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The paralogous and orthologous analyses of TLP gene family. a The plot of paralogous and orthologous TLP gene pairs between B. napus and A. thaliana, B. rapa, B. oleracea, respectively. b The statistics analysis of paralogous and orthologous of TLP gene family among four species
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Background:
Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and development of plants. Therefore, this study used a bioinformatics approach to conduct the systematic comparative genomics a...
Contexts in source publication
Context 1
... further analyzed the orthologous and paralogous of TLP gene family between B. napus and A. thaliana, B. rapa, or B. oleracea. The orthologous and paralogous network maps between B. napus and these three species were constructed by Circos program (Fig. 3a). Orthologs referred to genes that have evolved from vertical pedigrees from different species and typically retained the same function as the original gene. Here, 50 pairs of orthologous genes were identified in B. napus and A. thaliana; 78 pairs of orthologous genes were identified in B. napus and two diploid parents, B. rapa, B. ...
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... 3a). Orthologs referred to genes that have evolved from vertical pedigrees from different species and typically retained the same function as the original gene. Here, 50 pairs of orthologous genes were identified in B. napus and A. thaliana; 78 pairs of orthologous genes were identified in B. napus and two diploid parents, B. rapa, B. oleracea ( Fig. 3b, Table S1). Paralogs referred to genes that were found in the same species and derived from gene duplication, and might evolve new and previously related functions. A total of 4, 13, 13 and 63 pairs of paralogous genes were identified in A. thaliana, B. rapa, B. oleracea and B. napus ( Fig. 3b, Table S2). In addition, the divergence ...
Context 3
... napus and two diploid parents, B. rapa, B. oleracea ( Fig. 3b, Table S1). Paralogs referred to genes that were found in the same species and derived from gene duplication, and might evolve new and previously related functions. A total of 4, 13, 13 and 63 pairs of paralogous genes were identified in A. thaliana, B. rapa, B. oleracea and B. napus ( Fig. 3b, Table S2). In addition, the divergence time and selection types of orthologous TLP gene pairs were calculated according to the nonsynonymous substitutions (Ka) and synonymous (Ks). To avoid the misalignment, we only used the orthologous gene pairs with Ks < 1 according to previous report [33]. Finally, we obtained the Ks, Ka, Ka/Ks, ...
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... Group 2 did not consist of Arabidopsis TLPs, suggesting that the functional evolution of monocot TLP2 and TLP3 genes may have taken place. The results of our phylogenetic analyses are in accordance with the findings by Zeng and others [19,[22][23][24]. We furthermore used the Ka/Ks ratio as an indicator of selective pressure [17] and found strong diversifying selection between the paralogs and ortholog TLPs (Supplementary Table S3). ...
... We furthermore used the Ka/Ks ratio as an indicator of selective pressure [17] and found strong diversifying selection between the paralogs and ortholog TLPs (Supplementary Table S3). Other studies have not found diversifying selection between the paralogs or orthologs of TLPs [23,24], except for BnaC05g20780D to Bo5g043430.1 in Brassica napus [24]. ...
... We furthermore used the Ka/Ks ratio as an indicator of selective pressure [17] and found strong diversifying selection between the paralogs and ortholog TLPs (Supplementary Table S3). Other studies have not found diversifying selection between the paralogs or orthologs of TLPs [23,24], except for BnaC05g20780D to Bo5g043430.1 in Brassica napus [24]. ...
The Tubby-like proteins (TLPs) gene family is a group of transcription factors found in both animals and plants. In this study, we identified twelve B. distachyon TLPs, divided into six groups based on conserved domains and evolutionary relationships. We predicted cis-regulatory elements involved in light, hormone, and biotic and abiotic stresses. The expression patterns in response to light and hormones revealed that BdTLP3, 4, 7, and 14 are involved in light responses, and BdTLP1 is involved in ABA responses. Furthermore, BdTLP2, 7, 9, and 13 are expressed throughout vegetative and reproductive stages, whereas BdTLP1, 3, 5, and 14 are expressed at germinating grains and early vegetative development, and BdTLP4, 6, 8, and 10 are expressed at the early reproduction stage. The natural variation in the eleven most diverged B. distachyon lines revealed high conservation levels of BdTLP1-6 to high variation in BdTLP7-14 proteins. Based on diversifying selection, we identified amino acids in BdTLP1, 3, 8, and 13, potentially substantially affecting protein functions. This analysis provided valuable information for further functional studies to understand the regulation, pathways involved, and mechanism of BdTLPs.
... Next, the neighbor-joining method was used for sequence alignment and the phylogenetic tree was constructed using MEGA X software [46]. Then, according to our previously published method [47][48][49], the expansion analysis of AHP gene family of Chinese cabbage, Brassica oleracea, and Brassica napus was carried out using A. thaliana AHP gene family as reference ( Figure 3C-E). Based on the multiploidy relationships that species experienced ( Figure 3F), in theory, the relationship between the number of genes of A. thaliana, Chinese cabbage, B. oleracea, and B. napus is 1:3:3:6 [49]. ...
... Gene duplication patterns may reveal the generational types of genes and evolutionary ways of gene functions [33]. Almost all PeZF-HDs (except for PeZF-HD19) were duplicated through WGD or segmental duplication events, suggesting that WGD or segmental duplication played a key role in the expansion of PeZF-HDs, which was similar to the ZF-HDs in other plants, like tomato and Chinese cabbage [13,18]. ...
Zinc finger-homeodomain (ZF-HD) proteins play essential roles in plant growth, development and stress responses. However, knowledge of the expression and evolutionary history of ZF-HD genes in moso bamboo remains limited. In this study, a total of 24 ZF-HD genes were found unevenly distributed on 12 chromosomes in moso bamboo (Phyllostachys edulis). Phylogenetic analysis indicated that PeZF-HDs were divided into two subfamilies: ZHD and MIF. The ZHD subfamily genes were further classified into seven groups according to their orthologous relationships among the rice and Arabidopsis ZF-HD gene family. The gene structures and conserved motifs of PeZF-HDs were analyzed. Whole-genome duplication (WGD) or segmental duplication promoted the evolution and expansion of the moso bamboo ZF-HD gene family. Ka/Ks ratios suggested that the twenty-four duplication pairs had undergone purifying selection. Promoter analysis showed that most PeZF-HDs contained cis-elements associated with stress responses and hormones. Expression analysis demonstrated that many PeZF-HDs were responsive to abiotic stress treatment. Overall, this work investigated PeZF-HD genes in moso bamboo using bioinformatic approaches. The evolutionary research on gene structure, motif distribution and cis-regulatory elements indicated that PeZF-HDs play distinct roles in biological processes, which provides a theoretical basis for exploring the physiological functions of ZF-HDs and selecting candidate stress-related genes in moso bamboo.
... TLP7 is tethered to the PM but detaches upon stimulus and translocates to the nucleus. [53] BnaA08g01250D AT1G53240 mMDH1 encodes a mitochrondrial malate dehydrogenase. It is expressed at higher levels than the other mitochrondrial isoform mMDH2 (At3G15020) according to transcript and proteomic analyses. ...
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... By using the Arabidopsis TLP gene family as a reference, it was found in Brassica that TLP genes in Brassica napus are not directly amplified compared to those in the diploid parents. Instead, indirect amplification of the TLP gene family occurs in the two diploid parents [35]. ...
... In research on the Brassica TLP gene family, Wang et al. identified five origins of TLP duplication using the MCScanX program and found that TLP genes in Brassica originated only from WGD and DSD [35]. Based on the above analysis, an important duplication mode (TRD) was missing in this study. ...
... MCScanX is often used to identify the type of origin of gene duplication in the evolutionary analysis of gene families [1-3, 35,41,[43][44][45][46][47][48][49][50][51][52][53]. However, the duplication types identified by the duplicate_gene_classifier program of MCScanX lack the TRD type, and it is enforced that a gene can originate from only one duplication type. ...
Background
In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages.
Results
Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations.
Conclusions
This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.
... thaliana, B. rapa and B. oleracea) was calculated according to their CDSs. In addition, to minimize errors, only the gene pairs with Ks < 1 were remained for further analysis (Guo et al., 2017;Wang T, et al., 2020). ...
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... Cleft residues of TLPs have different types of crescent fold structures, which can be electropositive, electronegative or neutral [12,36,39,40]. TLPs that carry the characteristic of anti-fungal protein such as PR5a-d in Nicotiana tabacum, TLP in Brassica oleracea and TLP in Vitis vinifera all have acidic cleft, which is comprised of electronegative amino acid residues, Arg-Glu-Asp-Asp-Asp (R-E-D-D-D) [7,41,42] (Figure 3). ...
Unrelenting threats of fungal diseases have caused huge losses to farmers around the
world. Despite efforts and progress made in strengthening the conventional breeding
strategies, a sustainable solution is yet to be discovered. Thus, the development of
transgenic crops using anti-fungal genes such as thaumatin-like protein (TLP), a
member of class 5 pathogenesis-related protein (PR-5), is deemed as a viable solution
to achieve better resistance trait. However, the plant genome usually has multiple TLP
copies with varying signature domains and motifs. It is possible that not all of the copies
exert anti-fungal activity. In addition, the biological roles of TLPs underlying their
ability to improve the plants’ tolerance are still inconclusive. This mini review will
discuss the unique characteristics of TLPs, which might contribute to their anti-fungal
property as well as the various biological roles the proteins may play in the plants’
defense mechanism against fungal infection. Several TLPs that have been proven to
possess anti-fungal activity will also be discussed. Moreover, the impact of transgenic
plants overexpressing TLPs in combating fungal diseases will also be elaborated via
several successful transgenic researches. The information presented in this mini-review
will greatly highlight the potential of TLPs as an anti-fungal agent, especially in the
generation of transgenic plants with improved tolerance against fungal diseases.
... Considering the critical role of TLP proteins in host defenses during pathogen infection, investigations of the TLP gene family have been accomplished in several plant species, such as Cucumis melo (Liu et al. 2020), Gossypium barbadense , Vitis vinifera L. (Yan et al. 2017), Brassica napus (Wang et al. 2020), Hordeum vulgare (Iqbal et al. 2020), etc. However, limited information on TLP proteins in bread wheat, especially in relation to disease resistance, has been reported. ...
Thaumatin-like proteins (TLPs) play potential roles in plant resistance to various diseases. Identifying TLPs is necessary to determine their function and apply them to plant disease resistance. However, limited information is available about TLP-family genes in wheat, especially regarding their responses to Fusarium species, which cause Fusarium head blight in wheat. In this study, we conducted a comprehensive genome-wide survey of TLP genes in wheat and identified 129 TLP genes in the wheat genome, which were unevenly distributed on 21 wheat chromosomes, with 5A containing the highest number. Phylogenetic analysis showed that these 129 wheat TLP genes together with 24 Arabidopsis TLPs were classified into 7 groups based on the protein sequences. We systematically analyzed the genes in terms of their sequence characterization, chromosomal locations, exon–intron distribution, duplication (tandem and segmental) events and expression profiles in response to Fusarium infection. Furthermore, we analyzed differentially expressed TLP genes based on publicly available RNA-seq data obtained from a resistant near isogenic wheat line at different time points after Fusarium graminearum inoculation. Then, the expression of 9 differentially expressed TLP genes was confirmed by real-time PCR, and these 9 genes were all upregulated in the resistant Sumai 3 variety, which was generally consistent with the RNA-seq data. Our results provide a basis for selecting candidate wheat TLP genes for further studies to determine the biological functions of the TLP genes in wheat.
Graphical Abstract
... TLP'lerin korunmuş C-terminal TUB domaininin aksine, N-terminalindeki tekrarlar türler arasında büyük değişkenlik göstermektedir (Gagne et al., 2002;Kim et al., 2017). F-box proteinleri, hücre döngüsü, translasyon-transkripsiyon kontrolü ve sinyal iletimi başta olmak üzere farklı biyolojik süreçlerin düzenlenmesinde aktif bir şekilde rol oynamaktadır (Lai et al., 2012;Wang et al., 2020). Ayrıca TLP'lerin transkripsiyon faktörü olarak işlev gördüğü tahmin edilmektedir (Boggon et al., 2000). ...
... Ayrıca, çeltikte yapılan iki çalışmada, biyotik streslerden biri olan patojen istilasında konakçı ve patojen arasındaki etkileşimde TLP'lerin önemli işlevlere sahip olduğu gösterilmiştir (Cai et al., 2008;Kou et al., 2009). Daha öce yapılan çalışmalarda Arabidopsis'te 11 (Lai et al., 2004), çeltikte 14 (Liu et al., 2008), elmada 9 (Xu et al., 2016), Salvia miltiorrhiza 12 (Wang et al., 2021), Brassica napus 28 (Wang et al., 2020) ve mısırda 15 (Yulong et al., 2016) aday TLP geni tespit edilmiştir. Yapılan literatür taraması sonucunda Phaseolus vulgaris'e ait TLP genleriyle ilgili bir çalışmaya rastlanmamıştır. ...
... TLP'ler hayvanlarla kıyaslandığında çok az bitki türünde karakterizasyon çalışması yapılmıştır. Daha önce yapılan çalışmalarda Arabidopsis'te 11 (Lai et al., 2004) çeltikte 14 (Liu, 2008), elmada 9 (Xu et al., 2016), Salvia miltiorrhiza 12 (Wang et al., 2021), Brassica napus 28 (Wang et al., 2020) ve mısırda 15 (Yulong et al., 2016) aday TLP geni tespit edilmiştir. Bu çalışmada fasulye genomunda 10 TLP geni tespit edilmiştir. ...
... After WGT the number of BraCOBLs and BolCOBLs almost doubled compared to the number of AtCOBLs. However, the number of BnaCOBLs was close to the sum of the number of BraCOBLs and BolCOBLs after allopolyploidization. Furthermore, BnaCOBLs are highly syntenic to [52][53][54][55] and conserved in gene clusters of BraCOBLs and BolCOBLs (Fig 1). We propose that whole-genome triplication event contributed to the expansion of BnaCOBLs. ...
The COBRA-like ( COBL ) genes play key roles in cell anisotropic expansion and the orientation of microfibrils. Mutations in these genes cause the brittle stem and induce pathogen responsive phenotypes in Arabidopsis and several crop plants. In this study, an in silico genome-wide analysis was performed to identify the COBL family members in Brassica . We identified 44, 20 and 23 COBL genes in B . napus and its diploid progenitor species B . rapa and B . oleracea , respectively. All the predicted COBL genes were phylogenetically clustered into two groups: the AtCOB group and the AtCOBL7 group. The conserved chromosome locations of COBLs in Arabidopsis and Brassica , together with clustering, indicated that the expansion of the COBL gene family in B . napus was primarily attributable to whole-genome triplication. Among the BnaCOBLs , 22 contained all the conserved motifs and derived from 9 of 12 subgroups. RNA-seq analysis was used to determine the tissue preferential expression patterns of various subgroups. BnaCOBL9 , BnaCOBL35 and BnaCOBL41 were highly expressed in stem with high-breaking resistance, which implies these AtCOB subgroup members may be involved in stem development and stem breaking resistance of rapeseed. Our results of this study may help to elucidate the molecular properties of the COBRA gene family and provide informative clues for high stem-breaking resistance studies.
