- Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus. - Therefore, this study used a bioinformatics approach to conduct the systematic comparative genomics analysis of TLP gene family in B. - Instead, an indirect expansion of TLP gene family occurred in its two diploid parents. - In addition, the study further utilized RNA-seq to detect the expression pattern of TLP genes between different tissues and two subgenomes.. - Conclusions: This study systematically conducted the comparative analyses of TLP gene family in B. - It provided rich gene resources for exploring the molecular mechanism of TLP gene family. - Until now, the TLP gene family of B. - The Tubby gene was first isolated by positional cloning in obese mice, subsequently, other members of TLP gene family were successively identi- fied [10, 12]. - TLP gene family members contained a tubby domain about 270 amino acids in the C-terminal, and a plurality of different domains in the N-terminal. - Di- versity of the N-terminal indicated the diversity functions of TLP genes [11, 15]. - The hydrophobic α-helix was located at the C-terminus of TLP protein [16, 17]. - Unlike the diversity of N-terminal struc- tures in animals, the N-terminus of TLP protein in plants often contained a conserved F-box domain [16, 18]. - thaliana, Zea mays, Malus domestica, Cicer arietinum and other plants, a genome-wide TLP gene family has been studied [27–30]. - Identification and comparative analysis of TLP gene family in B. - In order to explore the structure and biological function of TLP family genes in B.. - thaliana corresponding genes (E-value<7E-136 ~ 0), which provided a good guidance for studying the function of TLP family genes in B. - Chromosome distribution analysis of TLP family genes in B. - To more intuitively understand the distribution of TLP family genes on the chromosomes of B. - Conservative motif and gene structure analyses of TLP gene family. - napus, indicating its presence or absence as a marker for the identification of TLP genes. - This indicated that these conserved motifs were relatively conservative and might play a very important role in the function of TLP gene family. - Gene structure analysis showed that TLP gene family structure Table 1 The summary of TLP gene family members in B. - 1 Phylogenetic relationship and chromosome distribution analyses of TLP gene family. - a The construction of phylogenetic tress using the TLP gene family among B. - 2 The converted motif and gene structure analyses of TLP gene family in B. - a The motif identification of TLP gene family in B. - b The gene structure of TLP gene family in B. - We further analyzed the orthologous and paralogous of TLP gene family between B. - In addition, the divergence time and selection types of orthologous TLP gene pairs were calculated according to the nonsynonymous substitutions (Ka) and synonymous (Ks). - 1, indi- cating purifying selection on these orthologous TLP gene pairs. - Furthermore, we estimated the divergence time of orthologous TLP gene pairs according to syn- onymous substitution rate (Table S3). - The results indi- cated that the divergence time was million years ago (Mya) for 28 orthologous TLP gene pairs be- tween B. - The divergence time was from 0.12 to 29.80 Mya for the orthologous TLP gene pairs between B.. - Similar, the divergence time of orthologous TLP gene pairs was Mya be- tween B. - No proximal and tandem dupli- cation were detected for TLP gene family among these four species. - Actually, by checking gene collinearity within a genome, we found that and 18.2% of TLP genes were located in collinear blocks for B. - The percentage of TLP genes located in the collinear blocks was significantly larger than the average genome- wide level for B. - Expansion analysis of TLP gene family in Brassica species In order to further explore whether the expansion of TLP gene family in B. - To elucidate the evolution of TLP gene family in Brassica, we performed gene loss and rep- lication retention analysis. - thaliana, the number of TLP genes did not increase significantly. - 3 The paralogous and orthologous analyses of TLP gene family. - a The plot of paralogous and orthologous TLP gene pairs between B. - b The statistics analysis of paralogous and orthologous of TLP gene family among four species. - We obtained quantitative changes in the number of TLP genes in different evolutionary stages based on the phylo- genetic reconstruction (Fig. - The TLP gene in B. - rapa, it was clear that the loss of TLP gene did not occur directly in B. - The loss of TLP genes occurred during the WGD event of the diploid parents B. - Gene expression pattern analysis of TLP gene family in B.. - To explore the potential function of TLP family genes in different tissues of B. - napus, the transcriptome data was used to calculate the expression of TLP family genes in two tissues, including roots and leaves. - The results showed that most of TLP genes had higher expres- sion levels in roots and leaves except for the low expres- sion levels of the two genes in GroupB. - In addition, we also compared the expression differences of TLP genes in roots and leaves in subgenome A and sub- genome C for each group (Fig. - The results showed that the expression patterns of TLP genes between subgenome A and subgenome C were similar. - These genes might be involved Table 3 The synteny analyses of TLP genes and all genes in B. - Collinear blocks contained TLP gene. - TLP gene in collinear block. - Total TLP genes. - Systematical and comprehensive analyses of TLP gene family in B. - This study systematically compared and analyzed the TLP gene family of B. - 4 The duplication or loss analyses of TLP genes in B. - The methods, techniques, and experiences of these studies laid the foundation for an in-depth analysis of TLP gene family. - In the structural analysis of TLP genes, it was found that the gene family struc- ture of B. - So many paralogous genes also gave us a new understanding of the TLP gene family in B. - Evolution and expansion of TLP gene family in Brassica species. - In the analysis of the duplication and loss of TLP gene family during evolution, we found a very interesting gene, the A. - 5 The expression hierarchical clustering of TLP genes in B. - In addition, this study found that the loss of TLP family genes was not directly in the B. - Thus, the expansion of this gene family in B. - In addition, we also identified TLP gene family in other Brassica species for comparative analyses. - The TLP genes in B. - 6 Histogram of TLP gene expression in root and leaf of in B. - Exploring TLP gene function in more species. - In recent years, with the deepening of TLP gene research, it has been found that they played a major role in plant growth, development and stress response. - Studying the dis- tribution, gene structure and expression analysis of TLP family genes in plant was great significant for further study of their function. - The widespread presence of TLP genes indicated that they played an extremely important role in the life process [28, 29]. - Although the function of TLP family genes in ani- mals and plants has not yet been fully clarified, some re- search results have been obtained on the mining and research of their function and structure. - The highly con- served nature of TLP domain indicated that they had im- portant physiological functions in multicellular eukaryotes [16–18]. - In particular, studies of plant TLP gene family have revealed that multiple TLP genes were involved in plant responses to biotic and abiotic stresses [15, 27]. - The comparative genomics study of TLP gene family of B. - napus in this research system will inevitably lay a solid foundation for the functional study of TLP gene family.. - In conclusion, we comprehensively analyzed the evolution- ary pattern, gene structure, orthologous and paralogous genes, duplication type, gene synteny, gene duplication or losses, and gene expression pattern of TLP genes in B.. - Therefore, this is the first comprehensive and systematic analyses of TLP gene family in B. - This study provides useful resources for future studies on the structure and function of TLP genes in B. - In addition, our analyses showed that the directly expansion of TLP genes existed in B.. - Collection of genomic data and identification of TLP gene family. - Gene structural and conservative motif analyses of TLP genes in B. - Information on the location of TLP genes in B. - The gff file of TLP family genes was submitted to the GSDS program to obtain a schematic diagram of the gene structure. - meme4-1/cgi-bin/meme.cgi) was used to analyze the amino acid sequence of TLP genes in B. - Evolution analysis of TLP gene family in B. - The ClustalW program was used to perform multiple alignments of the amino acid sequences of the TLP gene family using default parameter values (https://www.gen- ome.jp/tools-bin/clustalw). - The phylogenetic tree of TLP gene family was constructed with Neighbor-Joining (NJ) method using Mega7.0 software (http://megasoftware.net) [51, 52]. - The pos- ition information on the chromosome of TLP family genes was extracted from gff file, and the chromo- some map was drawn using Perl program.. - To estimate the divergence of orthologous genes, the sequences of orthologous TLP gene pairs between B.. - Analysis of expression pattern of TLP gene family in B.. - The average value was used to com- pare the expression level of TLP genes between subge- nome A and C, or root and leaf. - The list of orthologous TLP gene pairs between B. - The list of paralogous TLP gene pairs in each of other examined species. - The duplicated type of TLP genes in B. - The duplication or loss analyses of TLP genes in B
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