Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians

Abstract

BackgroundPlanarians are non-parasitic Platyhelminthes (flatworms) famous for their regeneration ability and for having a well-organized brain. Dugesia japonica is a typical planarian species that is widely distributed in the East Asia. Extensive cellular and molecular experimental methods have been developed to identify the functions of thousands of genes in this species, making this planarian a good experimental model for regeneration biology and neurobiology. However, no genome-level information is available for D. japonica, and few gene regulatory networks have been identified thus far.ResultsTo obtain whole-genome information on this species and to study its gene regulatory networks, we extracted genomic DNA from 200 planarians derived from a laboratory-bred asexual clonal strain, and sequenced 476 Gb of data by second-generation sequencing. Kmer frequency graphing and fosmid sequence analysis indicated a complex genome that would be difficult to assemble using second-generation sequencing short reads. To address this challenge, we developed a new assembly strategy and improved the de novo genome assembly, producing a 1.56 Gb genome sequence (DjGenome ver1.0, including 202,925 scaffolds and N50 length 27,741 bp) that covers 99.4% of all 19,543 genes in the assembled transcriptome, although the genome is fragmented as 80% of the genome consists of repeated sequences (genomic frequency ≥ 2). By genome comparison between two planarian genera, we identified conserved non-coding elements (CNEs), which are indicative of gene regulatory elements. Transgenic experiments using Xenopus laevis indicated that one of the CNEs in the Djndk gene may be a regulatory element, suggesting that the regulation of the ndk gene and the brain formation mechanism may be conserved between vertebrates and invertebrates.ConclusionThis draft genome and CNE analysis will contribute to resolving gene regulatory networks in planarians. The genome database is available at: http://www.planarian.jp.Electronic supplementary materialThe online version of this article (10.1186/s40851-018-0102-2) contains supplementary material, which is available to authorized users.

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

“…After removal of low quality, truncated and adapter chimera sequences, read depth was 173, 192 and 196 M read pairs. To analyse this experiment we generated novel annotations (see Methods) of the most recent S. mediterranea genome assembly [47] and the recently sequenced D. japonica genome [48]. We mapped 96% and 85% of S. mediterranea and D. japonica reads to gene models in their respective gene annotations.…”

“…The S. mediterranea S2F2 genome [47] was downloaded from Planmine, and the D. japonica v 1.0 genome [48] was downloaded from http://www.planarian.jp. De novo gene models were created for both S. mediterranea and D. japonica.…”

The Cellular and Molecular Basis for Planarian Regeneration

“…Classical inquiry into planarian regeneration involved diverse injuries and transplantations. A suite of molecular and cellular tools have enabled a recent era of intensive molecular genetic inquiry into planarian regeneration (Umesono et al, 1997;Sá nchez Alvarado and Newmark, 1999;Newmark and Sá nchez Alvarado, 2000;Reddien et al, 2005a;Hayashi et al, 2006;Wagner et al, 2011;Wurtzel et al, 2015;An et al, 2018;Fincher et al, 2018;Grohme et al, 2018;Plass et al, 2018;Zeng et al, 2018). Much excellent and fascinating work on planarian biology will not be reviewed here, such as the role of myriad molecules that give planarian stem cells (neoblasts) their attributes, the molecular genetics of the planarian germline, organ formation and function, signaling pathway function and evolution, cilia, genome repair and protection, aging, epigenetics, regulatory RNAs, immune biology, and planarian embryogenesis.…”

The evolutionary terrestrialization of planarian flatworms (Platyhelminthes, Tricladida, Geoplanidae): a review and research programme

“…It has been suggested that many of the problems associated with the amplification and sequencing of planarian molecular markers may be solved by applying next generation sequencing (NGS) methodologies (Sluys and Riutort 2018). This new era has started already, and in recent years genomes and transcriptomes of freshwater planarians have already been sequenced (Egger et al 2015;An et al 2018;Grohme et al 2018;, contributing new anonymous nuclear markers that can be used as phylogenetic tools. There are even bioinformatic pipelines that can help in the discovery of these markers using NGS data as input (Frías-López et al 2016).…”