Telford, M. J. | Search bioRxiv

bioRxiv2018

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

Cell lineages provide the framework for understanding how multicellular organisms are built and how cell fates are decided during development. Describing cell lineages in most organisms is challenging, given the number of cells involved; even a fruit fly larva has ~50,000 cells and a small mammal has more than 1 billion cells. Recently, the idea of using CRISPR to induce mutations during development as heritable markers for lineage reconstruction has been proposed and trialled by several groups. While an attractive idea, its practical value depends on the accuracy of the cell lineages that can be generated by this method. Here, we use computer simulations to estimate the performance of this approach under different conditions. Our simulations incorporate empirical data on CRISPR-induced mutation frequencies in Drosophila. We show significant impacts from multiple biological and technical parameters - variable cell division rates, skewed mutational outcomes, target dropouts and different mutation sequencing strategies. Our approach reveals the limitations of recently published CRISPR recorders, and indicates how future implementations can be optimised to produce accurate cell lineages.

developmental biology↗

bioRxiv2017

Molecular data from Orthonectid worms show they are highly degenerate members of phylum Annelida not phylum Mesozoa.

SummaryThe Mesozoa are a group of tiny, extremely simple, vermiform endoparasites of various marine animals (Fig. 1). There are two recognised groups within the Mesozoa: the Orthonectida (Fig. 1a,b; with a few hundred cells including a nervous system made up of just 10 cells [1]) and the Dicyemids (Fig. 1c; with at most 42 cells [2]). They are classic Problematica [3] - the name Mesozoa suggests an evolutionary position intermediate between Protozoa and Metazoa (animals) [4] and implies their simplicity is a primitive state, but molecular data have shown they are members of Lophotrochozoa within Bilateria [5-8] which would mean they derive from a more complex ancestor. Their precise phylogenetic affinities remain uncertain, however, and ascertaining this is complicated by the very fast evolution observed in genes from both groups, leading to the common systematic error of Long Branch Attraction (LBA) [9]. Here we use mitochondrial and nuclear gene sequence data, and show beyond doubt that both dicyemids and orthonectids are members of the Lophotrochozoa. Carefully addressing the effects of systematic errors due to unequal rates of evolution, we show that the phylum Mesozoa is polyphyletic. While the precise position of dicyemids remains unresolved within Lophotrochozoa, we unequivocally identify orthonectids as members of the phylum Annelida. This result reveals one of the most extreme cases of body plan simplification in the animal kingdom; our finding makes sense of an annelid-like cuticle in orthonectids [1] and suggests the circular muscle cells repeated along their body [10] may be segmental in origin.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC=\"FIGDIR/small/235549_fig1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@76ca5org.highwire.dtl.DTLVardef@16df6eaorg.highwire.dtl.DTLVardef@6da877org.highwire.dtl.DTLVardef@14f3056_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1:C_FLOATNO The mesozoans Intoshia variabili and Dicyema typus A. Differential Interference contrast micrograph of an Intoshia variabili female showing repeated bands of ciliated cells. Picture G. Slyusarev (St Petersburg State University, Russia).\n\nB. Confocal image of a phalloidin stained female specimen of Intoshia linei reveals repeated set of circular muscles. Picture G. Slyusarev (St Petersburg State Univ.).\n\nC. Rhombogen stage of a dicyemid (Dicyema typus from the Octopus) adapted from Hyman L.H. The Invertebrates: Protozoa through Ctenophora McGraw-Hill, New York 1940(19). Anterior to right in all images.\n\nC_FIG

evolutionary biology↗