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399 results for “gene family”
Data from: A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)
The pleurocarpous mosses (i.e., Hypnanae) are a species-rich group of land plants comprising about 6,000 species that share the development of female sex organs on short lateral branches, a derived trait within mosses. Many of the families within Hypnales, the largest order of pleurocarpous mosses, trace their origin to a rapid radiation less than 100 million years ago, just after the rise of the angiosperms. As a result, the phylogenetic resolution among families of Hypnales, necessary to test evolutionary hypotheses, has proven difficult using one or few loci. We present the first phylogenetic inference from high-throughput sequence data (transcriptome sequences) for pleurocarpous mosses. To test hypotheses of gene family evolution, we built a species tree of 21 pleurocarpous and six acrocarpous mosses using over one million sites from 659 orthologous genes. We used the species tree to investigate the genomic consequences of the shift to pleurocarpy and to identify whether patterns common to other plant radiations (gene family expansion, whole genome duplication, or changes in the molecular signatures of selection) could be observed. We found that roughly six percent of all gene families have expanded in the pleurocarpous mosses, relative to acrocarpous mosses. These gene families are enriched for several gene ontology (GO) terms, including interaction with other organisms. The increase in copy number coincident with the radiation of Hypnales suggests that a process such as whole genome duplication or a burst of small-scale duplications occurred during the diversification. In over 500 gene families we found evidence of a reduction in purifying selection. These gene families are enriched for several terms in the GO hierarchy related to "tRNA metabolic process." Our results reveal candidate genes and pathways that may be associated with the transition to pleurocarpy, illustrating the utility of phylotranscriptomics for the study of molecular evolution in non-model species.
Data from: Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae
Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with the previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for the comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for the inference of spider relationships and ancient divergence dates.
Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae
Gene duplication allows for functional divergence and innovation that provide selective advantages. However, in flowering plants genetic studies have revealed that single-gene mutations affecting one of two or more closely related paralogs often fail to cause detectable morphological defects, suggesting functional redundancy. Flowering plants have hundreds of genes encoding leucine-rich repeat receptor-like protein kinases (LRR-RLKs), several of which play important roles in anther development but little is known about their evolutionary history and possible functional divergence. We investigated the evolutionary relationship of the LRR-RLK gene family by phylogenetic analysis and found that these closely related paralogs resulted from multiple duplication events, such as the one resulting in BAM1 and BAM2. We further used qRT-PCR to verify gene expression changes in immature anthers from the bam1/bam2 single and double mutants compared with wild type providing strong evidence that the BAM1 and BAM2 genes have evolved different functions, with differential effects on anther gene expression. Moreover, careful examination of anther development in bam1 and bam2 single mutants revealed previously unrecognized extra cell division in tapetum cell layers. Thus our results from phylogenetic, molecular and morphological analyses uncover sequence and functional differences between paralogs whose single mutants lack obvious fertility defects, effectively revealing functional divergence of duplicate genes.
Data from: Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes
Background: Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be diverse transcriptional regulators, playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. Results: In this study, we identified 428 bZIP genes encoding 585 distinct proteins in six legumes, Glycine max, Medicago truncatula,Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Lotus japonicus. The legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. Four kinds of intron patterns (a–d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. We predicted the DNA-binding patterns and the dimerization properties, based on the characteristic features in the basic and hinge regions and the Leu zipper, respectively, which indicated that some highly conserved amino acid residues existed across each major group. The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. We also detected several key legume bZIP genes involved in drought- and salt-responses by comparing fold changes of expression values in drought-stressed or salt-stressed roots and leaves. Conclusions: In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses.
Data from: Identification and distribution of the NBS-LRR gene family in the Cassava genome
Background: Plant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analysing the genomic organization of resistance genes in this crop. Results: With searches for Pfam domains and manual curation of the cassava gene annotations, we identified 228 NBS-LRR type genes and 99 partial NBS genes. These represent almost 1% of the total predicted genes and show high sequence similarity to proteins from other plant species. Furthermore, 34 contained an N-terminal toll/interleukin (TIR)-like domain, and 128 contained an N-terminal coiled-coil (CC) domain. 63% of the 327 R genes occurred in 39 clusters on the chromosomes. These clusters are mostly homogeneous, containing NBS-LRRs derived from a recent common ancestor. Conclusions: This study provides insight into the evolution of NBS-LRR genes in the cassava genome; the phylogenetic and mapping information may aid efforts to further characterize the function of these predicted R genes.
Data from: Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
Background: SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined. Results: In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3′UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle. Conclusions: Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.
Fig. 3 in Karyotype characterization of Mugil incilis Hancock, 1830 (Mugiliformes: Mugilidae), including a description of an unusual co-localization of major and minor ribosomal genes in the family
Fig. 3. Metaphase plates of Mugil incilis after FISH with 45SrDNA (a) and 5SrDNA (c), respectively (b and d) DAPI counterstained. Arrows indicate chromosome pair number 1.
GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees Pipeline.
<p>Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families. </p>
Table 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 1.</b> Arrangement and annotation of the mitochondrial genome of Cubaris murina.</p><table><tbody><tr><th></th><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th></th></tr></tbody><tbody><tr><th>Name</th><td>Type</td><td>Start</td><td>Stop</td><td>Strand</td><td>(bp)</td><td>Start</td><td>Stop</td><td>Inter-genic space</td><td>Overlap</td></tr><tr><th>Cox1</th><td>Coding</td><td>1</td><td>1536</td><td>+</td><td>1536</td><td>ATG</td><td>TAA</td><td>1</td><td></td></tr><tr><th>trnL2(tta)</th><td>tRNA</td><td>1538</td><td>1598</td><td>+</td><td>61</td><td></td><td></td><td>48</td><td></td></tr><tr><th>Cox2</th><td>Coding</td><td>1647</td><td>2282</td><td>+</td><td>636</td><td>ATA</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnK(aaa)</th><td>tRNA</td><td>2281</td><td>2336</td><td>+</td><td>56</td><td></td><td></td><td></td><td>8</td></tr><tr><th>trnD(gac)</th><td>tRNA</td><td>2329</td><td>2403</td><td>+</td><td>75</td><td></td><td></td><td></td><td>17</td></tr><tr><th>atp8</th><td>Coding</td><td>2387</td><td>2533</td><td>+</td><td>147</td><td>ATA</td><td>TAA</td><td></td><td>4</td></tr><tr><th>atp6</th><td>Coding</td><td>2530</td><td>3192</td><td>+</td><td>663</td><td>ATA</td><td>TAA</td><td>2</td><td></td></tr><tr><th>Cox3</th><td>Coding</td><td>3195</td><td>3989</td><td>+</td><td>795</td><td>ATG</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnR(cga)</th><td>tRNA</td><td>3988</td><td>4055</td><td>+</td><td>68</td><td></td><td></td><td>55</td><td></td></tr><tr><th>nad3</th><td>Coding</td><td>4111</td><td>4407</td><td>+</td><td>297</td><td>ATA</td><td>TAA</td><td></td><td>9</td></tr><tr><th>trnA(gca)</th><td>tRNA</td><td>4399</td><td>4446</td><td>+</td><td>48</td><td></td><td></td><td></td><td>8</td></tr><tr><th>nad1 CR putative</th><td>Coding</td><td>4439 5219</td><td>5218 5360</td><td>−</td><td>780 142</td><td>ATG</td><td>TAG</td><td></td><td>14</td></tr><tr><th>NCR1</th><td>tRNA</td><td>5361</td><td>5429</td><td>+</td><td>69</td><td></td><td></td><td></td><td>17</td></tr><tr><th>rrnS</th><td>rRNA</td><td>5413</td><td>6139</td><td>+</td><td>727</td><td></td><td></td><td>48</td><td></td></tr><tr><th>trnW(tga)</th><td>tRNA</td><td>6188</td><td>6244</td><td>+</td><td>57</td><td></td><td></td><td></td><td>7</td></tr><tr><th>trnS1(aga)</th><td>tRNA</td><td>6238</td><td>6296</td><td>−</td><td>59</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR2</th><td></td><td>6297</td><td>6666</td><td></td><td>370</td><td></td><td></td><td></td><td></td></tr><tr><th>trnL1(cta)</th><td>tRNA</td><td>6667</td><td>6731</td><td>−</td><td>65</td><td></td><td></td><td>29</td><td></td></tr><tr><th>cob</th><td>Coding</td><td>6759</td><td>7907</td><td>−</td><td>1,149</td><td>ATA</td><td>TAG</td><td>38</td><td></td></tr><tr><th>trnT(aca)</th><td>tRNA</td><td>7946</td><td>8017</td><td>−</td><td>72</td><td></td><td></td><td>29</td><td></td></tr><tr><th>nad5</th><td>Coding</td><td>8047</td><td>9648</td><td>+</td><td>1,602</td><td>ATG</td><td>TAG</td><td></td><td>3</td></tr><tr><th>trnF(ttc)</th><td>tRNA</td><td>9646</td><td>9707</td><td>+</td><td>62</td><td></td><td></td><td></td><td>15</td></tr><tr><th>trnH(cac)</th><td>tRNA</td><td>9693</td><td>9758</td><td>−</td><td>66</td><td></td><td></td><td></td><td>23</td></tr><tr><th>nad4</th><td>Coding</td><td>9736</td><td>11,082</td><td>−</td><td>1,312</td><td>ATA</td><td>TAA</td><td>13</td><td></td></tr><tr><th>nad4L</th><td>Coding</td><td>11,096</td><td>11,374</td><td>−</td><td>279</td><td>ATA</td><td>TAA</td><td></td><td>13</td></tr><tr><th>trnP(cca)</th><td>tRNA</td><td>11,362</td><td>11,422</td><td>−</td><td>61</td><td></td><td></td><td>25</td><td></td></tr><tr><th>nad6</th><td>Coding</td><td>11,448</td><td>11,903</td><td>+</td><td>456</td><td>ATA</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnS2(tca)</th><td>tRNA</td><td>11,902</td><td>11,962</td><td>+</td><td>61</td><td></td><td></td><td>17</td><td></td></tr><tr><th>rrnL</th><td>rRNA</td><td>11,980</td><td>12,549</td><td>−</td><td>570</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR3</th><td></td><td>12,550</td><td>12,753</td><td></td><td>204</td><td></td><td></td><td></td><td></td></tr><tr><th>trnE(gaa)</th><td>tRNA</td><td>12,754</td><td>12,812</td><td>−</td><td>59</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR4</th><td></td><td>12,813</td><td>12,950</td><td></td><td>138</td><td></td><td></td><td></td><td></td></tr><tr><th>trnV(gta)</th><td>tRNA</td><td>12,951</td><td>13,019</td><td>−</td><td>69</td><td></td><td></td><td></td><td>5</td></tr><tr><th>trnQ(caa)</th><td>tRNA</td><td>13,015</td><td>13,077</td><td>−</td><td>63</td><td></td><td></td><td></td><td>6</td></tr><tr><th>trnM(atg)</th><td>tRNA</td><td>13,072</td><td>13,141</td><td>+</td><td>70</td><td></td><td></td><td>25</td><td></td></tr><tr><th>nad2</th><td>Coding</td><td>13,167</td><td>14,123</td><td>+</td><td>978</td><td>ATA</td><td>TAG</td><td></td><td>15</td></tr><tr><th>trnC(tgc)</th><td>tRNA</td><td>14,109</td><td>14,158</td><td>−</td><td>50</td><td></td><td></td><td></td><td></td></tr><tr><th>trnY(tac)</th><td>tRNA</td><td>14,159</td><td>14,205</td><td>−</td><td>47</td><td></td><td></td><td>7</td><td></td></tr></tbody></table>
Table 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 2.</b> Base composition (%) of nucleotide, AT content, and AT- and GC-skew of the mitochondrial genome of <i>Cubaris murina.</i> Values in bold indicate positive AT-skew.</p><table><tbody><tr><th></th><th></th><th></th><th>Base composition (%)</th><th></th><th></th><th></th><th></th></tr></tbody><tbody><tr><th>Total</th><td></td><td>A</td><td>C</td><td>G</td><td>T</td><td>%AT</td><td>AT skew</td><td>GC skew</td></tr><tr><th>14,212 bp</th><td>28.90%</td><td>15.80%</td><td>23.40%</td><td>31.90%</td><td>60.80%</td><td>−0.049</td><td>0.194</td></tr><tr><th></th><td></td><td></td><td>Base composition (%)</td><td></td><td></td><td></td><td></td></tr><tr><th>Gene Strand</th><td>A</td><td>C</td><td>G</td><td>T</td><td>%AT</td><td>AT skew</td><td>GC skew</td></tr><tr><th><i>cox1</i></th><td>(+)</td><td>22.4%</td><td>18.6%</td><td>24.2%</td><td>34.8%</td><td>57.2%</td><td>−0.217</td><td>0.131</td></tr><tr><th><i>cox2</i></th><td>(+)</td><td>20.6%</td><td>21.7%</td><td>27.7%</td><td>30.0%</td><td>50.6%</td><td>−0.186</td><td>0.121</td></tr><tr><th><i>atp8</i></th><td>(+)</td><td>21.1%</td><td>15.0%</td><td>34.7%</td><td>29.3%</td><td>50.4%</td><td>−0.163</td><td>0.396</td></tr><tr><th><i>atp6</i></th><td>(+)</td><td>20.4%</td><td>19.8%</td><td>29.1%</td><td>30.8%</td><td>51.2%</td><td>−0.203</td><td>0.190</td></tr><tr><th><i>cox3</i></th><td>(+)</td><td>17.2%</td><td>23.6%</td><td>28.6%</td><td>30.6%</td><td>47.8%</td><td>−0.280</td><td>0.096</td></tr><tr><th><i>nad3</i></th><td>(+)</td><td>20.2%</td><td>16.2%</td><td>32.3%</td><td>31.3%</td><td>51.5%</td><td>−0.216</td><td>0.332</td></tr><tr><th><i>nad1</i></th><td>(−)</td><td>31.7%</td><td>22.2%</td><td>27.6%</td><td>18.6%</td><td>50.3%</td><td><b>0.260</b></td><td>0.108</td></tr><tr><th><i>NCR1</i></th><td></td><td>28.9%</td><td>27.5%</td><td>19.7%</td><td>23.9%</td><td>52.8%</td><td>0.095</td><td>−0.165</td></tr><tr><th><i>NCR2</i></th><td></td><td>27.0%</td><td>22.2%</td><td>18.1%</td><td>32.7%</td><td>59.7%</td><td>−0.095</td><td>−0.102</td></tr><tr><th><i>cob</i></th><td>(−)</td><td>36.0%</td><td>12.0%</td><td>23.5%</td><td>28.5%</td><td>64.5%</td><td><b>0.116</b></td><td>0.324</td></tr><tr><th><i>nad5</i></th><td>(+)</td><td>28.5%</td><td>10.5%</td><td>21.7%</td><td>39.3%</td><td>67.8%</td><td>−0.159</td><td>0.348</td></tr><tr><th><i>nad4</i></th><td>(−)</td><td>38.4%</td><td>11.9%</td><td>22.8%</td><td>26.9%</td><td>65.3%</td><td><b>0.176</b></td><td>0.314</td></tr><tr><th><i>nad4L</i></th><td>(−)</td><td>41.9%</td><td>12.2%</td><td>17.6%</td><td>28.3%</td><td>70.2%</td><td><b>0.194</b></td><td>0.181</td></tr><tr><th><i>nad6</i></th><td>(+)</td><td>25.7%</td><td>10.5%</td><td>17.8%</td><td>46.1%</td><td>71.8%</td><td>−0.284</td><td>0.258</td></tr><tr><th><i>NCR3</i></th><td></td><td>36.8%</td><td>9.8%</td><td>19.1%</td><td>34.3%</td><td>71.1%</td><td>0.035</td><td>0.322</td></tr><tr><th><i>NCR4</i></th><td></td><td>35.5%</td><td>13.0%</td><td>15.2%</td><td>36.2%</td><td>71.7%</td><td>−0.010</td><td>0.078</td></tr><tr><th><i>nad2</i></th><td>(+)</td><td>28.9%</td><td>12.4%</td><td>22.6%</td><td>36.1%</td><td>65.0%</td><td>−0.111</td><td>0.291</td></tr></tbody></table>
Fig. 3 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 3. Continued. RAxML tree based on the concatenated 83 nuclear loci of the LEO dataset. Numbers on the branches are bootstrap values (BS)>50%; additionally, LPP and quartet support values (QSV) from MSC analysis (see suppl. Fig. S4) are given in the order BS/LLP/QSV for nodes along the backbone of Ochneae. The indicated classification of subfamilies and tribes follows Schneider & al. (2014). Numbers in parentheses after species names correspond to the specimen IDs (only for species with multiple accessions).
A Study to Assess the Genetic Variations in Bile Flow Disorders: Linking Progressive Familial Intrahepatic Cholestasis (PFIC)-Related Genes to Symptoms in Adults With Recurrent Cholestasis in Spain
ClinicalTrials.gov study NCT07191704. IPD Sharing: YES. Countries: 1. Publications: 0.
An Intervention to Increase Genetic Testing in Families Who May Share a Gene Mutation Related to Cancer Risk and An Intervention to Help Patients and Their Primary Care Providers Stay Up-to-date About
ClinicalTrials.gov study NCT05420064. IPD Sharing: YES. Countries: 1. Publications: 0.
Gene Analysis and Treatment Optimization in Chinese Homozygous Familial Hypercholesterolemia
ClinicalTrials.gov study NCT01878604. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Gene Therapy Study for Homozygous Familial Hypercholesterolemia (HoFH)
ClinicalTrials.gov study NCT02651675. IPD Sharing: NO. Countries: 4. Publications: 0.
Erythromycin Treatment for Readthrough of APC Gene Stop Codon Mutation in Familial Adenomatous Polyposis-minors' Adjusted Version
ClinicalTrials.gov study NCT02354560. IPD Sharing: Not stated. Countries: 0. Publications: 11.
Data from: Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae
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Data from: Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids
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Data from: Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
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Expression Analysis and Functional Characterization of CER1 Family Genes Involved in Very-LongChain Alkanes Biosynthesis in Brachypodium distachyon
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