DR.

LI BIAN (Orcid ID : 0000-0001-5250-5981)

DR. FENGHUI LI (Orcid ID : 0000-0003-2096-7908)

Article type : Resource Article

Chromosome-level genome assembly of the greenfin horse-faced filefish (Thamnaconus

septentrionalis) using Oxford Nanopore PromethION sequencing and Hi-C technology
Li Bian1,2*, Fenghui Li1,3*, Jianlong Ge1,2*, Pengfei Wang4,5, Qing Chang1,2, Shengnong Zhang1,2, Jie Li1,2,

Changlin Liu1,2, Kun Liu6, Xintian Liu7, Xuming Li8, Hongju Chen8, Siqing Chen1,2, Changwei Shao1,2, Zhishu

Lin9

1. Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China

2. Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for

Marine Science and Technology (Qingdao), Qingdao, China

3. National Demonstration Center for Experimental Fisheries Science Education, Shanghai Collaborative

Innovation for Aquatic Animal Genetics and Breeding, Shanghai Engineering Research Center of Agriculture,

Shanghai Ocean University, Shanghai, China

4. Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, Guangzhou, China

5. Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries

Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China

6. Qingdao Conson Oceantec Valley Development Co., Ltd, Qingdao, China

7. Weihai Fishery Technology Extension Station, Weihai, China

8. Biomarker Technologies Corporation, Beijing, China

9. Qingdao Municipal Ocean Technology Achievement Promotion Center, Qingdao, China

Correspondence:

Siqing Chen, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
This article has been accepted for publication and undergone full peer review but has not been
through the copyediting, typesetting, pagination and proofreading process, which may lead to
differences between this version and the Version of Record. Please cite this article as doi:
10.1111/1755-0998.13183
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Email: [email protected]

Changwei Shao, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao,

China.

Email: [email protected]

Zhishu Lin, Qingdao Municipal Ocean Technology Achievement Promotion Center, Qingdao, China.

Email: [email protected]

*These authors contributed equally to this work.

Abstract
The greenfin horse-faced filefish, Thamnaconus septentrionalis, is a valuable commercial
fish species that is widely distributed in the Indo-West Pacific Ocean. This fish has characteristic
blue-green fins, rough skin and a spine-like first dorsal fin. T. septentrionalis represents a
conservation issue because its population has declined sharply, and it is an important marine
aquaculture fish species in China. The genomic resources of the filefish are lacking, and no
reference genome has been released. In this study, the first chromosome-level genome of T.
septentrionalis was constructed using nanopore sequencing and Hi-C technology. A total of 50.95
Gb polished nanopore sequences were generated and were assembled to 474.31 Mb genome,
accounting for 96.45% of the estimated genome size of this filefish. The assembled genome
contained only 242 contigs, and the achieved contig N50 was 22.46 Mb, reaching a surprisingly
high level among all the sequenced fish species. Hi-C scaffolding of the genome resulted in 20
pseudochromosomes containing 99.44% of the total assembled sequences. The genome contained
67.35 Mb of repeat sequences, accounting for 14.2% of the assembly. A total of 22,067
protein-coding genes were predicted, 94.82% of which were successfully annotated with putative
functions. Furthermore, a phylogenetic tree was constructed using 1,872 single-copy gene families
and 67 unique gene families were identified in the filefish genome. This high-quality assembled
genome will be a valuable genomic resource for a range of genomic, conservation and breeding
studies of T. septentrionalis in future research.
Key words
Filefish, genome assembly, Oxford Nanopore sequencing, Hi-C

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1 Introduction
The greenfin horse-faced filefish (Thamnaconus septentrionalis, hereafter known as
“filefish”) belongs to the family Monacanthidae (Tetraodontiformes) and has characteristic
blue-green fins, rough skin and a spine-like first dorsal fin (Figure 1) (Su & Li, 2002). This fish is
widely distributed in the Indo-West Pacific Ocean, ranging from the Korean Peninsula, Japan and
the China Sea to East Africa. Filefish is a temperate demersal species inhabiting a depth range of
50-120 m (Su & Li, 2002). Filefish feed on plankton, such as copepods, ostracods, amphipods and
mollusks (Su & Li, 2002). This fish goes through annual long-distance seasonal migrations and
has diurnal vertical migration habits during wintering and spawning (Lin, Gan, Zheng, & Guan,
1984; Su & Li, 2002). Due to a high protein content and good taste, filefish is an important
commercial species in China, Korea and Japan. An interesting feature of filefish is its rough skin,
which is observed because the skin is covered with dense small scales. These scales are difficult to
remove, and people have to peel off the skin before eating. Given this property, filefish is also
called “skinned fish” in China.
As a commercially important species in China, the annual catch of filefish in the East China
Sea once reached 0.33 million tons in 1987 and 1989 (Chen, Zheng, & Li, 1998). However, the
wild resources have declined dramatically since 1990 due to overfishing, and the annual catch in
the same area was only 3,842 tons in 1994 (Chen, Li, & Hu, 2000). In subsequent years,
researchers have attempted to explore methods to properly culture filefish. Several key
technologies, including fertilized egg collection, sperm cryopreservation, larval rearing, and tank
and cage culturing, have been studied, and this species is cultivated commercially in China, Korea
and Japan (Guan et al., 2013; Kang et al., 2004; Li, Jiang, Xu, & Liu, 2002; Liu et al., 2017;
Mizuno, Shimizu-Yamaguchi, Miura, & Miura, 2012). The aquaculture practices for this species
can also be improved by genomics data, which facilitate genome-wide association studies
(GWAS) to identify DNA markers and causative genes associated with traits of interest (Yue &
Wang, 2017). In China, the demand sizes of filefish vary in different regions, and the smallest size
is only 150 g, which can be achieved within one year. One bottleneck of filefish cultivation is the
high mortality under high temperature, especially when the water temperature is above 25℃.

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Genomic information will enable GWAS to identify SNPs associated with fast-growth and
heat-tolerance traits, benefit genome-assisted breeding programs and make a sustainable and
profitable filefish cultivation industry. On the other hand, genomics resources will also support
better conservation studies of filefish. Given the wide distribution of this species, filefish may
undergo some degree of local adaptation, which can be resolved with genome-wide high quality
SNPs. However, the available genetic information of filefish is scarce. At present, only limited
genetic studies regarding microsatellite loci isolation and population structure are available for this
filefish (An et al., 2011; An, Lee, Park, & Jung, 2013; Bian et al., 2018; Xu, Chen, & Tian, 2010;
Xu, Tian, Liao, & Chen, 2009).
Spectacular improvements in high-throughput sequencing technology, especially
single-molecule sequencing methods, have notably reduced the sequencing costs, making a
genome project affordable for individual labs. Oxford Nanopore sequencing technology is
currently one of the most powerful methods for the rapid generation of long-read sequences and
has the potential to offer relatively low-cost genome sequencing of non-model animals. This
technology directly detects the input DNA without PCR amplification or synthesis; therefore, the
length of sequenced DNA can be notably long. The longest read generated by nanopore
sequencing has been up to 2,272,580 bases (Payne, Holmes, Rakyan, & Loose, 2018). Nanopore
sequencing has been used in several fish species to construct high-quality genome assemblies or to
increase the completeness of previous genome drafts (Austin et al., 2017; Ge et al., 2019; Jansen et
al., 2017; Kadobianskyi, Schulze, Schuelke, & Judkewitz, 2019; Tan et al., 2018). In the case of
red spotted grouper (Epinephelus akaara), a chromosome-level reference genome with a contig
N50 length of 5.25 Mb was constructed by taking advantage of nanopore sequencing and Hi-C
technology(Ge et al., 2019). In clown anemonefsh (Amphiprion ocellaris), a hybrid
Illumina/Nanopore method generated considerably longer scaffolds than the Illumina-only
approach with an 18-fold increase in N50 length and increased genome completeness by an
additional 16% (Tan et al., 2018).
In this study, the first chromosome-level genome of filefish was constructed using Nanopore
sequencing and Hi-C technology. These genomic data will benefit a comprehensive conservation

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study of filefish along the coast of China and Korea to implement better protection of wild
populations and enable us to screen for genetic variations correlated with fast-growth and
heat-tolerance traits of filefish in the future.
2 Materials and methods
2.1 Ethics statement
This study was approved by the Review Committee for the Use of Animal Subjects of
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences. In China,
academic research on filefish is highly encouraged and does not require particular permits.
2.2 Sample and DNA extraction
A single female fish (~325 g) was collected on August 2018 from the Tianyuan Fisheries Co.,
Ltd. The muscle tissue below the dorsal fin was taken and stored in the liquid nitrogen until DNA
extraction. Genomic DNA was extracted using the CTAB (cetyltrimethylammonium bromide)
method. The quality and concentration of the extracted genomic DNA was checked using 1%
agarose gel electrophoresis and a Qubit fluorimeter (Invitrogen, Carlsbad, CA, USA). This
high-quality DNA was used for subsequent Nanopore, Illumina and Hi-C sequencing.
2.3 Library construction and genome sequencing
To generate Oxford Nanopore long reads, approximately 15 μg of genomic DNA was
size-selected (30–80 kb) with BluePippin (Sage Science, Beverly, MA, USA) and processed
according to the Ligation Sequencing Kit 1D (SQK-LSK109) protocol. Briefly, DNA fragments
were repaired using NEBNext FFPE Repair Mix (New England Biolabs). After end-repair and
3’-adenylation with the NEBNext End repair/dA-tailing Module reagents (New England Biolabs),
the Oxford Nanopore sequencing adapters were ligated using NEBNext Quick Ligation Module
(E6056) (New England Biolabs). The final library was sequenced on 3 different R9.4 flow cells
using the PromethION DNA sequencer (Oxford Nanopore, Oxford, UK) for 48 hours. Guppy
software was used to conduct base calling of raw signal data. These obtained data were then
filtered to remove short reads (<5 kb) and the reads with low-quality bases and adapter sequences
(YSFRI, 2019c).
Illumina sequencing libraries were prepared to carry out genome size estimation, correction

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of genome assembly, and assembly evaluation. Paired-end (PE) libraries with insert sizes of 300
bp were constructed according to the Illumina standard protocol (San Diego, CA, USA) and
subjected to PE (2 × 150 bp) sequencing on an Illumina HiSeq X Ten platform (Illumina, San
Diego, CA, USA). After discarding the reads with low-quality bases, adapter sequences, and
duplicated sequences, the clean reads were used for subsequent analysis (YSFRI, 2019a).
2.4 Genome size estimation and genome assembly
A k-mer depth frequency distribution analysis (Liu et al., 2013) of the Illumina data was
conducted to estimate the genome size, heterozygosity, and content of repetitive sequences of the
filefish. Genome size (G) was estimated based on the following formula: G = k-mer number/
k-mer depth of homozygous peak, where k-mer number = total k-mers—abnormal k-mers (with
excessively low or excessively high frequency).
For genome assembly, Canu (version 1.5) (Koren et al., 2017) was conducted for initial read
correction, and the assembly was performed by Wtdbg (version1.0)
(https://github.com/ruanjue/wtdbg). The consensus assembly was generated by 2 rounds of Racon
(version 1.32) (Vaser, Sović, Nagaranjan, & Šikić, 2017) and 3 rounds of Pilon (version 1.21)
(Walker et al., 2014) polishing using the Illumina reads.
2.5 Hi-C library construction and sequencing
For Hi-C sequencing, the muscle tissue of filefish was used for library preparation according
to Rao et al (Rao et al., 2014). Briefly, the tissue cells were fixed with formaldehyde, and
restriction endonuclease Hind III was used to digest DNA. The 5’ overhang of the fragments was
repaired and labeled using biotinylated nucleotides, followed by ligation in a small volume. After
reversal of crosslinking, ligated DNA was purified and sheared to a length of 300-700 bp. The
DNA fragments with interaction relationships were captured with streptavidin beads and prepared
for Illumina sequencing. The final Hi-C libraries were sequenced on an Illumina HiSeq X Ten
platform (Illumina, San Diego, CA, USA) to obtain 2 × 150 bp paired-end reads (YSFRI, 2019b).
To assess the quality of Hi-C data, the plot of insert fragment length frequency was first made to
detect the quality of Illumina sequencing. Second, we used BWA-MEM (version 0.7.10-r789) (Li
& Durbin, 2009) to align the PE clean reads to the draft genome assembly. In the end, HiC-Pro

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(Servant et al., 2015) (version 2.10.0) was performed to find the valid reads from unique mapped
read pairs.
2.6 Chromosomal-level genome assembly using Hi-C data
We first performed error correction of the contigs by breaking them into segments measuring
50 kb on average and reassembled them with Hi-C data. The mismatched regions between Hi-C
assembly and original assembly were listed as candidate error regions, and the positions of low
Hi-C sequencing depth in these sequences were corrected. The corrected contigs and valid reads of
Hi-C were used to perform chromosomal-level genome assembly using LACHESIS (Burton et al.,
2013) with the following parameters: CLUSTER_MIN_RE_SITES=22;
CLUSTER_MAX_LINK_DENSITY=2; CLUSTER_NONINFORMATIVE_RATIO=2;
ORDER_MIN_N_RES_IN_TRUNK=10; and ORDER_MIN_N_RES_IN_SHREDS=10. To
evaluate the quality of the chromosomal-level genome assembly, a genome-wide Hi-C heatmap
was generated by ggplot2 in the R package.
2.7 Assessment of the genome assemblies
To assess the genome assembly completeness and accuracy, we first aligned the Illumina
reads to the filefish assembly using BWA-MEM (version 0.7.10-r789) (Li & Durbin, 2009).
Furthermore, CEGMA (version 2.5) (Parra, Bradnam, & Korf, 2007) was conducted to find core
eukaryotic genes (CEGs) in the genome with parameter set as identity>70%. Finally, the
completeness of the genome assembly was also evaluated by using BUSCO (version 2.0) (Simao,
Waterhouse, Ioannidis, Kriventseva, & Zdobnov, 2015) to search the genome against the
actinopterygii database, which consisted of 4584 orthologs.
2.8 Repeat annotation, gene prediction and functional annotation
We first used MITE-Hunter (Han & Wessler, 2010), LTR-FINDER (version 1.05) (Xu &
Wang, 2007), RepeatScout (version 1.0.5) (Price, Jones, & Pevzner, 2005) and PILER (Edgar &
Myers, 2005) to construct a de novo repeat library for filefish with default settings. These
predicted repeats were classified using PASTEClassifer (version 1.0) (Hoede et al., 2014) , and
then integrated with Repbase (19.06) (Bao, Kojima, & Kohany, 2015) to build a new repeat library
for final repeat annotation. In the end, RepeatMasker (version 4.0.6) (Tarailo-Graovac & Chen,

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2009) was performed to detect repetitive sequences in the filefish genome.
Ab initio-based, homolog-based, and RNA-sequencing (RNA-seq)-based methods were
conducted in combination to detect the protein-coding genes in filefish genome assembly.
Genscan (Burge & Karlin, 1997), Augustus (version 2.4) (Stanke & Waack, 2003), GlimmerHMM
(version 3.0.4) (Majoros, Pertea, & Salzberg, 2004), GeneID (version 1.4) (Blanco, Parra, &
Guigó, 2007), and SNAP (version 2006-07-28) (Korf, 2004) with default parameters were used for
ab initio-based gene prediction, and all of these programs were trained using the zebrafish gene
model before gene prediction. For Augustus gene prediction, the PASA gene model was also
retrieved as the initial gene model for training, and the best gene model with higher accuracy and
specificity was used. For the homolog-based method, the protein data of tiger pufferfish (Takifugu
rubripes), spotted green pufferfish (Tetraodon nigroviridis) and zebrafish (Danio rerio) from
GenBank were downloaded to conduct gene annotation using GeMoMa (version 1.3.1)
(Keilwagen et al., 2016). For the RNA-seq-based method, a mixture of 10 tissues（including brain,
eye, gill, heart, liver, intestine, spleen, ovary, kidney and muscle）of a female (not the same as
that in Nanopore sequencing) and the testis of a male filefish was used to construct an Illumina
sequencing library and subjected to PE (2 × 150 bp) sequencing on an Illumina HiSeq X Ten
platform (Illumina, San Diego, CA, USA) (YSFRI, 2019d). After discarding the reads with
low-quality bases, adapter sequences, and duplicated sequences, the retained high-quality clean
reads were first aligned to the assembly using Hisat (version 2.0.4) (Kim, Langmead, & Salzberg,
2015), and then assembled by Stringtie (version 1.2.3) (Pertea et al., 2015) followed by gene
prediction with TransDecoder (version 2.0) (http://transdecoder.github.io) and GeneMarkS-T
(version 5.1) (Tang, Lomsadze, & Borodovsky, 2015). A de novo transcriptome assembly was
conducted by Trinity (version 2.1.1) ( Haas et al., 2013), and PASA (version 2.0.2) (Haas et al.,
2003) was used for gene prediction. Finally, EVM (version 1.1.1) (Haas et al., 2008) and PASA
(version 2.0.2) (Haas et al., 2003) were performed to integrate the prediction results obtained from
the three methods. The EVM might lose some reliable genes during integration. We detected these
reliable genes by blasting the EVM missing genes against the homolog-based and RNA-seq-based
gene database with an e-value cutoff of 1E-5. The matched genes with good integrity were added

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back to the final gene dataset.
To functionally annotate the predicted genes, they were aligned to the nonredundant protein
sequences (NR), eukaryotic orthologous groups of proteins (KOG) (Tatusov et al., 2003), Kyoto
Encyclopedia of Genes and Genomes (KEGG) (Kanehisa & Goto, 2000) and TrEMBL
(Boeckmann et al., 2003) databases using BLAST (version 2.2.31) (Altschul, Gish, Miller, Myers,
& Lipman, 1990) with an e-value cutoff of 1E-5. Gene ontology (GO) (Consortium, 2004)
annotation was performed with Blast2GO (version 4.1) (Conesa et al., 2005). For noncoding RNA
prediction, we first used tRNAscan-SE (version 1.3.1) (Lowe & Eddy, 1997) to annotate transfer
RNAs (tRNAs). Furthermore, Infernal (version 1.1) (Nawrocki & Eddy, 2013) was used to search
for ribosomal RNAs (rRNAs) and microRNAs based on the Rfam (version 13.0)(Daub, Eberhardt,
Tate, & Burge, 2015) and miRbase (version 21.0) (Griffiths-Jones, Grocock, Van Dongen,
Bateman, & Enright, 2006) databases.
2.9 Comparative genomics
To resolve the phylogenetic position of the filefish, we first used OrthoMCL (version 2.0.9)
(Li, Stoeckert, & Roos, 2003) to detect ortholog groups by retrieving the protein data of eleven
teleost species including tiger pufferfish (Takifugu rubripes), yellowbelly pufferfish (Takifugu
flavidus), spotted green pufferfish (Tetraodon nigroviridis), red seabream (Pagrus major), medaka
(Oryzias latipes), large yellow croaker (Larimichthys crocea), three-spined stickleback
(Gasterosteus aculeatus), Nile tilapia (Oreochromis niloticus), Japanese seabass (Lateolabrax
maculatus), spotted gar (Lepisosteus oculatus) and zebrafish (Danio rerio) (Supporting
Information Table S1). The single-copy orthologous genes shared by all 12 species were further
aligned using MUSCLE (version 3.8.31) (Edgar, 2004) and concatenated to construct a
phylogenetic tree with PhyML (Guindon et al., 2010). The divergence time among species was
estimated by the MCMCTree program of the PAML package (version 4.7a) (Yang, 2007) .
Divergence times of L. oculatus-L. crocea (315~322 Mya), L. maculatus-L. crocea (95∼100 Mya)
and T. flavidus-T. rubripes (4.22∼4.70 Mya) from the TimeTree database (Kumar, Stecher,
Suleski, & Hedges, 2017) were used as the calibration times. CAFÉ (version 4.2) (De Bie,
Cristianini, Demuth, & Hahn, 2006) was used to identify expanded and contracted gene families.

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3.Results and discussion
3.1 Initial characterization of the filefish genome
The k-mer (k = 19 in this case) depth frequency distribution analysis of the 45.97 Gb clean
Illumina data was conducted to estimate the genome size, heterozygosity, and repeat content of
filefish (Table 1). The k-mer depth of 76 was found to be the highest peak in the plot, and a k-mer
number of 37,677,330,713 was used to calculate the genome size of filefish (Supporting
Information Figure S3). The sequences around k-mer depth of 38 were heterozygous sequences,
and k-mer depth greater than 153 represented repetitive sequences. The filefish genome size was
estimated to be 491.74 Mb, the heterozygosity was approximately 0.35%, and the contents of
repetitive sequences and guanine-cytosine were approximately 16.62% and 46.05%, respectively.
3.2 Genome assembly
A total of 50.95 Gb of high-quality clean reads, representing a 104‐fold coverage of the
genome, were generated from the PromethION DNA sequencer (Table 1, Supporting Information
Table S2-S3). After initial read correction with Canu, the data were assembled using Wtdbg
followed by Racon and Pilon polishing, which produced a 465.93 Mb genome assembly with a
surprisingly long contig N50 of 22.07 Mb (Supporting Information Table S4). The length of this
assembly was close to the genome size estimated by k-mer analysis (491.74 Mb), indicating an
appropriate assembly size was obtained from the Nanopore data. Among the sequenced
tetraodontiform species, the genome size of filefish was larger than that of Takifugu and
Tetraodon species, but smaller than that of Mola mola (Aparicio et al., 2002; Gao et al., 2014;
Jaillon et al., 2004; Pan et al., 2016) (Table 2).
For Hi-C data, overall 39.44 Gb clean reads were obtained and used for subsequent analysis
(Table 1). To assess the quality of Hi-C data, we first made a plot of insert fragment length
frequency, which showed a relatively narrow unimodal length distribution with the highest peak at
approximately 350 bp (Supporting Information Figure S4), indicating efficient purification of
streptavidin beads during library construction. The alignment results revealed that approximately
89.78% of the Hi-C reads were mapped on the genome, and 78.18% of the read pairs were
uniquely detected on the assembly (Supporting Information Table S5). Last, a total of 47,111,219

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valid read pairs, which accounted for 66.95% of the unique mapped read pairs, were detected by
HiC-Pro in the Hi-C dataset (Supporting Information Table S6). Taken together, our evaluation
suggested that the obtained Hi-C valid read pairs were sufficient for subsequent analysis.
Before chromosomal-level genome assembly, an error correction of the initial assembly was
performed by BWA-MEM with Hi-C data. The corrected filefish genome assembly was
approximately 474.30 Mb with only 242 contigs, the contig N50 reached 22.46 Mb, and the
longest contig was 32.32 Mb (Table 2, Supporting Information Table S7). The results indicated
that high-coverage nanopore long read-only assembly followed by multiple iterations of genome
polishing using Illumina reads is an effective method to generate high-quality genome assemblies.
A chromosomal-level genome was then assembled using LACHESIS, and the results showed
that overall 147 contigs spanning 471.65 Mb (99.44% of the assembly) were scaffolded into 20
pseudochromosomes, and 107 contigs spanning 469.46 Mb (98.98% of the assembly) were
successfully ordered and oriented (Table 3). The unanchored contigs were usually short contigs
that had low Hi-C interaction frequencies with others. Several of the pseudochromosomes were
scaffolded with only 2 or 3 contigs, representing a high contiguity of the genome. The final
assembled genome was 474.31 Mb with a scaffold N50 length of 23.05 Mb and a longest scaffold
of 34.81 Mb (Table 2, Supporting Information Table S7) (YSFRI, 2020). To the best of our
knowledge, this assembled genome was one of the most contiguous fish genome assemblies with
the highest contig N50 when compared with other published fish genomes. Both the anchored and
unanchored contigs went through the subsequent genome content analysis together.
To further evaluate the quality of the chromosomal-level genome assembly, a genome-wide
Hi-C heatmap was generated. The 20 pseudochromosomes could be easily distinguished and the
interaction signal strength around the diagonal was considerably stronger than that of other
positions within each pseudochromosome, which indicated a high quality of this genome assembly
(Figure 2).
3.3 Completeness of the assembled genome
Illumina reads were aligned to the filefish assembly, and 97.41% of the clean reads could be
mapped to the contigs (Supporting Information Table S8). Then the CEGMA analysis identified

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442 CEGs, accounting for 96.51% of all 458 CEGs in the program, and 226 CEGs could be
detected by using a highly conserved 248 CEGs dataset (Table 2, Supporting Information Table
S9). Last, approximately 94.33% (4324/4584) of actinopterigian complete BUSCOs were found in
the assembly (Table 2, Supporting Information Table S10). Overall, the assessment results
indicated that our filefish genome assembly was complete and of high quality.
3.4 Repeat annotation, gene prediction and gene annotation
A total of 67.35 Mb of repeat sequences that accounted for 14.2% of the assembly were
found in filefish (Supporting Information Table S11). This repeat content was close to the value
(16.62%) obtained from k-mer analysis. The predominant repeat types were TIRs (4.35%), LINEs
(2.40%) and LARDs (1.65%).
The combination of ab initio-based, homolog-based, and RNA-seq-based methods predicted
22,067 protein-coding genes with an average gene length, average exon length, and average intron
length of 11, 291bp, 230 bp, and 905 bp, respectively (Table 1, Table 4) (Bian, 2020). A total of
20,924 genes, which accounted for 94.82% of the predicted genes, were successfully annotated
with putative functions (Table 5). Approximately 94.33% (4324/4584) of actinopterigian complete
BUSCOs were detected in the annotated gene database (Supporting Information Table S12). The
noncoding RNA prediction identified 1,703 tRNAs, 649 rRNAs and 109 microRNAs (Supporting
Information Table S13).
3.5 Comparative genomics
Comparison of the filefish genome assembly with eleven other teleost species genomes found
a total of 22,665 gene families, 5,692 of which were shared among all eleven species, including
1,872 single‐copy orthologous genes (Supporting Information Table S14). Overall, 20,261 genes
of filefish could be clustered into 15,433 gene families, including 67 unique gene families
containing 193 genes (Supporting Information Table S14). The phylogenetic tree showed that four
tetraodontiform species were clustered together, and the divergence time between filefish and the
other three species was approximately 124.4 million years ago (Mya) (Figure 3). We also found 59
expanded gene families and 98 contracted gene families in filefish compared with the other fish
species (Supporting Information Figure S5). The Pfam annotations of some most expanded gene

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families included Tubulin/FtsZ family, sodium: neurotransmitter symporter family and sodium:
solute symporter family (Supporting Information Table S16). The annotations of the contracted
gene families included peptidase family M50, protein tyrosine kinase and root hair defective 3
GTP-binding protein (Supporting Information Table S17). These data will serve as valuable
resources for subsequent phylogenetic studies of filefish. A Venn diagram of orthologous gene
families among four tetraodontiform species was also constructed, and 971 unique gene families
containing 6485 genes were identified in the filefish genome (Figure 4).
4. Conclusion
In this study, we assembled the chromosome-level genome of T. septentrionalis, a first
reference genome of the genus Thamnaconus. The assembled genome was 474.31 Mb, which is
larger than the sequenced Takifugu and Tetraodon species but smaller than Mola mola. With the
powerful sequencing ability of Oxford Nanopore technology, the contig N50 of the assembled
genome achieved 22.46 Mb, and the longest contig was 32.32 Mb. To the best of our knowledge,
this contig N50 is the highest among all the sequenced fish genomes. This finding revealed that a
combination of high-coverage nanopore sequencing and Illumina data polishing can effectively
produce highly contiguous genome assemblies. The contigs were clustered and ordered onto 20
pseudochromosomes with Hi-C data, and several pseudochromosomes were scaffolded with only
2 or 3 contigs. The genome assembly and applied methodology supply valuable resources for
comparative genomics studies, especially for the vertebrate and fish genomics communities
(Supporting Information Figure S1-S2, Supporting Information Table S15). These data are also
useful for diverse conservation applications including identifying conservation units, assessing
gene flow, and detecting local adaptation of the populations along the coast of China and Korea.
Moreover, the genomic information presented in this study may establish a strong foundation for
genome-assisted breeding programs for filefish in the future.

Acknowledgements
We appreciate the help from Tianyuan Fisheries Co., Ltd who provided the filefish samples.
This work was supported by fund of Key Laboratory of Open-Sea Fishery Development, Ministry

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of Agriculture, P. R. China (LOF 2017-05), fund of Guangdong Provincial Key Laboratory of
Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese
Academy of Fisheries Sciences, SCSFRI, CAFS (FEEL-2017-10), Key Research and
Development Program of Shandong province, Department of Science & Technology of Shandong
province (2019GHY112073) and Central Public-interest Scientific Institution Basal Research
Fund, YSFRI, CAFS (20603022017014).
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Data Accessibility
This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the
accession WFAA00000000. The version described in this paper is version WFAA01000000. Raw
sequencing reads and genome assembly are available at GenBank as BioProject PRJNA565600.
Raw sequencing data (Nanopore, Illumina , Hi-C and RNA-seq data) have been deposited in SRA
(Sequence Read Archive) database as SRX6875837, SRX6862879, SRX6875660, and
SRX6875519. Genome assembly has been deposited in assembly database as GCA_009823395.1.
Gene annotation, transcriptome assembly and a high-quality genome-wide Hi-C heatmap of
filefish have been deposited in FigShare,
doi:10.6084/m9.figshare.11874825.v1(https://figshare.com/articles/Thamnaconus_septentrionalis_
genome_supporting_data/11874825).

Author Contributions
S.C., C.S. and Z.L. designed and managed the project. L.B., F.L. and J.G. interpreted the data
and drafted the manuscript. P.W., S.Z., C.L. and X.L. prepared the materials. Q.C., J.L., K.L. and
H.C. preformed the DNA extraction, RNA extraction and libraries construction. L.B., F.L., X.L.
and C.S. performed the bioinformatic analysis. All authors contributed to the final manuscript
editing.

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 TABLE 1 Statistics of the sequencing data

Types Method Sequencing Library size Clean data Coverage

platform (bp) (Gb) (×)†

Genome Illumina Illumina HiSeq X 300 45.97 93.48

Genome Nanopore PromethION ultra-long 50.95 103.61

Genome Hi-C Illumina HiSeq X 300 39.44 80.20

Transcriptome Illumina Illumina HiSeq X 300 11.31 23.00

† The coverage was calculated using an estimated genome size of 491.74 Mb.

TABLE 2 Assembly statistics of filefish and other tetraodontiform genomes

Species T. septentrionalis Takifugu rubripes† Takifugu flavidus Tetraodon nigroviridis Mola mola

Sequencing technology Oxford Nanopore PacBio Sequel PacBio Sequel Plasmid library + BAC library Illumina Hiseq 2000

sequencing sequencing

Assembly size (Mb) 474.31 384.13 366.29 342.40 639.45

Number of scaffolds 155 128 867 25773 5552

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 N50 scaffold size (Mb) 23.05 16.71 15.68 0.73 8.77

Number of contigs 242 530 1111 41566 51826

N50 contig length (Mb) 22.46 3.14 4.36 0.03 0.02

Complete BUSCOs (%)‡ 94.33 96.40 93.41 90.66 96.49

CEGMA assessment (%) 96.51 99.34 98.47 96.72 99.56

† The assembly statistics of other tetraodontiform genomes were from NCBI assembly database. The GenBank assembly accession numbers were as follows:

Takifugu rubripes (GCA_901000725.2), Takifugu flavidus (GCA_003711565.2), Tetraodon nigroviridis (GCA_000180735.1), Mola mola (GCA_001698575.1). ‡

Numbers shown are percentages of complete BUSCO genes covered by the assemblies. § Numbers shown are percentages of 458 core eukaryotic genes presented in

the assemblies.

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 TABLE 3 Statistics of the pseudochromosome assemblies using Hi-C data

Group Contig number Contig length (bp)

Group 1 3 34,805,468

Group 2 3 34,142,503

Group 3 3 29,239,029

Group 4 13 27,092,115

Group 5 3 24,789,104

Group 6 7 24,144,372

Group 7 10 23,815,151

Group 8 3 23,107,901

Group 9 11 22,985,309

Group 10 5 23,048,615

Group 11 2 22,982,431

Group 12 6 23,025,906

Group 13 3 22,547,364

Group 14 11 22,005,842

Group 15 16 20,921,416

Group 16 3 20,603,809

Group 17 2 19,738,352

Group 18 5 17,694,734

Group19 13 18,094,054

Group 20 25 16,862,837

Total contigs clustered 147 471,646,312

Total contigs ordered and oriented 107 469,464,378

TABLE 4 Summary of predicted protein-coding genes in the filefish genome

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 Method Software Species Number of predicted genes

Genscan 28,628

Augustus 44,749

Ab inito GlimmerHMM 34,576

GeneID 24,446

SNAP 58,914

Takifugu rubripes 19,643

Homology-based GeMoMa Tetraodon nigroviridis 21,885

Danio rerio† 19,808

PASA 30,768

RNA-seq GeneMarkS-T 47,856

TransDecoder 78,130

Integration EVM 22,067

† The GenBank accession numbers were as follows: Takifugu rubripes (GCA_000180615.2), Tetraodon

nigroviridis (GCA_000180735.1), Danio rerio (GCA_000002035.4)

TABLE 5 Summary of functional annotations for predicted genes

Annotation database Annotated number of predicted genes Percentage (%)
GO 11,257 51.01%
KEGG 13,714 62.15%
KOG 14,760 66.89%
TrEMBL 20,795 94.24%
NR 20,905 94.73%
All Annotated 20,924 94.82%
Predicted Genes 22,067 -

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 FIGURE 1 The greenfin horse-faced filefish (Thamnaconus septentrionalis)

FIGURE 2 The genome-wide Hi-C heatmap of the filefish. LG 1-20 are the abbreviations of Lachesis

Group 1-20, representing the 20 pseudochromosomes.

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FIGURE 3 Phylogenetic analysis of the filefish with other teleost species. Lepisosteus oculatus was used as

the outgroup. The calibration times were L. oculatus-L. crocea (315~322 Mya), L. maculatus-L. crocea

(95∼100 Mya) and T. flavidus-T. rubripes (4.22∼4.70 Mya). The estimated species divergence time (million

years ago) and the 95% confidential intervals were labeled at each branch site.

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 FIGURE 4 Venn diagram of orthologous gene families among four tetraodontiform species.

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