0000000000909691
AUTHOR
Ingo Ebersberger
What is in a lichen? A metagenomic approach to reconstruct the holo-genome of Umbilicaria pustulata
AbstractLichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are generally poor candidates for experimentation. Obtaining contiguous, high quality genomes for such symbiotic communities is technically challenging. Here we present the first assembly of a lichen holo-genome from metagenomic whole genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis – the fungus Umbilicaria pustulata (33 Mbp) and the green alga Trebouxia sp. (53 Mbp) – were assemble…
Transcriptome data reveal syndermatan relationships and suggest the evolution of endoparasitism in acanthocephala via an epizoic stage
The taxon Syndermata comprises the biologically interesting wheel animals ("Rotifera": Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparas…
Support for the monophyletic origin of Gnathifera from phylogenomics
The monophyletic origin of Spiralia within the metazoan tree of life is supported by many large-scale phylogenomic data. While there is now substantial molecular evidence for Lophotrochozoa being a monophyletic taxon within Spiralia, the phylogenetic affiliations of many other spiralian phyla remain unclear. Here we focus on the question of a monophyletic taxon Gnathifera, which was originally characterized by jaw morphology as comprising the taxa Rotifera, Acanthocephala and Gnathostomulida. Based on a large-scale molecular sequence dataset of 11,146 amino acid residues, we reconstructed phylogenetic trees of spiralian phyla using maximum-likelihood and Bayesian approaches. We obtain the f…
EST sequencing of Onychophora and phylogenomic analysis of Metazoa
Onychophora (velvet worms) represent a small animal taxon considered to be related to Euarthropoda. We have obtained 1873 5' cDNA sequences (expressed sequence tags, ESTs) from the velvet worm Epiperipatus sp., which were assembled into 833 contigs. BLAST similarity searches revealed that 51.9% of the contigs had matches in the protein databases with expectation values lower than 10(-4). Most ESTs had the best hit with proteins from either Chordata or Arthropoda (approximately 40% respectively). The ESTs included sequences of 27 ribosomal proteins. The orthologous sequences from 28 other species of a broad range of phyla were obtained from the databases, including other EST projects. A conc…
Additional file 6: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Snail collection sites. (PDF 330 kb)
Additional file 3: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Results and figure for the climate niche divergence PCA. (PDF 14 kb)
Additional file 1: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Results of the a) sequencing effort and b) assembly statistics. (PDF 257 kb)
Additional file 2: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Phylogenetic inference on species relationships. (PDF 255 kb)
Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
AbstractBackgroundLife history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related EuropeanRadixspecies.ResultsSnails of the genusRadixoccupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural …
A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain
The intron positions found in globin genes of plants, protozoa and invertebrates have been interpreted as evidence for a three-intron-four-exon structure of the ancestral globin gene. In particular, the so-called 'central' introns, which are not found in vertebrate globin genes but are present in a variety of invertebrate and plant species, have been used as an argument for an ancestral gene structure featuring three introns. We have analyzed the presence or absence of central introns in the Gb genes 2beta, 9 and 7A of various European and Australasian species of the insect Chironomus. We find unrelated central introns at different positions in some of the species investigated, while other …
Additional file 5: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Results enrichment analyses. (XLSX 11 kb)
Additional file 4: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Selected genes with annotations. (XLSX 35 kb)
Additional file 7: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Radix mt-genome primers. (XLS 36 kb)
Additional file 8: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Annotations and evolutionary models of the clusters used for phylogenetic inference. (XLSX 10 kb)
Data from: Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Background: Life history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related European Radix species. Results: Snails of the genus Radix occupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural…