Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion

Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new nonmodel genome resource for the study of ciliate ecology and genomic biology and provides a detailed functional counterpart to ecological research on S. arcuata.

Thinking embodiment with genetics: epigenetics and postgenomic biology in embodied cognition and enactivism

The role of the body in cognition is acknowledged across a variety of disciplines, even if the precise nature and scope of that contribution remain contentious. As a result, most philosophers working on embodiment—e.g. those in embodied cognition, enactivism, and ‘4e’ cognition—interact with the life sciences as part of their interdisciplinary agenda. Despite this, a detailed engagement with emerging findings in epigenetics and post-genomic biology has been missing from proponents of this embodied turn. Surveying this research provides an opportunity to rethink the relationship between embodiment and genetics, and we argue that the balance of current epigenetic research favours the extension of an enactivist approach to mind and life, rather than the extended functionalist view of embodied cognition associated with Andy Clark and Mike Wheeler, which is more substrate neutral.

Genomes of skipper butterflies reveal extensive convergence of wing patterns

For centuries, biologists have used phenotypes to infer evolution. For decades, a handful of gene markers have given us a glimpse of the genotype to combine with phenotypic traits. Today, we can sequence entire genomes from hundreds of species and gain yet closer scrutiny. To illustrate the power of genomics, we have chosen skipper butterflies (Hesperiidae). The genomes of 250 representative species of skippers reveal rampant inconsistencies between their current classification and a genome-based phylogeny. We use a dated genomic tree to define tribes (six new) and subtribes (six new), to overhaul genera (nine new) and subgenera (three new), and to display convergence in wing patterns that fooled researchers for decades. We find that many skippers with similar appearance are distantly related, and several skippers with distinct morphology are close relatives. These conclusions are strongly supported by different genomic regions and are consistent with some morphological traits. Our work is a forerunner to genomic biology shaping biodiversity research.

Direct determination of diploid genome sequences

ABSTRACTDetermining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses and, in general, failing to capture sequences novel to a given genome.Some de novo assemblies have been constructed, free of reference bias, but nearly all were constructed by merging homologous loci into single ‘consensus’ sequences, generally absent from nature. These assemblies do not correctly represent the diploid biology of an individual. In exactly two cases, true diploid de novo assemblies have been made, at great expense. One was generated using Sanger sequencing and one using thousands of clone pools.Here we demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies. We make a single library from ~1 ng of high molecular weight DNA, using the 10x Genomics microfluidic platform to partition the genome. We applied this technique to seven human samples, generating low-cost HiSeq X data, then assembled these using a new ‘pushbutton’ algorithm, Supernova. Each computation took two days on a single server. Each yielded contigs longer than 100 kb, phase blocks longer than 2.5 Mb, and scaffolds longer than 15 Mb. Our method provides a scalable capability for determining the actual diploid genome sequence in a sample, opening the door to new approaches in genomic biology and medicine.

Linear Causation Schemes in Post-genomic Biology: The Subliminal and Convenient One-to-one Genotype-Phenotype Mapping Assumption

<p class="p1"><span class="s1"><strong>Abstract </strong></span>| In this essay we question the validity of basic assumptions in molecular biology and evolution on the basis of recent experimental data and through the lenses of a systems and nonlinear perspective<span class="s2"><strong>. </strong></span>We focus our discussion on two well-established foundations of biology: the flow of information in molecular biology (i<span class="s2"><strong>.</strong></span>e<span class="s2"><strong>.</strong></span>, the central dogma of molecular biology), and the “causal” linear signaling pathway paradigm<span class="s2"><strong>.</strong></span>Under both paradigms the subliminal assumption of a one-to-one genotype-phenotype mapping (GPM) constitutes an underlying working hypothesis in many cases<span class="s2"><strong>. </strong></span>We ask if this is empirically sustainable in post-genomic biology<span class="s2"><strong>. </strong></span>We conclude that when embracing the notion of complex networks and dynamical processes governing cellular behavior — a view now empirically validated — one-to-one mapping can no longer be sustained<span class="s2"><strong>. </strong></span>We hypothesize that such subliminal and sometimes explicit assumption may be upheld, to a certain degree, because it is convenient for the private appropriation and marketing of scientific discoveries<span class="s2"><strong>. </strong></span>Hopefully, our discussion will help smooth the undergoing transition towards a more integrative, explanatory, quantitative and multidisciplinary systems biology<span class="s2"><strong>. </strong></span>The latter will likely also yield more preventive and sustainable medical and agricultural developments, respectively, than a reductionist approach.</p>