PF00520/PF07885 and PF00027) and a CNGC-specific motif were identified in the B.
- Of the 26 BoCNGC genes identified in the latest genome assembly version in Ensembl Plants, 16 and 24 were detected in earlier versions from Bolbase (v.1.3) and GenBank (v.2.1) respectively (Table 1)..
- The physiological and biochemical properties of the 26 BoCNGC proteins were determined by computing dif- ferent parameters, and are tabulated in Table 1.
- Phylogenetic analysis of BoCNGC genes.
- The sequence alignment revealed high similar- ity between the amino acid sequences of the three species, especially at the conserved domain regions (Additional file 2).
- The topology of the inferred max- imum likelihood scoring tree revealed that the BoCNGC gene family can be divided into four major groups (i.e., Groups I–IV), which are based on the A.
- Chromosomal distribution and diversification of BoCNGC genes.
- The 26 BoCNGC genes were mapped onto B.
- The BoCNGC genes were unevenly distributed, with some chromosomes (i.e., C1.
- Chromosome 6 did not carry any of the BoCNGC genes (Fig.
- We investigated gene duplication events to clarify the genome expansion mechanism of the B.
- An evaluation of the physical distance between BoCNGC gene loci revealed that eight genes (i.e., BoCNGC18 / BoCNGC19 , BoCNGC21/BoCNGC22/BoCNGC24 , and BoCNGC20/BoCNGC25/BoCNGC26 ) were tandemly du- plicated.
- The BoCNGC gene clusters likely formed via tandem and segmental duplication events may have expanded and enhanced the functional diversity of the gene family..
- Ten of the 20 AtCNGC genes were retained as a single copy in the equivalent blocks of both Brassica species.
- overlap/tandem repeat regions of the B.
- The mean Ka/Ks value of all orthologous gene pairs in the B.
- Most of the BoCNGC genes had Ka/Ks ratios greater than 1.
- 2 Chromosomal localization, synteny, and expansion of the B.
- a Physical locations and distances of the BoCNGC genes across the eight Brassica oleracea chromosomes.
- b Circos plot presenting gene duplication (tandem and segmental) events and synteny of the BoCNGC genes.
- The BoCNGC genes are presented as numbers on the B.
- Additional file 8).
- Additionally, there was a relatively conserved IQ domain and a less conserved CaMBD adjacent to a CNBD present in 24 of the 26 BoCNGC proteins.
- Two proteins (i.e., BoCNGC18 and BoCNGC19) were observed to lack the CaMBD and IQ domains because their sequences are truncated at the C-terminal end of the CNBD.
- Alignments between BoCNGCs, AtCNGCs, and BrCNGCs revealed a high se- quence divergence at the C-terminal of the CNBD, in which several Group IV-b members lack the CaMBD and IQ motif (Additional files 9 and 10).
- To characterise the structural diversity of the BoCNGC family members, we analysed the exon–intron organization of individual BoCNGC genes.
- The majority of the BoCNGC genes from phylogenetic Groups I–III contained six or seven exons, while the Group IV members had 8–11 exons (Fig.
- Closely clustered BoCNGC genes in the same clades were similar regard- ing the number of exons and intron lengths.
- Most of the introns in BoCNGC genes were phase 0 introns, which occur in between complete codons.
- A comparison between the exon–intron organizations of BoCNGC genes and the AtCNGC genes clustered in the same phylogenetic groups revealed several differences (Additional file 11).
- Most of the phase 1 introns were present in AtCNGC genes, implying that intron loss dur- ing evolution resulted in a decrease in the number of introns in BoCNGC genes, particularly those in Groups I – III and IV-a..
- The functions of the remaining motifs (i.e., 6, 8, and 9) remain to be determined..
- 4 Schematic diagram presenting the BoCNGC gene structures and the conserved motifs in the encoded proteins.
- The neighbour-joining phylogenetic tree is provided on the left side of the figure, followed by the exons – introns, which are indicated as red boxes and black lines, respectively.
- The order of the motifs corresponds to the motif positions in the protein sequence.
- However, the length of the box does not correspond to the length of the motif.
- Identifying the targets of the predicted microRNAs (miRNAs) may provide insights into the biological func- tions of miRNAs influencing plant development, signal transduction, and stress adaptations [43].
- These miRNAs were localized to the 3′ arm of the stem- loop hairpin structure.
- The accessibility of the target site varied from 2.883 (bol-miR838d) to 16.4 (bol-miR5021), where lower values correspond to a greater possibility of contact between the miRNA and target site.
- The major- ity of the genes were assigned to biological process (22), followed by molecular function (7) and cellular compo- nents (3).
- Of the 26 BoCNGCs , 19 were expressed at relatively high levels (fragments per kilobase of exon model per million mapped reads value >1) in at least one tissue, including 15 in the roots and si- liques, 16 in leaves, and 17 in stems, buds, and flowers.
- Some of the syntenic duplicates have di- verged in expression patterns indicating sunfunctiona- lization.
- Most of the Group III and IV genes were expressed at low levels in the leaves, stems, calli, roots, and siliques, while BoCNGC26 was not expressed in any tissue..
- A review of the reported expression profiles of ortho- logus Arabidopsis CNGCs in the tissues of wild and mutant plants suggest that a) the mRNAs of this gene family are expressed in all plant tissues, b) expression in leaves is greater than in roots, stem and flower, c) group-I, II and IV CNGCs are highly expressed in flowers and apex of Arabidopsis mutants (Additional file 21) [46].
- expression levels, including the up-regulation of the ex- pression of 10 BoCNGC genes in infiltrated seedlings, with the highest levels observed for BoCNGC21 .
- Interestingly, none of the Group III and IV-a genes were affected..
- The expression of 13 of the 26 BoCNGC genes was up-regulated in cold-stressed plants, although the expression levels were lower than the levels induced by Xcc (i.e., biotic stress) (Fig.
- Moreover, most of the duplicated gene pairs and genes en- coding interacting proteins produced similar expression pat- terns (especially in response to Xcc).
- oleracea CNGC genes, and de- termined that the BoCNGC gene family is larger than the CNGC families of most of the reported crops [4]..
- b Effect of biotic stress on the expression levels of BoCNGC genes in the leaves of 25 days old seedlings inoculated with Xanthomonas campestris pv.
- c Effect of abiotic stress on the expression levels of BoCNGC genes in the leaves of 25 days old seedlings subjected to cold stress at 4 °C for 24 h.
- between orthologs, and the ecology of the organism [48].
- where basic residues located on either side of membrane spanning region play a role in the stabilization of the protein in membrane [49].
- The net charge of a protein is a fundamental physical property, and its value directly influences the solubility, aggrega- tion, and crystallization of the protein [50].
- Because of the close relationship between B.
- Interestingly, we revealed the absence of the CaMBD and IQ domain in BoCNGC18 and BoCNGC19, which raised the possibil- ity that these were abnormal CNGC proteins.
- Additionally, of the 26 BoCNGC genes, nine in- cluded target sites for diverse groups of novel and con- served miRNAs.
- As a member of the classical triangle of U [62], the assembled genome of B.
- The less number of CNGC genes in Brassica genomes suggest that most of the duplicated gene copies were lost post- polyploidization.
- Reversion of the few duplicated CNGC genes to single copy might be due to neutral loss of un- necessary duplicates over time.
- Synteny analysis revealed that more than 80% of the BoCNGC genes are located in conserved syntenic blocks, which lost and gained some genes.
- Our findings suggest that the WGT and segmental du- plication events were important for the expansion of the B.
- To the best of our knowledge, this manuscript is the first to describe a comprehensive and systematic analysis of the B.
- Besides, our results might help in under- standing the functions of BoCNGCs related to the regu- lation of signal transduction pathways, and elucidate the expression profiles of the corresponding genes during plant development and stress responses.
- The results of the bioinformatics and comparative genomic analyses are also valuable for studying CNGC protein functions, with potential implications for the economic, agronomic, and ecological enhancement of B.
- The bioinformatics analysis and comparative genomic analysis also provides valuable information in the study of CNGC protein functions for the improvement of the economic, agronomic, and ecological benefits of Chin- ese cabbage.
- www.arabidopsis.org/) [67] were used as queries to per- form a homology-based search of the Ensembl Plants.
- This search was con- ducted with the default parameters of the BLASTP pro- gram.
- The identified BoCNGC genes were named ac- cording to their positions in the phylogenetic tree..
- Multiple sequence alignment and phylogenetic analysis The identified CNGC proteins were aligned using the default settings of the ClustalX 2.0 program [72].
- brad/) [73] using the default settings of the ClustalX 2.0 program.
- Chromosomal locations and gene duplication events Details regarding the chromosomal locations of the BoCNGC genes were obtained from the Ensembl Plants database.
- To investigate the BoCNGC expression profiles, we used the Illumina RNA-sequencing data available in the Gene Expression Omnibus database (accession number GSE42891) [24].
- The midvein of the first fully opened leaf (just above the petiole) was inoculated with the Xcc sus- pension using a 1-ml syringe.
- The lengths of each exon and intron can be mapped to the scale given in the bottom.
- Additional file 12: Functional annotation of the identified conserved MEME motifs.
- The heights of the amino acids indicates the degree of conservation.
- Additional file 18: Distribution of BoCNGC genes in major functional terms (GO terms Level 2) for categories Molecular Function (a), Biological Process (b) and Cellular Component (c).
- The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript..
- The transcriptomic data of BoCNGC genes used in current analyses are available in the Gene Expression Omnibus database (accession number GSE42891)..
- Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys Edulis).
- Genomic characterization, phylogenetic comparison and differential expression of the cyclic nucleotide-gated channels gene family in pear (Pyrus bretchneideri Rehd.
- Regulatory roles of conserved phosphorylation sites in the activation T-loop of the MAP kinase ERK1.
- Substrate preference and phosphatidylinositol monophosphate inhibition of the catalytic domain of the per-Arnt-Sim domain kinase PASKIN.
- Network organization of the human autophagy system.
- The roles of post-translational modifications in the context of protein interaction networks.
- Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex.
- High-throughput sequencing identification of novel and conserved miRNAs in the Brassica Oleracea leaves.
- Deciphering the diploid ancestral genome of the mesohexaploid Brassica Rapa

Xem thử không khả dụng, vui lòng xem tại trang nguồn
hoặc xem Tóm tắt