Sequencing, de novo assembly and annotation of the genome of the scleractinian coral, Pocillopora acuta

Abstract

Coral reefs are the most divers marine ecosystem. However, under the pressure of global changes and anthropogenic disturbances corals and coral reefs are declining worldwide. In order to better predict and understand the future of these organisms all the tools of modern biology are needed today. However, many NGS based approaches are not feasible in corals because of the lack of reference genomes. Therefore we have sequenced, de novo assembled, and annotated, the draft genome of one of the most studied coral species, Pocillopora acuta (ex damicornis). The sequencing strategy was based on four libraries with complementary insert size and sequencing depth (180pb, 100x; 3Kb, 25x; 8kb, 12x and 20 kb, 12x). The de novo assembly was performed with Platanus (352 Mb; 25,553 scaffolds; N50 171,375 bp). 36,140 genes were annotated by RNA-seq data and 64,558 by AUGUSTUS (Hidden-Markov model). Gene functions were predicted through Blast and orthology based approaches. This new genomic resource will enable the development of a large array of genome wide studies but also shows that the de novo assembly of a coral genome is now technically feasible and economically realistic.

Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases

“…While the predicted number of genes is similar, the genome size of M. capitata is over twice that of P. acuta (Shumaker et al, 2019;Vidal-Dupiol et al, 2019). One explanation for the higher methylation in M. capitata is that with greater energy availability -through translocation from high density Symbiodiniaceae populations and energy stores in perforate tissues -there is greater capacity for maintenance methyltransferase to maintain high methylation, and thus reduce gene expression variability and spurious expression (Liew et al, 2018;.…”

“…Previously sequenced and assembled coral genomes were used for mapping of DNA methylation data. These include Montipora capitata (Shumaker et al, 2019) and Pocillopora acuta (Vidal-Dupiol et al, 2019). Both of the coral genomes have a high and similar number of predicted genes (63,227 in M.capitata and 64,558 in P. acuta ).…”

“…Bisulfite-converted genomes were created in-silico with Bowtie 2-2.3.4 [Linux x84_64 version; (Langmead & Salzberg, 2012)) using through Bismark v0.21.0 (Krueger & Andrews, 2011). Trimmed reads were aligned to the BS-converted P. acuta genome (Vidal-Dupiol et al, 2019) and the BS-converted M. capitata genome (Shumaker et al, 2019) with Bismark v0.21.0 with alignment stringency set by and the default MAPQ score threshold of 20. To check mapping rates for endosymbionts and quantify percent methylation, trimmed reads from P. actua libraries were also aligned to the Cladicopium goreaui genome [type C1, previously Symbiodinium goreaui (Liu et al, 2018)] using the same settings as specified above.…”

“…The M. capitata genome annotation yielded gene (a combination of AUGUSTUS and GeMoMa predictions), coding sequence, and intron tracks (Shumaker et al, 2019). Similarly, gene (AUGUSTUS predictions), coding sequence, and intron information was obtained from the P. acuta genome (Vidal-Dupiol et al, 2019). Flanking regions upstream and downstream of genes were generated with BEDtools v2.29.2 for each genome separately (Quinlan & Hall, 2010); flankBED was used to generate 1000 bp flanks upstream and downstream of annotated genes from each genome.…”

Population genomics ofPocilloporacorals: insights from RAD-sequencing

“…After sampling, all colonies fragments were bleached with menthol according to previously detailed protocols (Vidal-Dupiol et al, 2019;Wang et al, 2012). Total genomic DNA was extracted according to the protocol of (Sambrook et al, 1989), followed by a purification using Qiagen DNeasy blood and tissue spin columns (Qiagen).…”