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Research Article
Genome-wide survey reveals the phylogenomic relationships of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes)
expand article infoLu Liu‡, Qi Liu§, Tianxiang Gao|
‡ Shandong Jiaotong University, Weihai, China
§ Wuhan Onemore-tech Co., Ltd, Wuhan, China
| Zhejiang Ocean University, Zhoushan, China
¶ Zhejiang Marine Fisheries Research Institute, Zhoushan, China

Corresponding author: Tianxiang Gao ( gaotianxiang0611@163.com )

Academic editor: Maria Elina Bichuette
© 2022 Lu Liu, Qi Liu, Tianxiang Gao.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Liu L, Liu Q, Gao T (2022) Genome-wide survey reveals the phylogenomic relationships of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes). ZooKeys 1129: 55-72. https://doi.org/10.3897/zookeys.1129.91543
ZooBank: urn:lsid:zoobank.org:pub:B99966E1-EF69-46FD-8CDF-D6D1417102C1
Open Access

Abstract

Fish are the largest vertebrate group, consisting of more than 30 000 species with important ecological and economical value, while less than 3% of fish genomes have been published. Herein, a fish, Chirolophis japonicus, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the C. japonicus genome was assembled (49 901 contigs with 42.61% GC contents), leading to a prediction of 46 729 protein-coding gene models. A total of 554 136 simple sequence repeats was identified in the whole genome of C. japonicus, and dinucleotide microsatellite motifs were the most abundant, accounting for 59.49%. Phylogenomic analysis of 16 genomes based on the 694 single-copy genes suggests that C. japonicus is closely related with Anarrhichthys ocellatus, Cebidichthys violaceus, and Pholis gunnellus. The results provide more thorough genetic information of C. japonicus and a theoretical basis and reference for further genome-wide analysis.

Keywords

Chirolophinae, draft genome, genome assembly, genome evolution, next-generation sequencing, Stichaeidae, Zoarcales

Introduction

Chirolophis Swainson, 1839 belongs to the family Stichaeidae of the order Perciformes, which is widely distributed between cold and temperate areas in the Pacific Ocean and along the coasts of Europe in the Atlantic Ocean (Jing et al. 2005; Balanov et al. 2020). Chirolophis contains nine species (https://www.fishbase.se/search.php) which are important commercial bony fishes, especially in China (Chen et al. 2017). Among these species, Chirolophis japonicus (Herzenstein, 1890), also known as Azuma emmnion (Jordan & Snyder, 1902), lives in rocky shallow coastal waters of the Pacific Ocean, including the Yellow Sea, the Bohai Sea, the northern Sea of Japan, and the Okhotsk Sea to the Bering Sea (Shiogaki 1983; Jing et al. 2005; Balanov et al. 2020). They display strong cryptic habits and are almost impossible to be observed by SCUBA diving observations. Studies on this species are relatively rare, mainly including mitochondrial genome data (Yang et al. 2016), the origin of the cortical protrusion of head (Sato 1977), and reproductive biology research (Chen 2017).

Genome-based phylogenetic studies have provided new opportunities for exploring the phylogeny of fishes. With the development of molecular biology and sequencing technology, more and more species are being sequenced and genomes published, ranging from model fishes to many commercial species. There are nearly 9900 species published genomes in the Eukaryota on the NCBI database (https://www.ncbi.nlm.nih.gov/genome/), accessed on 7 July 2022. Genome survey sequencing (GSS) was considered useful for providing basic genome information. Besides productively identifying genome-wide simple sequence repeats (SSRs) effectively, it can predict putative gene functions efficiently and target the potential exon-intron boundaries. A series of research advances has been made in the study of phylogenomic relationships of organisms, such as plants (Ran et al. 2018; Li et al. 2019b), animals (Koepfli et al. 2015; Heras et al. 2020), and fungi (Spatafora et al. 2016; Liu et al. 2022), which have provided insight into evolutionary history.

In the order Perciformes, the genomes of only three species, Anarrhichthys ocellatus (Ayres, 1855), Cebidichthys violaceus (Girard, 1854), and Pholis gunnellus (Linnaeus, 1758), have been published so far (Li et al. 2019a; Heras et al. 2020; Potter and Consortium 2022). Meanwhile, the complete mitogenomes of two species, Chirolophis ascanii and Chirolophis japonicus (or Azuma emmnion), provided robust phylogenetic relationships (Yang et al. 2016; Chen et al. 2017; Margaryan et al. 2021). Completed genome sequences of C. japonicus would improve our understanding of phylogeny, even though the genomic information of C. japonicus remains unknown.

In this present study, we perform a genomic survey for C. japonicus using next-generation sequencing technology for the first time, investigate its genomic feature and reconstruct the phylogenomic relationships with single-copy orthologs genes of C. japonicus. The draft genome assembly of C. japonicus can help us find more useful information for taxonomic studies, adaptive evolutionary mechanisms, and phylogenetic studies, as well as understand the genomic evolution of Chirolophis, and provide a molecular basis of C. japonicus.

Materials and methods

Material collection

In this study, a male specimen of C. japonicus with body length 186 mm and body weight 225 g was collected from coastal waters of Qingdao (35°40'N, 119°30'E), China in July 2021 (Fig. 1). Firstly, we identified it by morphological characteristics and DNA barcoding (mitochondrial DNA COI gene), then the examined sample was quickly preserved in −80 °C ultra-low temperature freezer. All subsequent animal experiments took place at Fisheries Ecology and Biodiversity Laboratory (FEBL) of Zhejiang Ocean University, Zhoushan, China. Experiments were conducted under the guidelines and approval of the Ethics Committee for Animal Experimentation of Zhejiang Ocean University (ZJOU-ECAE20211876). Secondly, a piece of fresh muscle tissue was clipped from the base of dorsal fin and preserved in absolute 95% ethanol.

Figure 1. 

Chirolophis japonicus (Herzenstein, 1890), 186 mm, from Qingdao.

Genomic DNA extraction and next-generation sequencing

The total cell DNA was extracted using the phenol-chloroform method (Sambrook et al. 1982), following the protocol in a previous study (Yang et al. 2021), and then carried out with DNA/Protein Analyzer and 1% agarose gel electrophoresis. High-quality DNA was randomly interrupted using ultrasonic crusher, and the obtained short reads (300–350 bp) were sequenced with Illumina NovaSeq 6000 with a paired-end library following the manufacturer’s instructions (OneMore-Tech, Wuhan, China) in January 2022.

Sequence quality control, genome assembly, and K-mer analysis

Quality control was performed on the raw data from the Illumina sequencing platform using the FastQC v. 0.11.9 (Andrews 2010) and Trimmomatic v. 0.39 (Bolger et al. 2014) based on four criteria: 1) removal of the A-tail and adaptors, 2) deletion of the low-quality reads where N contents are more than 10%, 3) filtration of the reads whose base quality is less than 10, and 4) discard of duplicated reads. The genome size, heterozygosity, and repeat content of C. japonicus was estimated based on a K-mer method (Liu et al. 2013). De novo assembly of the C. japonicus genome was conducted using MaSuRCA v. 3.3.3 (Zimin et al. 2013) based on clean data. The quality of the assembled genome was evaluated by Quast v. 5.0.2 and BUSCO v. 5.3.2 (Simão et al. 2015). The mitochondrial DNA analyses followed the method of previous studies (Yang et al. 2016, 2021; Nie et al. 2021). In brief, the software NOVOPlasty v. 4.2.1 (Dierckxsens et al. 2017) and GetOrganelle v. 1.7.6.1 (Jin et al. 2020) were used to assemble the mitogenome with clean data. The mitogenome of C. japonicus was annotated using MFannot tool (http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl) and GeSeq (Tillich et al. 2017), then manually annotated and drawn with OGDraw v. 1.3.1 (Lohse et al. 2013; Greiner et al. 2019). The clean data and complete assembled mitochondrial genome were uploaded to GenBank.

Gene prediction and functional annotation

The gene predictors Augustus v. 3.3.3 (Stanke and Waack 2003), SNAP (Johnson et al. 2008), and GeneMark-ES v. 4.69 (Lomsadze et al. 2005) were trained on the gene models, and all the gene models were integrated using EvidenceModeler v. 1.1.1 (Haas et al. 2008). The amino acid sequences from C. japonicus were annotated by GO (Ashburner et al. 2000), Eggnog (Huerta-Cepas et al. 2019), CAZymes (Cantarel et al. 2009), InterPro (Hunter et al. 2009), KEGG (Kanehisa et al. 2006), KOG https://www.creative-proteomics.com/services/kog-annotation-analysis-service.html, and Pfam (El-Gebali et al. 2019), using Diamond v. 2.0.2 with the e-value less than 1 × 10−5 (Buchfink et al. 2015).

Microsatellite identification and non-coding RNA annotation

In this study, MIcroSAtellite identification tool (MISA) v. 2.1 was used to identify simple sequence repeats (SSR) in the draft genome of C. japonicus (Thiel et al. 2003). The tRNA and rRNA were predicted by tRNAscan-SE v. 3.0 (Lowe and Eddy 1997) and RNAmmer v. 1.2 (Lagesen et al. 2007), respectively.

Phylogenomic analysis of C. japonicus

A total of 15 genomes of other bony fish were downloaded from the NCBI database (Table 1). The amino acid sequences of single-copy orthologs genes among the 16 species were found using OrthoFinder v. 2.5.4 (Emms and Kelly 2019), and these sequences were aligned by using MAFFT v. 7 (Katoh and Standley 2013). In order to reconstruct the phylogenomic relationship of C. japonicus, a maximum likelihood (ML) tree was analyzed/constructed using RaxML v. 8.2.12 based on the amino acid sequences of single-copy orthologs genes (Stamatakis 2014). The best model was PROTGAMMAILGF with 100 bootstrap replicates. Finally, the phylogram was viewed using FigTree v. 1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).

Table 1.
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Information on genomes used in this study.

Species Biosample Bioproject References
Anarrhichthys ocellatus SAMN10245424 PRJNA496475
Archocentrus centrarchus SAMN09948522 PRJNA489129 Koepfli et al. 2015
Cebidichthys violaceus SAMN06857690 PRJNA384078 Heras et al. 2020
Chirolophis japonicus This study
Cyclopterus lumpus SAMN12629502 PRJNA625538
Gasterosteus aculeatus SAMN15223905 PRJNA707557 Berner et al. 2019; Nath et al. 2021
Gymnodraco acuticeps SAMEA104242997 PRJEB37639
Liparis tanakae SAMN10970109 PRJNA523297
Micropterus salmoides SAMN15299117 PRJNA687018 Broughton and Reneau 2006; Sun et al. 2021
Myoxocephalus scorpius SAMEA4028818 PRJEB12469
Pholis gunnellus SAMEA7522838 PRJEB45449
Pseudoliparis sp. SAMN10662039 PRJNA512070 Mu et al. 2021
Seriola lalandi SAMN04902367 PRJNA319656 Purcell et al. 2018
Taurulus bubalis SAMEA7522994 PRJEB45317
Toxotes jaculatrix SAMN18445299 PRJNA723051
Ophiodon elongatus SAMN13559843 PRJNA595583 Longo et al. 2020

Data availability statement

Raw sequencing data for genome have been deposited at the Sequence Read Archive SRR21530970. These data can be quickly accessed by checking the project ID PRJNA879413 at NCBI Project.

Results

Sequencing data statistics and K-mer analysis

In this study, a total of 65.4 Gb clean reads was obtained by next-generation sequencing from an Illumina NovaSeq 6000 platform. The Q20 value, Q30 value, and GC content were 98.17%, 94.83%, and 43.14%, respectively. The K-mer analysis with a depth of 71 shows that genome size of C. japonicus was 596 Mb with 0.50% heterozygosity rate and 30.30% repeat sequences (Table 2, Suppl. material 1), resulting in C. japonicus being a diploid.

Table 2.
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The genome characteristics of Chirolophis japonicus based on the K-mer method.

Species K-mer number K-mer depth Genome size (Mb) Heterozygous ratio (%) Repeat sequences (%)
C. japonicus 4.353×1010 71 596 0.50 30.30

Genomic and mitochondrial features

The genome sequences of C. japonicus were sequenced from a male with an Illumina NovaSeq 6000 platform, spanning 595.7 Mb with GC contents of 42.61% that were assembled using the software MaSuRCA (Table 3; Zimin et al. 2013). A total of 49 901 contigs was generated with the largest contigs of 365 029 bp. The final contigs N50 and L50 were 29 108 bp and 5388 bp long, respectively (Table 3). A total of 69 rRNA was identified, including 66 8S rRNA, two 18S rRNA, and single 28S rRNA. In addition, 846 tRNA were annotated using the tRNAscan-SE.

Table 3.
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Gene prediction and annotation of Chirolophis japonicus.

Category Database Number of reads Percent (%)
Protein-coding gene model 46 729
Annotated InterPro 37 169 79.54
Eggnog 37 742 80.98
GO 9353 20.02
KEGG_KO 17 747 37.98
Pfam 26 530 56.77
KOG 35 440 75.84
CAZymes 765 1.64
Assembly BUSCO coverage 88.9

The complete mitogenome of C. japonicus is 16,522 bp long with a GC content of 45.97%. It consists of two ribosomal RNA genes (rnl and rns), 20 tRNA genes, and 13 protein-coding genes (PCGs) without an intron (Fig. 2).

Figure 2. 

The complete mitogenome structure of Chirolophis japonicus.

Chirolophis japonicus genome annotation

A total of 46 729 protein-coding genes was predicted by a combination of different software, including Augustus v. 3.3.3 (Stanke and Waack 2003), SNAP (Johnson et al. 2008) and GeneMark-ES v4.69 (Lomsadze et al. 2005). Among these, 79.54%, 80.98%, 20.02%, 39.98%, 56.77%, 75.84%, and 1.64% genes were annotated in the InterPro, Eggnog, GO, KEGG_KO, Pfam, KOG, and CAZymes databases, respectively.

Distribution and features of SSR

A total of 554 136 of SSR was identified in the complete genome of C. japonicus, including 166 077 of mononucleotide microsatellite motifs (29.97%), 329 685 of dinucleotide microsatellite motifs (59.49%), 37 615 of trinucleotide microsatellite motifs (6.79%), 17 896 of tetranucleotide microsatellite motifs (3.23%), 1568 of pentanucleotide microsatellite motifs (0.28%), and 1322 of hexanucleotide microsatellite motifs (0.24%;) (Fig. 2). A/T, AC, GAG, AGAC, CTCTC, and CCCTAA were the highest repeats in mono-, di-, tri-, tetra-, penta-, and hexanucleotide microsatellite motifs, respectively (Fig. 3).

Figure 3. 

The distributions and frequencies of microsatellite motifs of Chirolophis japonicus a mononucleotide microsatellite motifs b dinucleotide microsatellite motifs c trinucleotide microsatellite motifs d tetranucleotide microsatellite motifs e pentanucleotide microsatellite motifs f hexanucleotide microsatellite motifs.

Phylogenomic relationships of Chirolophis japonicus

In the present study, the phylogenomic relationship of a total of 16 bony fish (Table 1, Fig. 4) was reconstructed. A total of 694 single copy genes (Suppl. material 2) was identified from 16 male fish genomes using OrthoFinder (Emms and Kelly 2019), which consisted of 361 031 characters from amino acid sequences. The phylogenomic tree suggested that Chirolophis japonicus is closely related with Anarrhichthys ocellatus, Cebidichthys violaceus, and Pholis gunnellus, and provided robust phylogenetic relationships within the order Zoarcales, with full support. Although Chirolophis japonicus and Cebidichthys violaceus belong to the family Stichaeidae, they did not form a clade based on the amino acid sequences of 694 single-copy genes. In addition, Ophiodon elongatus, Cyclopterus lumpus, Liparis tanakae, Pseudoliparis sp., Taurulus bubalis, and Myoxocephalus scorpius clustered into a clade; other species, including Gymnodraco acuticeps, Archocentrus centrarchus, Seriola lalandi, Toxotes jaculatrix, Micropterus salmoides and Gasterosteus aculeatus, formed a separate clade. In addition, the phylogenomic analysis based on the amnio acid of 13 protein-coding genes of mitogenome show that Chirolophis japonicus is closely related with the Chirolophis ascanii (Fig. 5).

Figure 4. 

A maximum likelihood (ML) phylogenomic tree of Chirolophis japonicus based on amino acid sequences of 694 single-copy genes. Chirolophis japonicus is in bold. Maximum likelihood bootstrap values (90%) of each clade are indicated along branches. A scale bar in the upper right indicates substitutions per site.

Figure 5. 

The maximum likelihood (ML) phylogenomic tree of fungi based on amino acid of 13 protein-coding genes (PCGs): ATP6, ATP8, COX1, COX2, COX3, CYTB, ND1, ND2, ND3, ND4, ND4L, ND5 and ND6. Support values for ML analysis greater than 60% is given on relative clade. A scale bar in the upper left indicates substitutions per site.

Discussion

Currently, there are more than 30 000 species of fishes, including bony, jawless, and cartilaginous fishes, living on the earth, some with great ecological and economic value. In 2002, the first fish genome, Fugu rubripes (also known as “torafugu”) was published, which provided a framework for future studies of fish genomes (Aparicio et al. 2002). With the rapid development of the whole genome sequencing (WGS) technology, a large number of fish genomes have since been sequenced, such as fish as model organisms Oryzias latipes and Danio rerio, and economically important fishes such as Cyprinus carpio and Ctenopharyngodon idella (Kasahara et al. 2007; Howe et al. 2013; Xu et al. 2014; Wu et al. 2022). In addition, the Chinese “Aquatic 10-100-1000 Ge- nomics Program” and the “Fish 10K Project” have facilitated the understanding of fish genomes (Liu et al. 2017; Fan et al. 2020). Until now, a total of 819 fish genomes has been released in the NCBI database (https://www.ncbi.nlm.nih.gov/genome/, assessed on 7 July 2022), which is less than3% of the known 30 000 species.

In the present study, a new fish genome, Chirolophis japonicus, was sequenced. The genomes size was estimated to be 596 Mb based on the K-mer analysis, and the genome spanned 595.7 Mb, assembled using the MaSuRCA (Table 3; Zimin et al. 2013), which followed the predicted genome size of the K-mer method. Among the published teleost genomes, the size ranges from 322.5 Mb (Fugu rubripes) to 40 Gb (Protopterus annectens) (Aparicio et al. 2002; Wang et al. 2021), with an average length less than 1 Gb (Fan et al. 2020). Meanwhile, the genome of three species in Zoarcales, including Anarrhichthys ocellatus (612.19 Mb), three genomes of Cebidichthys violaceus (575.66 Mb, 593.00 Mb, 606.18 Mb), and two genomes of Pholis gunnellus (588.7 Mb, 590.3 Mb), are slightly larger than that of C. japonicus (https://www.ncbi.nlm.nih.gov/genome/, assessed on 7 July 2022). In addition, the heterozygous ratio of C. japonicus was 0.50%, probably mid-level compared to other teleost genomes (Aird et al. 2011; Li et al.2019c; Xu et al. 2020; Yang et al. 2021).

At present, phylogenomic analysis has become an important method for studying the evolutionary relationships of an organism, such as plants (Ran et al. 2018; Li et al. 2019b), animals (Koepfli et al. 2015; Heras et al. 2020), and fungi (Spatafora et al. 2016; Liu et al. 2022). Although the phylogenetic relationships of the genus Chirolophis have been published based on the mitogenomes (Yang et al. 2016; Chen et al. 2017; Margaryan et al. 2021), we provided a phylogenomic relationship according to the 694 single-copy genes (Fig. 3, Suppl. material 2) among C. japonicus and 15 other species. The results of the phylogenomic tree shows that C. japonicus is closely related with three species in the order Zoarcales, while C. japonicus and Cebidichthys violaceus, belonging to the family Stichaeidae, are without a clade (Fig. 2). Thus, solving this problem requires more fish genomes to be sequenced.

Microsatellite DNA markers shows many advantages, such as codominant, extensive distribution, abundant polymorphisms, and a convenient analysis, and was considered to be an effective tool in genetic analysis and evolutionary research (Yang et al. 2022). In this study, the highest number and type of repeats is dinucleotide repeats, which was consistent with data for Ophichthus evermanni (Yang et al. 2022), Padon nehereus (Yang et al. 2021), Cociella crocodilus (Zhao et al. 2021), Acanthogobius ommaturus (Chen et al. 2020), Sillago sihama (Qiu et al. 2020), and other species. SSR polymorphic loci are mainly distributed among mononucleotide and dinucleotide repeats. Based on this, the search of polymorphic SSR markers from low repetitive motifs will greatly help in subsequent population genetics research of C. japonicus. The complexity of repeated motif usually reflects DNA mutation rate and evolutionary level (Katti et al. 2001). The frequency from mononucleotides to trinucleotides was up to 96.25%, which implies that C. japonicus has experienced a long evolutionary history and accumulated more genetic variation.

Finally, the genome assembly of C. japonicus can help us understand the genome evolution of Chirolophis and teleosts, as well as provide a molecular basis for breeding and cultivation.

Acknowledgements

We sincerely thank the reviewers for their constructive comments. We would like to thank Yuan Zhang and Chenghao Jia for assistance in sample collection and sorting. This work was supported by the Zhejiang Provincial Key Research and Development Program (2021C02047); The Doctoral Research Foundation of Shandong Jiaotong University, Grant/Award Numbers: BS201902051.

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Supplementary materials

Supplementary material 1 

K-mer analyses (K = 71) of Chirolophis japonicus, X-axis and Y-axis represent the K-mer depth and frequency for the corresponding depth

Lu Liu, Qi Liu, Tianxiang Gao

Data type: image

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (21.74 kb)
Supplementary material 2 

Maximum likelihood phylogenomic tree of Chirolophis japonicus

Lu Liu, Qi Liu, Tianxiang Gao

Data type: phylogenomic tree

Explanation note: Maximum likelihood phylogenomic tree of Chirolophis japonicus based on amino acids of 694 single-copy genes.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (5.51 MB)
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