Abstract
Cataloging an accurate functional gene set for the Symbiodiniaceae species is crucial for addressing biological questions of dinoflagellate symbiosis with corals and other invertebrates. To improve the gene models of Fugacium kawagutii, we conducted high-throughput chromosome conformation capture (Hi-C) for the genome and Illumina combined with PacBio sequencing for the transcriptome to achieve a new genome assembly and gene prediction. A 0.937-Gbp assembly of F. kawagutii were obtained, with a N50 > 13 Mbp and the longest scaffold of 121 Mbp capped with telomere motif at both ends. Gene annotation produced 45,192 protein-coding genes, among which, 11,984 are new compared to previous versions of the genome. The newly identified genes are mainly enriched in 38 KEGG pathways including N-Glycan biosynthesis, mRNA surveillance pathway, cell cycle, autophagy, mitophagy, and fatty acid synthesis, which are important for symbiosis, nutrition, and reproduction. The newly identified genes also included those encoding O-methyltransferase (O-MT), 3-dehydroquinate synthase, homologous-pairing protein 2-like (HOP2) and meiosis protein 2 (MEI2), which function in mycosporine-like amino acids (MAAs) biosynthesis and sexual reproduction, respectively. The improved version of the gene set (Fugka_Geneset _V3) raised transcriptomic read mapping rate from 33% to 54% and BUSCO match from 29% to 55%. Further differential gene expression analysis yielded a set of stably expressed genes under variable trace metal conditions, of which 115 with annotated functions have recently been found to be stably expressed under three other conditions, thus further developing the “core gene set” of F. kawagutii. This improved genome will prove useful for future Symbiodiniaceae transcriptomic, gene structure, and gene expression studies, and the refined “core gene set” will be a valuable resource from which to develop reference genes for gene expression studies.
Highlights
Fugacium kawagutii is one of the Symbiodiniaceae dinoflagellates, which are mostly essential endosymbionts of reef corals and many other invertebrates [1]
With the advance in high-throughput sequencing (HTS), six draft genomes from four genera (Symbiodinium, Breviolum, Cladocopium, and Fugacium) have been sequenced. These genomes have assembly rates ranging from 41.07% to 88.98% and rates at which genes are supported by expressed sequencing tag (EST) ranging from 62.5% to 77.2% (Table 1)
We improved genome assembly with high-throughput chromosome conformation capture (Hi-C) data, and refined the set of gene models based on the high-quality mRNA sequences from the PacBio ISO-Seq platform and the Illumina HiSeq × ten platform
Summary
Fugacium kawagutii is one of the Symbiodiniaceae dinoflagellates, which are mostly essential endosymbionts of reef corals and many other invertebrates [1]. Recent years have witnessed a rapid increase in high-throughput genome, transcriptome sequencing, and significant enhancement of molecular understanding of the symbiosis, while current genome data (genome and gene models) are still with quality compromises due to the complexities of the genome architecture, especially for the immense dinoflagellate genomes. These studies have assembled 41.07% to 88.98% of their respective genomes, predicting 26,609–69,018 protein coding genes. For F. kawagutii, for instance, a recent repeated sequencing [10] provided improvement to the original assembly [9], illustrating the need for continued effort to refine the genome data. We screened for genes that showed no significant changes in expression under different treatment conditions, and further developed the recently initiated “core gene set” of F. kawagutii, a valuable resource for developing reference genes for gene expression studies
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