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401 results for “nuclear gene”
Phylogenomics of Gesneriaceae using targeted capture of nuclear genes
<p>Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperm-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group. </p>
Nuclear Genome Organization in Fungi: From Gene folding to Rabl Chromosomes
<p>We discuss the current knowledge on the fungal genome organization, from the association of chromosomes within the nucleus to topological structures at individual genes and the genetic factors required for the hierarchical organization. Chromosome conformation capture followed by high-throughput sequencing (Hi-C) has elucidated how fungal genomes are globally organized in Rabl configuration where centromere or telomere bundles are associated with opposite faces of the nuclear envelope. Here, we explore the presence, in fungal taxa, of the typical proteins associated with genome organization in eukaryotes.</p>
New genetic markers for Sapotaceae phylogenomics: more than 600 nuclear genes applicable from family to population levels
<p>Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short tandem repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from<em>Capurodendron delphinense</em> and <em>Bemangidia lowryi</em>, both from the Tseboneae tribe, as well as the published <em>Manilkara zapota</em> transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (<em>C. delphinense</em>) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. All together, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.</p>
Fig. 17. Phylogenetic hypothesis using nuclear gene sequences TMO-4C4 and 18S in A New Genus and Species of Pygmy Pipehorse from Taitokerau Northland, Aotearoa New Zealand, with a Redescription of Acentronura Kaup, 1853 and Idiotropiscis Whitley, 1947 (Teleostei, Syngnathidae)
Fig. 17. Phylogenetic hypothesis using nuclear gene sequences TMO-4C4 and 18S retrieved with Maximum Likelihood (ML), Maximum Parsimony (MP), and Bayesian Inference (MrBayes), representing 17 species from clade 6 from the analysis of Hamilton et al. (2017) and the new taxon. Tree rooted with the southern Australian trunk-brooder pipefish Heraldia nocturna. Nodal support at the generic level is shown in ML/MP/MrBayes order. See Data Accessibility for tree file.
Fig. 3 in Phylogenetic analysis of the Common Krait (Bungarus caeruleus) in Pakistan based on mitochondrial and nuclear protein coding genes
Fig. 3. Mitochondrial and nuclear genes (ND4, Cyt b, COI, 12S rRNA, 16S rRNA, C-mos, RAG-1, and NT3) Bayesian phylogeny for Common Krait (Bungarus caeruleus).
Fig. 2 in Phylogenetic analysis of the Common Krait (Bungarus caeruleus) in Pakistan based on mitochondrial and nuclear protein coding genes
Fig. 2. Mitochondrial and nuclear genes (ND4, Cyt. b, COI, 12S rRNA, 16S rRNA, C-mos, RAG-1, NT3, and BDNF) based Maximum Likelihood phylogeny for Common Krait (Bungarus caeruleus).
Fig. 4 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 4. Distribution of specimen ages and the number of loci recovered in the phylogenomic study of Ochnaceae. A, Histogram of the collection years of all Ochnaceae specimens; B & C, Relationship between the year of collection of the specimens and the number of loci recovered for tissue obtained from herbarium material (excluding specimens with silica-dried leaf material), analysed for Ochneae and all the remaining Ochnaceae separately, either using the consensus-alignment (B) or the sample-specific (C) reference-based assembly approach. Pearson correlation coefficients and confidence intervals are given for each group.
Fig. 2 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 2. RAxML trees based on the concatenated nuclear loci of Ochnaceae. A, Early-diverging branches of Ochnaceae and relationships within Quiinoideae based on the FAM dataset; B, Phylogenetic relationships of Sauvagesieae, Luxemburgieae and Testuleeae based on the SLT dataset. Numbers on the branches are bootstrap values>50%. Numbers in parentheses after species names correspond to the specimen IDs (only for species with multiple accessions). The indicated classification of subfamilies and tribes follows Schneider & al. (2014).
Fig. 1 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 1. Overview of the phylogenetic relationships of the major clades of Ochnaceae based on the FAM dataset together with images of representative species. The classification follows Schneider & al. (2014). Ochninae is by far the most species-rich clade comprising about two-thirds of the family's species and six genera (Brack. = Brackenridgea; Cmp. = Campylospermum, clades A and B; I. = Idertia; Ochna; Ouratea; Rh. = Rhabdophyllum). Letters around the tree refer to the photos (mostly flowers except where indicated) and the relative position of the displayed taxa on the tree. A, Medusagyne oppositifolia (Medusagynoideae); B, Froesia venezuelensis (Quiinoideae); C, Luxemburgia schwackeana (Luxemburgieae); D, Rhytidanthera sulcata; E, Cespedesia spathulata; F, Poecilandra retusa; G, Godoya antioquiensis; H, Wallacea insignis; I, Sauvagesia semicylindrifolia; J, Sauvagesia erecta (Sauvagesieae); K, Infructescence of Lophira lanceolata with accrescent sepals (Lophirinae); L, Flower of Elvasia kollmannii (Elvasiinae); M, Perissocarpa umbellifera; N, Fruiting Rhabdophyllum arnoldianum; O, Brackenridgea nitida; P, Campylospermum glaberrimum; Q, Ochna serrulata; R, Fruit of Ochna integerrima with drupelets sitting on enlarged receptacle; S, Fruit of Ouratea sp. with enlarged red receptable; T, Ouratea sp. — Photos: A, K & N from www.africanplants.senckenberg.de (Dressler & al., 2014–); B by Julio Schneider; C by William Milliken/ Royal Botanic Gardens, Kew; D by Sandra Reinales; E by Reinaldo Aguilar; F, H & M by Francisco Farroñay; G by John Clark; I, J, S & T by Domingos Cardoso; L by Claudio Nicoletti de Fraga; O by John Elliott; P by Warran McCleland; Q by Marja Broersma; R by Pierre Grard.
Figure 2 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 2. Strict consensus of the 1040 equally most parsimonious trees (L = 445; CI = 0.724; RI = 0.886) obtained from the phylogenetic analysis of sphaeriid nuclear ITS1 rDNA sequences. The inferred evolutionary gain and loss of a ~160 nt fragment are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Figure 3 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 3. The single most-parsimonious tree (L = 951; CI = 0.568; RI = 0.793) obtained from the maximum parsimony analysis of combined (16S + ITS1) sequence dataset. Maximum likelihood analysis produced a largely congruent topology (HKY model; Ln likelihood = - 7034.61154) with the only difference being Pisidium dubium sister to Sphaerium/Musculium clade. Taxonomic names are arranged according to suggested sphaeriinid taxonomy in the present study and five major monophyletic lineages are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups. MP bootstrap values are shown to the left of the slash and decay index values to the right above the branches. Numbers below the branches indicate ML bootstrap values.
Figure 1 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 1. Strict consensus of the four equally most parsimonious trees (L = 526; CI = 0.447; RI = 0.743) obtained from the phylogenetic analysis of sphaeriid mitochondrial 16S rDNA sequences. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
<p>This repository accompanies the manuscript "<strong>Evaluating the role of the nuclear microenvironment in gene function by population-based modeling</strong>", available in <em>Nature Structural & Molecular Biology</em>.</p> <p>It contains the files for the population of 3D structures for GM12878 in 200-kb resolution generated using IGM (https://github.com/alberlab/igm) and the derived structural features. Please see README.txt for more information.</p> <p>For any inquiries please reach out to Dr. Frank Alber (falber@g.ucla.edu).</p>
Figure 6 in Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
Figure 6. Divergence time and diversification rate upshifts of Orchidaceae (A) Achronogram inferred using TreePL with the topology of the summary tree from four coalescent trees and with branch length calculated from a concatenated data set containing 299 genes, showing temporal evolutionary patterns of subtribe and higher ranks of Orchidaceae. Numbers near nodes indicate the estimated ages of corresponding nodes. The branch colors indicate the net diversification rate estimated using BAMM, and corresponding rates are shown in the legend at the top of the chronogram. Triangles or lines on terminal branches represent the range of species number of corresponding taxa as indicated to the left side of the chronogram. Ageological time scale is shown at the bottom of the chronogram, with an estimated temperature change curve for the Late Cretaceous (Veizer et al., 2000) and the Cenozoic (Westerhold et al., 2020). Also shown are the K‐Pg boundary, Paleocene– Eocene Thermal Maximum (PETM), an origin of the modern rainforests (Carvalho et al., 2021), and the origin of epiphytism shared by MCVECP (Malaxideae, Cymbidieae, Vandeae, Epidendreae, Collabieae, and Podochileae) clade inferred in this study. The orange up arrows on branches indicate the net diversification rate upshifts inferred in BAMM using subtribe‐level sampling fractions; the blue up arrows on branches and in the triangles indicate the net diversification rate upshifts inferred in Epidendreae and Vandeae using genus‐level sampling fractions. The same color scheme of taxon names in Figures 1–4 is used here. (B) A histogram plot shows the temporal pattern of divergence events of ancestors of orchid subtribes, genera, and species. The height of each bin indicates the number of divergent events within five million years, and the vertical dashed lines indicate mean ages of divergent events of each rank. (C) The temporal change pattern of the Orchidaceae net diversification rate. K‐Pg boundary, an origin of the modern rainforests, PETM, and the origin of epiphytism shared by members of the MCVECP clade are indicated.
Figure 5 in Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
Figure 5. Evolutionary pattern of growth forms in Orchidaceae Acladogram showing the reconstructed ancestral states of growth forms of Orchidaceae. Corresponding taxon names (genera of Apostasioideae and Cypripedioideae, subtribes of Orchidoideae and Epidendroideae, and tribes of Vanilloideae) are shown on the right side of the tree, and the same color scheme of taxon names in Figures 1–4 is used here. Branch colors indicate the reconstructed growth forms as described on the left side of the tree. The green, purple, blue, and orange vertical bars on branches indicate transitions to epiphytism, full mycoheterotrophy, lithophytism, and terrestrial form, respectively. Numbers in four columns between branch tips and taxon names indicate the times of transitions within the taxon group as indicated at the top: between terrestrial (T) and epiphytic (E), other types to full mycoheterotrophy (M), and other types to lithophytic (L). Orc: Orchideae; Ner: Nervilieae; Are: Arethuseae; Mal: Malaxideae.
Figure 4 in Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
Figure 4. Asummary cladogram of Orchidaceae, part 4 (the Cymbidieae tribe) A portion of the summary Orchidaceae phylogenetic tree generated from four coalescent trees reconstructed using gene‐sets with 1 195, 1 016, 834, and 639 genes, respectively, showing relationships of genera of Cymbidieae. Photographs of representative species of Cymbidieae are presented on the right side. See also legend for Figure 1.
Figure 1 in Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
Figure 1. Asummary cladogram of Orchidaceae, part 1 (the Apostasioideae, Vanilloideae, Cypripedioideae, and Orchidoideae subfamilies) A portion of the summary Orchidaceae phylogenetic tree generated from four coalescent trees reconstructed using gene‐sets with 1 195, 1 016, 834, and 639 genes, respectively. The relationships among genera of four subfamilies, Apostasioideae, Vanilloideae, Cypripedioideae, and Orchidoideae are shown. The branches have maximal multi‐locus bootstrap support values (MBS) in all coalescent trees, unless indicated by colored shapes with corresponding support value shown below the tree. The triangle at the tip of a branch indicates that the corresponding genus contains more than one sampled species, and the number of sampled species of the genus is shown in the parentheses after the genus name. The green tree symbol before a genus name indicates that the genus has epiphytic species. The subfamily, tribe, and subtribe names are shown to the right of genus names. Photographs, with species or genus names below, of some genera/species in the four subfamilies, are presented on the right side. The legends and symbols used here are also the same for Figures 2, 3, and 4.
Figure 3 in Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
Figure 3. Asummary cladogram of Orchidaceae, part 3 (the Epidendreae tribe) A portion of the summary Orchidaceae phylogenetic tree generated from four coalescent trees reconstructed using gene‐sets with 1,195, 1,016, 834, and 639 genes, respectively, showing relationships of genera of Epidendreae. Photographs of representative genera/species of Epidendreae are presented on the right side. See also legend for Figure 1.
Figure 2 in Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
Figure 2. Asummary cladogram of Orchidaceae, part 2 (the Epidendroideae subfamily, except the Epidendreae and Cymbidieae tribes) A portion of the summary Orchidaceae phylogenetic tree generated from four coalescent trees reconstructed using gene‐sets with 1,195, 1,016, 834, and 639 genes, respectively, showing relationships of genera of 12 Epidendroideae tribes: Neottieae, Sobralieae, Triphoreae (Tri), Xerorchideae, Gastrodieae, Nervilieae (Ner), Tropidieae, Arethuseae, Malaxideae, Collabieae, Podochileae, and Vandeae. Photographs of representative genera/species of the tribes shown in the tree are presented on the right side. See also legend for Figure 1.
Inter-generational nuclear crosstalk links the control of gene expression to programmed genome rearrangements during the Paramecium sexual cycle
<p>Multinucleate cells are found in many eukaryotes, but how multiple nuclei coordinate their functions is still poorly understood. In the cytoplasm of the ciliate <em>Paramecium tetraurelia</em>, two micronuclei (MIC) serving sexual reproduction coexist with a somatic macronucleus (MAC) dedicated to gene expression. During sexual processes, the MAC is progressively destroyed while still ensuring transcription and new MACs develop from copies of the zygotic MIC. Several gene clusters are successively induced and switched off before vegetative growth resumes. Concomitantly, programmed genome rearrangements (PGR) remove transposons and their relics from the new MACs. Development of the new MACs is controlled by the old MAC, since the latter expresses genes involved in PGR, including the <em>PGM</em> gene encoding the essential PiggyMac endonuclease that cleaves the ends of eliminated sequences. Using RNA deep sequencing and transcriptome analysis, we show that impairing PGR up-deregulates key PGR genes, together with ~600 other genes possibly also involved in PGR. Among these genes, 42% are no longer induced when no new MACs are formed, including 180 genes that are co-expressed with <em>PGM </em>under all tested conditions. We propose that bi-directional crosstalk between the two coexisting generations of MACs links gene expression to the progression of MAC development.</p>
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