Binning enables efficient host genome reconstruction in cnidarian holobionts

Abstract

BackgroundMany cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities—together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.ResultsOur results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.ConclusionsBinning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.

Transcriptome of Sphaerospora molnari (Cnidaria, Myxosporea) blood stages provides proteolytic arsenal as potential therapeutic targets against sphaerosporosis in common carp

“…Free living cnidarians have variable accounts of their retained complete BUSCO genes, e.g. Acropora digitifera 69% (675/978) [39]; Exaiptasia pallida 84.5% (826/978) [39]; Scleractinian coral Porites lutea 56.4% [40]. Other metazoan parasites have also retained a higher level of genes e.g.…”

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage

“…Adapter and primer trimming of amplicon raw reads were performed through an inhouse pipeline 50 . Based on a pipeline including FLASH v.1.2.11 51 , USE-ARCH v.10 52 , UPARSE 53 , and the Ribosomal Database Project (RDP) classifier v.2.9 54 , all amplicons datasets were processed as recently described [55][56][57][58] (For details see: https ://www.drive 5.com/usear ch/manua l10/ex_miseq .html). In brief, all sequences that were not merged by FLASH (default settings with modifications [M = 300]), sequences with > 1 N (ambiguous base) in the sequence read and expected errors > 0.5 were discarded.…”

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

“…The bin quality metrics were computed with BUSCO2 ( Simão et al, 2015 ) ( Table 1 ) and QUAST ( Gurevich et al, 2013 ). Both the stringent metagenomics binning procedure (a procedure also expedient in other holobiont organisms ( Celis et al, 2018 )) and the very low proportion of multiple orthologue hits in the BUSCO2 assessment ( Table 1 ) attest to the lack of evidence for residual non-placozoan contamination within the scaffolds used for gene prediction.…”