Next Article in Journal
Assessment of a Loop-Mediated Isothermal Amplification (LAMP) Assay for the Rapid Detection of Pathogenic Bacteria from Respiratory Samples in Patients with Hospital-Acquired Pneumonia
Previous Article in Journal
Isolation and Identification of Microvirga thermotolerans HR1, a Novel Thermo-Tolerant Bacterium, and Comparative Genomics among Microvirga Species
Previous Article in Special Issue
Cell Cycle, Division Rate, and Feeding of the Heterotroph Phalacroma rotundatum in a Chilean Fjord
Open AccessArticle

Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii

by Tangcheng Li 1,2,†, Liying Yu 1,†, Bo Song 3,†, Yue Song 4, Ling Li 1, Xin Lin 1,* and Senjie Lin 1,2,5,*
1
State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
2
Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
3
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
4
BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
5
Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao 266237, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Microorganisms 2020, 8(1), 102; https://doi.org/10.3390/microorganisms8010102
Received: 23 October 2019 / Revised: 1 January 2020 / Accepted: 8 January 2020 / Published: 11 January 2020
(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)
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. View Full-Text
Keywords: RNA-seq; Symbiodiniaceae; Fugacium kawagutii; gene set; genome; core genes; Hi-C RNA-seq; Symbiodiniaceae; Fugacium kawagutii; gene set; genome; core genes; Hi-C
Show Figures

Figure 1

MDPI and ACS Style

Li, T.; Yu, L.; Song, B.; Song, Y.; Li, L.; Lin, X.; Lin, S. Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii. Microorganisms 2020, 8, 102.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop