Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions

<p>Abstract</p> <p>Background</p> <p>One of the many gene families that expanded in early vertebrate evolution is the neuropeptide (NPY) receptor family of G-protein coupled receptors. Earlier work by our lab suggested that several of the NPY receptor genes found in extant vertebrates resulted from two genome duplications before the origin of jawed vertebrates (gnathostomes) and one additional genome duplication in the actinopterygian lineage, based on their location on chromosomes sharing several gene families. In this study we have investigated, in five vertebrate genomes, 45 gene families with members close to the NPY receptor genes in the compact genomes of the teleost fishes <it>Tetraodon nigroviridis </it>and <it>Takifugu rubripes</it>. These correspond to <it>Homo sapiens </it>chromosomes 4, 5, 8 and 10.</p> <p>Results</p> <p>Chromosome regions with conserved synteny were identified and confirmed by phylogenetic analyses in <it>H. sapiens, M. musculus, D. rerio, T. rubripes </it>and <it>T. nigroviridis</it>. 26 gene families, including the NPY receptor genes, (plus 3 described recently by other labs) showed a tree topology consistent with duplications in early vertebrate evolution and in the actinopterygian lineage, thereby supporting expansion through block duplications. Eight gene families had complications that precluded analysis (such as short sequence length or variable number of repeated domains) and another eight families did not support block duplications (because the paralogs in these families seem to have originated in another time window than the proposed genome duplication events). RT-PCR carried out with several tissues in <it>T. rubripes </it>revealed that all five NPY receptors were expressed in the brain and subtypes Y2, Y4 and Y8 were also expressed in peripheral organs.</p> <p>Conclusion</p> <p>We conclude that the phylogenetic analyses and chromosomal locations of these gene families support duplications of large blocks of genes or even entire chromosomes. Thus, these results are consistent with two early vertebrate tetraploidizations forming a paralogon comprising human chromosomes 4, 5, 8 and 10 and one teleost tetraploidization. The combination of positional and phylogenetic data further strengthens the identification of orthologs and paralogs in the NPY receptor family.</p

Serendipitous meta-transcriptomics : the fungal community of Norway Spruce (Picea abies)

After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant’s phyllosphere. Notably, we could classify these transcripts as originating predominantly fromDothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.S1 Fig. Samples collected from Norway spruce. For each sample a brief description and sample ID are shown below a representative image of the associated plant tissue, while the sampling date is shown above.S2 Fig. Bioinformatics workflow of RNA data processing. We assembled reads from all samples into a single assembly (left column), computed Tau scores, GC content, and mapped the transcripts to the genome as well as to the Uniref90 protein database. For enriching for fungal transcripts (right column), we applied GC content and expression breadth filters to the reads and assembly respectively, clustered sequences by similarity, and performed functional annotation as well as phylogenetic analyses.S3 Fig. Putative taxonomic characterization of transcripts via protein alignments. Bar plot showing the number of transcripts by taxonomy (super)kingdoms. Parent summarises taxons hierarchically higher than the represented (super)kingdoms, NA summarises transcripts with no sequence similarity in the UniRef90 database. The number of transcripts is indicated at the top of every bar.S4 Fig. Taxonomic class and phylum of the fungal transcripts. (a) Number of transcripts per fungal phylum. The phylum are sorted by abundance top to bottom with Ascomycota (n = 81,181) and Basidiomycota (n = 4,839) being the most represented; the remaining phyla varying from n = 11 to n = 2. (b) A graph of the taxonomic hierarchy from species to phylum of the fungal transcripts, showing the broad species diversity of the largest clusters: Ascomycota (bottom) and Basidiomycota (top). (c) Similar to (a) for the fungal classes, with the Eurotiomycetes and Dothideomycetes classes being over-represented among the fungal transcripts. (d) Similar to (b) for the fungal classes (n = 24).S5 Fig. Characterisation of transcripts lacking taxonomic assignment by their GMAP alignments to the P. abies genome. (a) Boxplot of the tau scores for the no taxon transcripts split based on their GMAP alignments to the P. abies genome. The tau score ranges from 1 for complete specificity to 0 for equal expression in all samples. The transcripts having a GMAP alignment in the genome (99% of the GMAP hits cover 80% of the transcripts with at least a 90% identity) show a wide tau score distribution indicative of the presence of ubiquitously expressed transcripts as well as that of more tissue-specific transcripts. The transcripts having no GMAP alignment show a distribution typical of only tissue-specific expression (mean tau score of 0.98). (b) Percentage GC density distribution of the no taxon transcripts split based on their GMAP alignments to the P. abies genome. Transcripts having a GMAP alignment to the genome present a GC distribution typical of the P. abies transcripts. The transcripts without a GMAP alignment show a distribution enriched for higher percentage GC, similar to that of fungi. The shoulder observed under the peak of transcripts with GMAP alignments may indicate transcripts where the assembly contained gaps or created chimeras. (c) Scatterplot of log2 FPKM expression values vs. the percentage GC content for the transcripts with a GMAP alignment. Colouring indicates density, which is shaded from yellow (high) to blue (low). The expression of transcripts with a GMAP alignment resembles that of the Embryophita phylum. (d) Scatterplot of log2 FPKM expression values vs. the percentage GC content for transcripts with a GMAP alignment. Colouring as in (c). The expression of transcripts with no GMAP alignment resembled that of the fungal kingdom.S6 Fig. Phylogeny built on four nuclear genes. Shown are maximum-likelihood phylogenies based on fungal nucleotide sequences assembled from the spruce samples in context of known sequences, with highest sequence similarity to: (a) phosphoenolpyruvate carboxykinase; (b) NADP-dependent medium chain alcohol dehydrogenase; (c) beta lactamase; and (d) unspecific lipid transporter. Only branch with support values > 0.9 are shown. While clusters with more representative sequences yield better branch support (a, b), placement of clusters with fewer sequences is less certain (c, d). However, in all cases, at least one sequence is grouped with Dothideomycetes, and for (a,b) with Leotiomycetes.S1 Table. Sample IDs, description, and ENA submission IDs. Correspondence between the sample IDs as described in Nystedt et al., (2013), this manuscript and the ENA are shown in columns one to three. The fourth column contains a succinct description of the samples, refer to Nystedt et al., (2013) for full details.http://www.plosone.orgam201

Phylogenetic maximum likelihood analyses of the voltage-gated sodium channel α subunits

<p>Phylogenetic maximum likelihood analyses of the voltage-gated sodium channel α subunit (SCNα) gene family based on amino acid sequence alignments. The sequences and alignments described in <em>Widmark et. al. (2011) Molecular Biology and Evolution 28(1):859-71</em> (1) were used to re-analyze the phylogenetic relationships of vertebrate SCNα subtypes with more powerful methods.</p> <p><strong>File information:</strong></p> <p>Two datasets were made; the full subset of identified SCNα sequences in alignment file 1 (<em>9.6_SCNexons.aln</em>) used for the phylogenetic analyses in Figs. 1 and 3; and the identified SCN1A, SCN4A, SCN5A and SCN8A sequences in alignment file 2 (<em>8.14_SCNexons(1,4,5,8).aln</em>) used for the phylogenetic analyses in Figs. 2 and 4. The latter dataset includes only sequences representing each of the four chromosomes harboring SCNα genes in tetrapod genomes (1). Alignment files are provided in the CLUSTAL format. For sequence and alignment curation details see <em>Widmark et. al. (2011)</em> (1).</p> <p>The trees in Figs. 1 and 2 are supported by bootstrap values (see below). Both the final bootstrapped trees and all the bootstrap replicates are provided as txt-files in NEWICK format. The trees in Figs. 3 and 4 are supported by aLRT values (see below). The aLTR-supported trees are also provided in NEWICK format.</p> <p>In all files the first three letters of the sequence names are abbreviations of the species names, followed by the chromosome assignment of the genes and the abbreviated α subunit name (full names for the human sequences).</p> <p><strong>Phylogenetic methods:</strong></p> <p>The phylogenetic analyses were done using the PhyML 3.0 algorithm in PhyML-aBayes (3.0.1 beta) or through the web-based form of the PhyML 3.0 algorithm, both available from http://www.atgc-montpellier.fr/phyml. </p> <p>Trees supported by SH-like approximate likelihood ratio tests (aLTR) were done with standard settings: LG model of amino acid substitution; 4 substitution rate categories; equilibrium frequencies from the model; fixed proportion of invariable sites (0.0); gamma shape parameters estimated from the alignment; starting tree estimated using BIONJ; NNI method selected for tree topology improvement with both topology and branch length optimization.</p> <p>Trees supported by non-parametric bootstrap analyses with 100 replicates were done with the following settings: the JTT model of amino acid substitution was chosen based on analysis of the amino acid alignments in  ProtTest 1.4 (<em>http://darwin.uvigo.es/software/prottest.html</em>); 8 substitution rate categories; equilibrium frequencies, proportion of invariable sites and gamma shape parameters estimated from the alignment; starting tree estimated using BIONJ; NNI and SPR methods selected for tree topology improvement with both topology and branch length optimization. </p> <p>Statistical support values are shown at the nodes. The trees were rooted with the identified <em>Drosophila melanogaster</em> sequence.</p> <p><strong>Species abbreviations:</strong></p> <p>Species abbreviations are applied as follows: Homo sapiens (Hsa, human),  Mus musculus (Mmu, mouse), Monodelphis domestica (Mdo, opossum), Gallus gallus (Gga, chicken), Danio rerio (Dre, zebrafish), Oryzias latipes (Ola, medaka), Gasterosteus aculeatus (Gac, stickleback), Tetraodon nigroviridis (Tni, green spotted puffer), Ciona savignyi (Csa, tunicate), Branchiostoma floridae (Bfl, lancelet), Drosophila melanogaster (Dme, fruit fly).</p> <p><strong>References:</strong></p> <p>1. Widmark J, Sundström G, Ocampo Daza D, Larhammar D (2011) Differential evolution of voltage-gated sodium channels in tetrapods and teleost fishes. Molecular biology and evolution 28:859-71. DOI: 10.1093/molbev/msq257.</p> <p>2. Guindon S et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology 59:307-21. DOI: 10.1093/sysbio/syq010.</p> <p>3. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-5. DOI: 10.1093/bioinformatics/bti263.</p> <p> </p> <p><em>Description updated 2012-12-06.</em></p

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions-7

Mpared to mouse, , and . Chromosomes, scaffolds, gene positions, gene order and species abbreviations are given in the same way as in Fig. 6.<p><b>Copyright information:</b></p><p>Taken from "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"</p><p>http://www.biomedcentral.com/1471-2148/8/184</p><p>BMC Evolutionary Biology 2008;8():184-184.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2453138.</p><p></p

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions-8

O mouse, , and . Chromosomes, scaffolds, gene positions, gene order and species abbreviations are given in the same way as in Fig. 6.<p><b>Copyright information:</b></p><p>Taken from "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"</p><p>http://www.biomedcentral.com/1471-2148/8/184</p><p>BMC Evolutionary Biology 2008;8():184-184.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2453138.</p><p></p

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions-9

Romosomes as the NPY receptor genes in and human. Note that position of genes is shuffled to simplify the picture. Striped boxes indicate gene losses. Position for genes on Hsa2 and Hsa7 is indicated in the boxes.<p><b>Copyright information:</b></p><p>Taken from "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"</p><p>http://www.biomedcentral.com/1471-2148/8/184</p><p>BMC Evolutionary Biology 2008;8():184-184.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2453138.</p><p></p

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions-6

mouse, , and . Chromosomes, scaffolds, gene positions, gene order and species abbreviations are given in the same way as in Fig. 6.<p><b>Copyright information:</b></p><p>Taken from "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"</p><p>http://www.biomedcentral.com/1471-2148/8/184</p><p>BMC Evolutionary Biology 2008;8():184-184.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2453138.</p><p></p

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions-4

(NKR), C (OGDH), D (PX19), E (SORB) and F (TSPAN). Trees were constructed and visualized in the same way as in Fig. 4.<p><b>Copyright information:</b></p><p>Taken from "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"</p><p>http://www.biomedcentral.com/1471-2148/8/184</p><p>BMC Evolutionary Biology 2008;8():184-184.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2453138.</p><p></p

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions-1

Ed as control to verify quality and content of samples.<p><b>Copyright information:</b></p><p>Taken from "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"</p><p>http://www.biomedcentral.com/1471-2148/8/184</p><p>BMC Evolutionary Biology 2008;8():184-184.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2453138.</p><p></p

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions-0

En collapsed. Human bradykinin receptor B1 was used to root the tree.<p><b>Copyright information:</b></p><p>Taken from "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"</p><p>http://www.biomedcentral.com/1471-2148/8/184</p><p>BMC Evolutionary Biology 2008;8():184-184.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2453138.</p><p></p