Chromosomal-level assembly of yellow catfish genome

using third-generation DNA sequencing and Hi-C analysis

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Gaorui Gong1,#, Cheng Dan1,#, Shijun Xiao2,#, Wenjie Guo1, Peipei Huang3,
Yang Xiong1, Junjie Wu1, Yan He1, Jicheng Zhang2, Xiaohui Li1, Nansheng
Chen4,5, Jian-Fang Gui1,3,*, Jie Mei1,*

1
College of Fisheries, Key Laboratory of Freshwater Animal Breeding,
Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.

2
Wuhan Frasergen Bioinformatics, East Lake High-Tech Zone, Wuhan,
China.

3
State Key Laboratory of Freshwater Ecology and Biotechnology, Institute
of Hydrobiology, Chinese Academy of Sciences, University of the Chinese
Academy of Sciences, Wuhan, China.

4
Institute of Oceanology, Chinese Academy of Sciences, Qingdao,
Shandong, China

5
Department of Molecular Biology and Biochemistry, Simon Fraser
University, Burnaby, Canada

#
These authors contributed equally to this work.

* Corresponding author. Tel: +86-27-87282113; Fax: +86-27-87282114.

Email address: jmei@mail.hzau.edu.cn (Dr. Jie Mei, ORCID: 0000-0001-

5308-3864)

jfgui@ihb.ac.cn (Dr. Jian-Fang Gui)

Abstract

Background: The yellow catfish, Pelteobagrus fulvidraco, belonging to Siluriformes

order, is an economically important freshwater aquaculture fish species in Asia,
especially in Southern China. The aquaculture industry has recently been facing
tremendous challenges in germplasm degeneration and poor diseases resistance. As
the yellow catfish exhibits notable sex dimorphism in growth, with adult males about

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two to three fold bigger than females, how aquaculture industry takes advantage of
such sex dimorphism is another challenge. To address these issues, a high-quality
reference genome of the yellow catfish would be a very useful resource.

Finding: To construct a high-quality reference genome for the yellow catfish, we

generated 51.2 Gb short reads and 38.9 Gb long reads using Illumina and PacBio
sequencing platforms, respectively. The sequencing data were assembled into a
732.8 Mb genome assembly with a contig N50 length of 1.1 Mb. Additionally, we
applied Hi-C technology to identify contacts among contigs, which were then used to
assemble contigs into scaffolds, resulting in a genome assembly with 26
chromosomes, and a scaffold N50 length of 25.8 Mb. Using 24,552 protein-coding
genes annotated in the yellow catfish genome, the phylogenetic relationships of the
yellow catfish with other teleosts showed that yellow catfish separated from the
common ancestor of channel catfish ~81.9 million years ago. 1,717 gene families
were identified to be expanded in the yellow catfish and those gene families are
mainly enriched in immune system, signal transduction, glycosphingolipid
biosynthesis and fatty acid biosynthesis.

Conclusion: Taking advantage of Illumina, PacBio and Hi-C technologies, we

constructed the first high-quality chromosomal-level genome assembly for the yellow
catfish P. fulvidraco. The genomic resources generated in this work not only offer a
valuable reference genome for functional genomics studies of yellow catfish to
decipher the economic traits and sex determination, but also provide important
chromosome information for genome comparisons in the wider evolutionary research
community.

Key Words: yellow catfish, PacBio, Hi-C, genomics, chromosomal assembly

Data description

Introduction

The yellow catfish, Pelteobagrus fulvidraco, (Richardson, 1846; NCBI Taxonomy

ID: 1234273; Fishbase ID: 28052) is a teleost fish belonging to the order Siluriformes
(Figure 1), and is an economically important freshwater fish species in Asia.1 In
recent years, yellow catfish has become one of the most important aquaculture
species in China with an increasing market value because of its high meat quality
and lack of intermuscular bones besides the spine2. However, due to the ultra-

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intensive aquaculture and loss of genetic diversity, artificial breeding of yellow catfish
is facing tremendous challenges such as germplasm degeneration and poor
diseases resistance3. Meanwhile, as an XY sex-determining type fish species, yellow
catfish is also an excellent model for studying sex determination and sexual size
dimorphism in fish4,5. As female and male yellow catfish exhibit remarkable sex
dimorphism in their growth rate, with adult yellow catfish males about two to three
fold bigger than the females. In the last decade, sex-specific allele markers were
developed and YY super-male fish were generated from gynogenesis of XY
physiological female fish. Finally, XX male, XY female, YY super-male and females
have been created and provide a unique model to study sex determination in fish
species1,6,7. Recently, transgene and gene knockout technologies have been
successively applied in yellow catfish to reveal the function of pfpdz1 gene, a novel
PDZ domain-containing gene, in whose intron the sex-linked marker was located.
The pfpdz1 gene plays an important role in male sex differentiation and maintenance
in yellow catfish8. Taken together these features provide a platform for gene-editing
methods to study gene function.

In spite of the importance of yellow catfish both in sex-determination research

and in aquaculture, the genomic resources for the species are still limited. So far,
only transcriptome, SSR and SNP data have been reported for yellow catfish5, the
genome sequence for this important species is still missing, hindering the genome-
based functional gene identification controlling important economic traits and the
application of genome-assisted breeding in yellow catfish. In this work, we combined
genomic sequencing data from Illumina short reads and PacBio long reads to
generate the first reference genome for yellow catfish, and applied Hi-C data to
scaffold the genome sequences into the chromosomal level. The completeness and
continuity of the genome were comparable with other model teleost species. We
believe that the high-quality reference genome generated in this work will definitely
facilitate research on population genetics and functional genes identification related
to important economic traits and the sex determinant for yellow catfish, which will in
turn accelerate the development of more efficient sex control techniques and improve
the artificial breeding industry for this economically important fish species.
Sample and sequencing

A XX genotype female yellow catfish (Figure 1), reared in the breeding center of
Huazhong Agricultural University in Wuhan City, Hubei Province, was used for

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preparing DNA for sequencing. To obtain sufficient high-quality DNA molecules for
the PacBio Sequel platform (Pacific Biosciences of California, Menlo Park, CA, USA),
one yellow catfish was dissected and fresh muscle tissues were used for DNA
extraction using the phenol/chloroform extraction method as in previous study9. The
quality of the DNA was checked by agarose gel electrophoresis, and an excellent
integrity of DNA molecules were observed. Other tissues, including ocular, skin,
muscle, gonadal, intestinal, liver, kidney, blood, gall and air bladder tissues were
snap frozen in liquid nitrogen for at least one hour and then stored at −80 °C.

The extracted DNA molecules were sequenced with both Illumina HiSeq X Ten
platform (Illumina Inc., San Diego, CA, USA) and PacBio Sequel platforms. Short
reads generated from the Illumina platform were used for the estimation of the
genome size, the level of heterozygosity and repeat content of the genome, and long
reads from the PacBio platform were used for genome assembly. To this end, one
library with an insertion length of 250 bp was generated for the HiSeq X Ten platform
and three 20 kb libraries were constructed for the PacBio platform according to the
manufacturer’s protocols, resulting the generation of ~51.2 Gb short reads and ~38.9
Gb long reads, respectively. (Table 1) The polymerase and subreads N50 length
reached 21.3 kb and 16.2 kb, providing ultra-long genomic sequences for the
following assembly.

Genome features estimation from Kmer method

The short-reads from Illumina platform were quality filtered by HTQC v1.92.310 using
the following method. Firstly, the adaptors were removed from the sequencing reads.
Second, read pairs were excluded if any one end has an average quality lower than
20. Third, ends of reads were trimmed if the average quality lower than 20 in the
sliding window size of 5 bp. Finally, read pairs with any end was shorter than 75 bp
were removed.

The quality filtered reads were used for genome size estimation. Using the Kmer
method described in previous method11, we calculated and plot the 17-mer depth
distribution in SI Figure 1. The formula G = N17-mer /D17-mer,where the N17-mer is the total
number of 17-mers,and D17-mer denotes the peak frequency of 17-mers, were used to
estimate the genome size of yellow catfish. As a result, we estimated a genome size
of 714 Mb, as well as a heterozygosity rate of 0.45% and repeat ratio of 43.31%. To
confirm the robustness of the genome size estimation, we performed additional

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analysis with Kmer of 21, 25 and 27, and found the estimated genome size ranged
from 706 to 718 Mb (Supplementary Table 1).

Genome assembly by third-generation long reads

With 6 SMRT cells in PacBio Sequel platform, we generated 38.9 Gb subreads by

removing adaptor sequences within sequences. The mean and N50 length were 9.8
and 16.2 kb, respectively. The long subreads were used for genomic assembly of
yellow catfish. Firstly, Falcon v0.3.0 package 12 with a parameter of length_cutoff as
10 kb and pr_length_cutoff as 8 kb was used. As a result, we obtained a 690 Mb
genome with a contig N50 length of 193.1 kb. Secondly, canu v1.513 was employed
separately for genome assembly with default parameters, leading to 688.6 Mb yellow
catfish genome with contig N50 of 427.3 kb.

Although the size of genome assembly from both Falcon and canu was
comparable with the estimation based on Kmer method, the continuity of the genome
need further improvement. Genome puzzle master (GPM)14 is a tool to guide the
genome assembly from fragmented sequences using overlap information among
contigs from genomes.14 Based on the complementarity of the two genomes, the
contig could be merged and the gaps filled by sequences bridging the two contigs.15
Taking advantage of the sequence complementation of the two assemblies from
Falcon and canu, we therefore applied GPM14 to merge long contigs using reliable
overlaps between sequences. Finally, a ~730 Mb genome assembly of yellow catfish
with 3,564 contigs and contig N50/L50 of 1.1 Mb/126 was constructed. The final
genome sequences were then polished by arrow16 using PacBio long reads and by
pilon release 1.12 17 using Illumina short reads to correct errors in base level. The
length distribution for contigs in the final assembly is presented in Supplementary
Figure 2.

In situ Hi-C library construction and chromosome assembly using Hi-C data

Hi-C is a technique allowing to unbiased identify chromatin interactions across

the entire genome18. The technique was introduced in as a genome-wide version of
3C (Capturing chromosome conformation)19, and was used as a powerful tool in the
chromosome genome assembly of many projects in recent years20. In this work, Hi-C
experiments and data analysis on blood sample was used for the chromosome
assembly of the yellow catfish. Blood sample from the same yellow catfish for
genomic DNA sequencing was used for library construction for Hi-C analysis. 0.1 ml

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blood were cross-linked for 10 min with 1% final concentration fresh formaldehyde
and quenched with 0.2 M final concentration glycine for 5 min. The cross-linked cells
were subsequently lysed in lysis bufer (10 mMTris-HCl (pH 8.0), 10 mM NaCl, 0.2%
NP40, and complete protease inhibitors (Roche)). The extracted nuclei were re-
suspended with 150 μl 0.1% SDS and incubated at 65°C for 10 min, then SDS
molecules were quenched by adding 120 μl water and 30 μl 10% Triton X-100, and
incubated at 37 °C for 15 min. The DNA in the nuclei was digested by adding 30 μl
10x NEB buffer 2.1(50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, 100 μg/ml BSA, pH
7.9) and 150U of MboI, and incubated at 37 °C overnight. On the next day, the MboI
enzyme was inactivated at 65 °C for 20 min. Next, the cohesive ends were filled in by
adding 1 μl of 10 mM dTTP, 1 μl of 10 mM dATP, 1 μl of 10 mM dGTP, 2 μl of 5 mM
biotin-14-dCTP, 14 μl water and 4 μl (40 U) Klenow, and incubated at 37 °C for 2 h.
Subsequently, 663 μl water,120 μl 10x blunt-end ligation buffer (300 mM Tris-HCl,
100 mM MgCl2, 100 mM DTT, 1 mM ATP, pH 7.8), 100 μl 10% Triton X-100 and 20
U T4 DNA ligase were added to start proximity ligation. The ligation reaction was
placed at 16 °C for 4 h. After ligation, the cross-linking was reversed by 200 µg/mL
proteinase K (Thermo) at 65°C overnight. Subsequent chromatin DNA manipulations
were performed as a similar method described in the previous study19. DNA
purification was achieved through QIAamp DNA Mini Kits (Qiagen) according to
manufacturers` instructions. Purified DNA was sheared to a length of ~400 bp. Point
ligation junctions were pulled down by Dynabeads® MyOne™ Streptavidin C1
(Thermofisher) according to manufacturers` instructions. The Hi-C library for Illumina
sequencing was prepared by NEBNext® Ultra™ II DNA library Prep Kit for Illumina
(NEB) according to manufacturers` instructions. The final library was sequenced on
the Illumina HiSeq X Ten platform (San Diego, CA, United States) with 150 PE mode.

487 million raw reads were generated from the Hi-C library and were mapped to
the polished yellow catfish genome using Bowtie 1.2.2 (RRID:SCR_005476) 21 with
the default parameters. The iterative method was used to increase the interactive Hi-
C reads ratio 22. Two ends of paired reads were mapped to the genome
independently, but only the reads that two pairs were uniquely mapped to genome
were used. Self-ligation, non-ligation and other invalid reads, such as StartNearRsite,
PCR amplification, random break, LargeSmallFragments and ExtremeFragments,
were filtered using the method and hiclib as described in previous reports23. The
contact count among each contig were calculated and normalized by the restriction
sites in sequences (Figure 2). We then successfully clustered 2,965 contigs into 26

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groups with the agglomerative hierarchical clustering method in Lachesis24, which
was consistent with the previous karyotype analyses of Pseudobagrus fulvidraco25.
Lachesis was further applied to order and orient the clustered contigs, and 2,440
contigs were reliably anchored on chromosomes, presenting 66.8% and 94.2% of the
total genome by contig number and base count, respectively. Then, we applied
juicebox26 to correct the contig orientation and to remove suspicious fragments in
contig to unanchored groups by visual inspection. Finally, we obtained the first
chromosomal-level high-quality yellow catfish assembly with a contig N50 of 1.1 Mb
and scaffold N50 of 25.8 Mb, providing solid genomic resource for the following
population and functional analysis. (Table 2). We compared length distribution of
contig anchored and un-anchored on chromosomes (Supplementary Figure 3), and
found that anchored contigs were significantly longer than those of unanchored
contigs. We therefore speculated that short lengths of unanchored contigs limited
effective Hi-C reads mapping, leading to insufficient supporting evidence for their
clustering, ordering and orientation on chromosomes. The gap distribution on
chromosomes are shown in Supplementary Figure 4. We found that gaps were
mainly distributed at two ends of chromosomes, which could be explained by the
repeat distribution at chromosome terminals. The length and the statistics of contigs
and gaps of each chromosome were summarized in Supplementary Table 2.

Genome quality evaluation

First of all, we compared the genome assembly continuity of the yellow catfish
genome to those of other teleost species. We found that both contig and scaffold N50
lengths of the yellow catfish reached considerable continuity (Figure 3), providing us
a high-quality genome sequences for the following functional investigations. The
assembled genome were also subjected to BUSCO v3.027 (RRID:SCR_015008,
version 3.0) with the actinopterygii_odb9 database to evaluate the completeness of
the genome. Among 4,584 total BUSCO groups searched, 4,179 and 92 BUSCO
core genes were completed and partially identified, respectively, leading to a total of
91.2% BUSCO genes in the yellow catfish genome. After aligning short reads from
Illumina platform to the genome, the insertion length distribution for sequencing
library of 250 bp exhibited a single peak around the sequencing library length design
(Supplementary Figure 5). Paired-end reads data were not used during the contig
assembly, thus the high alignment ratio and single peak insertion length distribution
demonstrated the high-quality of contig assembly for yellow catfish. Using the
Illumina short read alignment to the reference genome of the yellow catfish by BWA

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0.7.16 software (RRID:SCR_010910), we identified 21,143 homozygous SNP loci by
GATK (RRID:SCR_001876) package28.

Repeat and gene annotation

We first used Tandem Repeat Finder29 to identify repetitive elements in yellow catfish
genome. RepeatModeler (http://www.repeatmasker.org/RepeatModeler.html,
RRID:SCR_015027) were used to detect transposable elements (TE) in the genome
by a de novo manner. The de novo and known repeats library from Repbase30 were
then combined, and the TEs were detected by mapping sequences to the combined
library in yellow catfish genome using the software RepeatMasker 4.0.7
(RRID:SCR_012954)31.

For protein-coding gene annotation, de novo-, homology- and RNA-seq-based

methods were used. Augustus (RRID:SCR_008417)32 was used to predict coding
genes in de novo prediction. For homology-based method, protein sequences of
closely related fish species, including Astyanax mexicanus, Danio rerio, Gadus
morhua, Ictalurus punctatus, Oryzias latipes，Takifugu rubripes，Tetraodon
nigroviridis and Oreochromis niloticus were downloaded from Ensembl33 and were
aligned against to the yellow catfish genome using TBLASTN (RRID:SCR_011822)
software34. Short reads from RNA-Seq (SRR1845493) were also mapped upon the
genome using TopHat v2.1.1 (RRID:SCR_013035) package35, and the gene
structure were formed using Cufflinks (RRID:SCR_014597)36. Finally, 24,552
consensus protein-coding genes were predicted in the yellow catfish genome by
integrating all gene models by MAKER37. The gene number, gene length distribution,
CDS length distribution, exon length distribution and intron length distribution were
comparable with those in other teleost fish species (Figure 4).

Local BLASTX (RRID:SCR_001653) and BLASTN (RRID:SCR_001598)

programs were used to search all predicted gene sequences to NCBI non-redundant
protein (nr), non-redundant nucleotide (nt), Swissprot database with a maximal e-
value of 1e-5 38. Gene ontology (GO)39 and Kyoto Encyclopedia of Genes and
Genomes (KEGG)40 pathway annotation were also assigned to genes using the
software Blast2GO41.As a result, 24,552 genes were annotated to at least one
database. (Table 3)

Gene family identification and Phylogenetic analysis of yellow catfish

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To cluster families from protein-coding genes, proteins from the longest transcripts of
each genes from yellow catfish and other fish species, including Ictalurus punctatus,
Clupeaharengus, Danio rerio, Takifugu rubripes, Hippocampus comes, Cynoglossus
semilaevis, Oryzias latipes, Gadus morhua, Lepisosteus oculatus, Dicentrarchus
labrax, and Gasterosteus aculeatus, were extracted and aligned to each other using
BLASTP (RRID:SCR_001010) programs38 with a maximal e-value of 1e-5. OrthMCL42
was used to cluster gene family using protein BLAST result. As a result, 19,846 gene
families were constructed for fish species in this work and 3,088 families were
identified as single-copy ortholog gene families.

To reveal phylogenetic relationships among yellow catfish and other fish species,
the protein sequences of single-copy ortholog gene family were aligned with
MUSCLE 3.8.31 (RRID:SCR_011812) program43, and the corresponding Coding
DNA Sequences (CDS) alignments were generated and concatenated with the
guidance of protein alignment. PhyML v3.3 (RRID:SCR_014629)44 were used to
construct the phylogenetic tree for the super-alignment of nucleotide sequences
using the JTT+G+F model. Using molecular clock data from the divergence time from
the TimeTree database45, the PAML v4.8 MCMCtree program46 was employed to
determine divergence times with the approximate likelihood calculation method. The
phylogenetic relationship of other fish species was consistent with previous studies47.
The phylogenetic analysis based on single-copy orthologs of yellow catfish with other
teleosts studied in this work estimated that the yellow catfish speciated around 81.9
million years ago from their common ancestor of the channel catfish (Figure 5). Given
yellow catfish and channel catfish belong to family Bagridae and Ictaluridae
respectively, the phylogenetic analysis showed that Bagridae and Ictaluridae were
separated at a comparable time scale, however, determining the exact time
estimation requires more Siluriformes genomes.

Gene family expansion and contraction analysis

According to divergence times and phylogenetic relationships, CAFE48 was used to

analyze gene family evolution and 1,717 gene families were significantly expanded in
the yellow catfish (P < 0.05). The functional enrichment on GO and KEGG of those
expanded gene families identified 350 and 42 significantly enriched (q-value < 0.05)
GO terms (Supplementary Table 3) and pathways (Supplementary Table 4),
respectively. The expanded gene families were mainly found on immune system

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pathways, especially on Hematopoietic cell lineage (q-value = 2.2e-17), Intestinal
immune network for IgA production (q-value = 2.4e-17), Complement and
coagulation cascades (q-value = 1.4e-15) and Antigen processing and presentation
(q-value = 2.3e-9) on KEGG pathways, and Signal transduction pathways, including
NF-kappa B signaling pathway (q-value = 5.4e-9), Rap1 signaling pathway (q-value =
1.9e-6) and PI3K-Akt signaling pathway (q-value = 2.3e-4). Meanwhile, 208 GO
terms and 44 KEGG pathways, including endocrine system, signal transduction,
xenobiotics biodegradation and metabolism, sensory system were enriched using
significantly contracted gene families.

Conclusion

Combining Illumina and PacBio sequencing platforms with Hi-C technology, we

reported the first high-quality chromosomal level genome assembly for the yellow
catfish. The contig and scaffold N50 reached 1.1 and 25.8 Mb, respectively. 24,552
protein-coding genes were identified in the assembled yellow catfish, and 3,088 gene
families were clustered for fish species in this work. The phylogenetic analysis of
related species showed that yellow catfish diverged ~81.9 MYA from the common
ancestor of the channel catfish. Expanded gene families were significantly enriched
in several important biological pathways, mainly in immune system and signal
transduction, and important functional gene in those pathways were identified for
following studies. Given the economic importance of yellow catfish and the increasing
research interests for the species, the genomic data in this work offered valuable
resource for functional gene investigations of yellow catfish. Furthermore, the
chromosomal assembly of yellow catfish also provides valuable data for evolutionary
studies for the research community in general.

Availability of supporting data

The raw sequencing and physical mapping data are available from NCBI via the
accession number of SRR7817079, SRR7817060 and SRR7818403 via the project
PRJNA489116; as well as the National Omics Data Encyclopedia
(NODE) (http://www.biosino.org/node/index) via the project ID OEP000129
(http://www.biosino.org/node/project/detail/OEP000129). The genome, annotation
and intermediate files and results are also available via the GigaScience GigaDB
repository49. All supplementary figures and tables are provided in Supplemental
Table 1-3 and Supplementary Figure 1-5.

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Software and URLs

Software URLs
HTQC https://sourceforge.net/projects/htqc/
Falcon https://github.com/PacificBiosciences/FALCON/wiki/Manual
Canu https://github.com/marbl/canu
GMP https://github.com/Jianwei-Zhang/LIMS
Pilon https://github.com/broadinstitute/pilon/
Bowtie http://bowtie-bio.sourceforge.net/index.shtml
Hiclib https://bitbucket.org/mirnylab/hiclib/src
Lachesis https://github.com/shendurelab/LACHESIS
Juicebox https://www.aidenlab.org/juicebox/
BUSCO https://busco.ezlab.org/
BWA http://bio-bwa.sourceforge.net/
GATK https://software.broadinstitute.org/gatk/
RepeatModeler http://www.repeatmasker.org/RepeatModeler.html
RepeatMasker http://repeatmasker.org/
Augustus https://ngs.csr.uky.edu/Augustus
Balst https://blast.ncbi.nlm.nih.gov/Blast.cgi
TopHat https://ccb.jhu.edu/software/tophat/index.shtml
Cufflinks http://cole-trapnell-lab.github.io/cufflinks/
MAKER http://www.yandell-lab.org/software/maker.html
Blast2GO https://www.blast2go.com/
OrthMCL https://github.com/apetkau/orthomcl-pipeline
MUSCLE http://www.drive5.com/muscle/
PhyML https://github.com/stephaneguindon/phyml
TimeTree http://timetree.org/
PAML http://abacus.gene.ucl.ac.uk/software/paml.html

Abbreviations

3C: Capturing Chromosome Conformation; bp: base-pair; BUSCO: Benchmarking

Universal Single-Copy Orthologs; CDS: Coding DNA Sequences; Gb: Gigabase;
GO: Gene Ontology; Kb: kilobase; KEGG: Kyoto Encyclopedia of Genes and
Genomes; Mb: megabase; Mya: Million years ago; PE: paired-end; TE: Transposable
Element.

Competing interests

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The authors declare that they have no competing interests.

Funding

This work was supported by China Agriculture Research System (CARS-46) and the
Fundamental Research Funds for the Central Universities (2662017PY013).

Author Contributions

Jie Mei, Jian-Fang Gui and Nansheng Chen conceived the study; Dan Chen, Jicheng
Zhang, Wenjie Guo and Peipei Huang collected the samples and performed
sequencing and Hi-C experiments; Shijun Xiao, Gaorui Gong and Yan He estimated
the genome size and assembled the genome; Shijun Xiao, Gaorui Gong and Xiaohui
Li assessed the assembly quality; Gaorui Gong, Shijun Xiao, Yang Xiong and Junjie
Wu carried out the genome annotation and functional genomic analysis, Jie Mei,
Nansheng Chen, Shijun Xiao, Gaorui Gong and Jian-Fang Gui wrote the manuscript.
And all authors read, edited, and approved the final manuscript.

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Figure 1. Picture of a yellow catfish, Pelteobagrus fulvidraco. The fish was collected
from the breeding center of Huazhong Agricultural University in Wuhan City, Hubei Province,
China.

Figure 2. Yellow catfish genome contig contact matrix using Hi-C data. The color bar
illuminated the logarithm of the contact density from red (high) to white (low) in the plot. Note
that only sequences anchored on chromosomes were shown in the plot.
 Downloaded from https://academic.oup.com/gigascience/advance-article-abstract/doi/10.1093/gigascience/giy120/5106933 by guest on 27 September 2018
Figure 3. Genome assembly comparison of yellow catfish with other public teleost
genomes. X and Y axis representing the contig and scaffold N50’s, respectively. The
genomes sequenced with third generation sequencing were highlighted in red.

Figure 4. Length distribution comparison on total gene, CDS, exon and intron of
annotated gene models of the yellow catfish with other closely related teleost fish
species. Length distribution of total gene (A), CDS (B), exon (C) and intron (D) were
compared to P. fulvidraco, D. rerio, G. aculeatus, O. latipes, I. punctatus and T. rubripes.
 Downloaded from https://academic.oup.com/gigascience/advance-article-abstract/doi/10.1093/gigascience/giy120/5106933 by guest on 27 September 2018
Figure 5. Phylogenetic analysis of the yellow catfish with other teleost species. The
estimated species divergence time (MYA) and the 95% confidential intervals were labeled at
each branch site. The divergence used for time recalibration was illuminated as red dots in
the tree. The fish (I. punctatus and P. fulvidraco) from the order Siluriformes were highlighted
by pink shading.
Table 1. Sequencing data generated for yellow catfish genome assembly and
annotation. Note that paired-end 150 bp reads was generated from the Illumina HiSeq X
Ten platform.

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Library type Platform Library size (bp) Data size (Gb) Application

Short reads HiSeq X Ten 250 51.2 genome survey and

genomic base correction
Long reads PacBio SEQUEL 20,000 38.9 genome assembly

Hi-C HiSeq X Ten 250 146.1 chromosome construction

Table 2. Statistics for genome assembly of yellow catfish. Note that contigs were
analyzed after the scaffolding based on Hi-C data.

Length Number
Sample ID
Contig**(bp) Scaffold(bp) Contig** Scaffold
Total 731,603,425 732,815,925 3,652 1,227
Max 11,531,338 55,095,979 - -
N50 1,111,198 25,785,924 126 11
N60 643,552 24,806,204 212 14
N70 333,994 22,397,207 373 17
N80 128,419 21,591,549 742 21
N90 59,682 16,750,011 1,634 25
Table 3. Statistics for genome annotation of yellow catfish. Note that the e-value
threshold of the 1e-5 was applied during the homolog searching for the functional annotation.

Database Number Percent

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InterPro 20,178 82.18

GO 14,936 60.83

KEGG ALL 24,025 97.85

KEGG KO 13,951 56.82

Swissprot 20,875 85.02

TrEMBL 24,093 98.13

NR 24,308 99.01

Total 24,552