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Article

Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of Sillago Species

by
Fangrui Lou
1,
Yuan Zhang
2,
Na Song
2,
Dongping Ji
3 and
Tianxiang Gao
1,*
1
Fishery College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
2
Fishery College, Ocean University of China, Qingdao 266003, Shandong, China
3
Agricultural Machinery Service Center, Fangchenggang 538000, Guangxi, China
*
Author to whom correspondence should be addressed.
Animals 2020, 10(4), 633; https://doi.org/10.3390/ani10040633
Submission received: 24 February 2020 / Revised: 31 March 2020 / Accepted: 1 April 2020 / Published: 7 April 2020
(This article belongs to the Section Animal Genetics and Genomics)
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Abstract

:

Simple Summary

A comprehensive transcriptome analysis revealed the phylogeny of seven Sillago species. Selection force analysis in seven Sillago species detected 44 genes positively selected relative to other Perciform fishes. The results of the present study can be used as a reference for the further adaptive evolution study of Sillago species.

Abstract

Sillago species lives in the demersal environments and face multiple stressors, such as localized oxygen depletion, sulfide accumulation, and high turbidity. In this study, we performed transcriptome analyses of seven Sillago species to provide insights into the phylogeny and positively selected genes of this species. After de novo assembly, 82,024, 58,102, 63,807, 85,990, 102,185, 69,748, and 102,903 unigenes were generated from S. japonica, S. aeolus, S. sp.1, S. sihama, S. sp.2, S. parvisquamis, and S. sinica, respectively. Furthermore, 140 shared orthologous exon markers were identified and then applied to reconstruct the phylogenetic relationships of the seven Sillago species. The reconstructed phylogenetic structure was significantly congruent with the prevailing morphological and molecular biological view of Sillago species relationships. In addition, a total of 44 genes were identified to be positively selected, and these genes were potential participants in the stress response, material (carbohydrate, amino acid and lipid) and energy metabolism, growth and differentiation, embryogenesis, visual sense, and other biological processes. We suspected that these genes possibly allowed Sillago species to increase their ecological adaptation to multiple environmental stressors.

1. Introduction

The fish family Sillago are commonly known as sand whitings or sand borers, which are widely distributed in inshore waters of the Indian Ocean and the western Pacific Ocean and thrive in estuaries and shoals [1]. As minitype bottom-dwelling fishes of shallow sea regions, Sillago species are gregarious and have the ecological habit of drilling sand [2]. In addition, the Sillago species have become an important economical edible fish due to their palatable meat and long chain fatty acids that prevent thrombosis [2]. The inshore fishing of Sillago species has also developed rapidly in the past decades. It is worth noting that the overfishing will eventually lead to the ecological and economic damage of the Sillago resource. Additionally, more complex demersal environments caused by climate change and human activities, such as localized oxygen depletion, sulfide accumulation, and high turbidity, also pose a challenge to Sillago species differentiation and survival [3]. Therefore, it is necessary to develop the management and restoration of Sillago fishery resources.
Inferring the phylogenetic relationships is fundamental to successfully managing and recovering Sillago fishery resources, allowing the identification of the origin and relationship of species and the revelation of the evolutionary processes that lead to species diversity. At present, eleven Sillago species have been recorded in China [4]. Although there exist few taxa in Sillago, species identification and phylogenetic status are often confusing to taxonomists due to their similar phenotypic and physiological characteristics [2]. Additionally, local environmental divergences and rapid climatic changes could lead to the further diversification and speciation of Sillago, ultimately improving the complexity of phylogenetic research of Sillago species [5]. Although significant development has been reported in recent years, the knowledge of the phylogeny of Sillago species is still controversial, especially in the process of identifying cryptic lineages within the vast diversity of Sillago through the analysis of different phenotypic characteristics. Particular points of contention include (i) the incorrect use of species’ scientific names and (ii) species identification errors from identification based only on morphological features [1,2,4]. The application of comprehensive molecular phylogenies upended classical morphological hypotheses and led to the development of a new Sillago phylogenetic classification method. For example, four Sillago species, including Sillago caudicula [2], S. sinica [6], S. suezensis [7], and S. shaoi [4] were reclassified using molecular markers, although they were all wrongly classified as S. sihama based on phenotypic traits. It is impossible to construct a comprehensive phylogenetic relationship for Sillago species only by using a single or small number of gene fragments. This is the case because a small number of gene fragments contain limited genetic information, and therefore cannot provide high statistical support for some crucial branches of the phylogenetic tree [8]. Different gene fragments are also affected by sequence conservation, gene evolution rate differences, horizontal gene transfer, and other factors, which ultimately lead to conflicting gene trees [9]. Additionally, it is undeniable that all previous studies only analyzed the differentiation between Sillago species, while the genetically adaptive characteristics were still not clear. Therefore, it is very essential to investigate the molecular features of different Sillago species based on complete genetic information, which will provide us with an accurate understanding of differentiation and environmental adaptation in Sillago species.
The sequence differentiation of orthologous genes is related to speciation, and therefore, orthologous genes can be used to infer more accurate phylogenetic relationships among species [10]. Currently, the advent and increasingly widespread use of high-throughput sequencing technologies provides hundreds to thousands of orthologous genes for the phylogenetic analysis of species [11,12]. However, it is worth noting that the massive datasets generated by high-throughput sequencing, especially whole genome datasets, require more complex analytical methods to confirm the most informative orthologous loci and appropriate tree reasoning methods [13]. For vertebrates (including teleost), two whole-genome duplications (WGDs) eventually produced duplicate genes, which further affected the accuracy of distinguishing orthologous genes from duplicated paralogs [14,15]. In Sillago species, unfortunately, there is only the S. sinica genome project that has been sequenced [5]. Modern transcriptome datasets may avoid the defects mentioned above, because they can effortlessly generate massive genome-wide protein-coding sequences for phylogenetic studies, especially when whole genomic information is not available [10]. Meanwhile, we can focus on calculating and comparing the gene evolutionary rates based on orthologous gene datasets, and then infer the potential local environmental adaptation genes of organisms [16,17]. In brief, we believe that the phylogenetic relationships and genetic adaptation characteristics will be successively identified in Sillago species by orthologous gene analysis.
In order to reconstruct the complete phylogenetic relationship of Sillago species and detect their genomic characters associated with adaptive evolution, five valid Sillago species (including S. japonica, S. aeolus, S. sihama, S. parvisquamis, and S. sinica) and two unpublished new species (S. sp.1 and S. sp.2; unpublished data)—which were confirmed by using morphological, anatomical, and DNA-barcoding evidence—were studied. Next, seven RNA sequencing (RNA-seq) libraries were constructed together. First, clean reads produced by RNA-seq were applied to assemble seven relatively integrated transcriptomes of Sillago species. Subsequently, transcriptome data of seven Sillago species and other existing Perciformes species were detected for orthologous genes, and then the shared orthologous genes were used to reconstruct the phylogenetic tree and predict the differentiation time. Considering that these genes that experience positive selection may be beneficial to improving the ecological adaptation of Sillago species, we investigated the positively selected genes (PSGs) of Sillago species based on orthologous genes. Meanwhile, a gene function enrichment analysis was performed on these PSGs. These results can constitute important data with which to gain insights into the process of species differentiation and adaptive evolution in other Sillago species.

2. Materials and Methods

2.1. Ethics Approval and Consent to Participate

The Sillago species are not endangered or protected species in China or other countries. In addition, frost anesthesia was used to minimize suffering in all samples.

2.2. Sample Collection, RNA Extraction, and Illumina Sequencing

Seven Sillago species were obtained from the coast of China and Japan. Then, one adult female per species was immediately euthanized, and the muscle of each individual was rapidly sampled, snap-frozen in liquid nitrogen, and stored at −80 °C prior to the RNA extraction. The sampling location and the standard length (SL) of each sequenced individual are shown in Figure 1. The total RNA of the seven Sillago species was extracted using a standard TRIzol Reagent kit, following the manufacturer’s protocol. The quantitative evaluation of total RNA was conducted by using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). We then purified mRNA by depleting rRNA from total RNA, and the remaining mRNA was cleaned three times. Then, we fragmented the mRNA into fragments of appropriate size. The fragmented mRNA was used to construct a cDNA library. Afterwards, we added A-tails and adapters to the double stranded cDNA. Then, the cDNA libraries were diluted to 10 pM and then quantified by using the Agilent 2100 Bioanalyzer. Finally, each tagged cDNA library was sequenced on the Illumina HiSeq 2000 across one lane with paired-end 150 bp reads.

2.3. Transcriptome De Novo Assembly

The raw RNA-seq data of Sillago japonica, Sillago aeolus, Sillago sihama, Sillago parvisquamis, Sillago sinica, Sillago sp.1 and Sillago sp.2 reported in this paper have been deposited in the Sequence Read Archive (SRA) database of National Center for Biotechnology Information (NCBI) under BioProject number PRJNA596307, with accession number of SRR10743284, SRR10743285, SRR10743281, SRR10743280, SRR10743279, SRR10743282 and SRR10743283, respectively. The FastQC 0.11.2 software (version, Babraham Institute, Cambridgeshire, UK) was applied to assess the sequencing quality of all raw reads in FASTQ format. Then, clean reads were obtained by removing reads with sequencing adapters, unknown nucleotides (N ratio > 10%), and low quality (quality scores < 20) using Trimmomatic 0.36 [18]. Additionally, the S. sinica genome dataset served as a reference sequence and was used for subsequent de novo assembly [5]. All remaining high-quality clean reads were sorted according to S. sinica genome index sequences and were aligned to the reference assembly generated from paired-end reads by using the bwa-mem algorithm in the BWA (Version 0.7.12, Microsoft Corporation, Redmond, WA, USA; [19]) software with default parameters, with the resulting output as ‘sam’ files. All sam files of each species were merged into a ‘bam’ file using the SAMtools (Version 1.3.1; Microsoft Corporation, Redmond, WA, USA; [20]) software. Finally, the Trinity (Version 2.4.0, Microsoft Corporation, Redmond, WA, USA; [21]) software was used for the transcriptome de novo assembly of each species, with the parameters as follows: --genome_guided_max_intron 10000. In order to perform further quantitative assessment of the assembly completeness, we applied the BUSCO software (version 4.0, Microsoft Corporation, Redmond, WA, USA) package with default settings, and downloaded the Ensembl Actinopterygii assembly as a reference.

2.4. Orthology Determination and Phylogenetic Tree Reconstruction

In order to reconstruct a more accurate phylogenetic tree, we performed an extensive orthologous gene comparison among the seven Sillago species and thirteen other Perciformes species (hereafter referred to as the “research species”) with transcriptome or genome datasets, including Epinephelus fuscoguttatus (GCNQ00000000.1), Epinephelus coioides (GCA_900536245.1), Perca fluviatilis (GCA_003412525.1), Chionodraco hamatus (GCA_009756495.1), Gymnodraco acuticeps (GGFR00000000.1), Dissostichus eleginoides (GHKE00000000.1), Trematomus bernacchii (GBXS00000000.1), Argyrosomus regius (GFVG00000000.1), Nibea albiflora (GCA_900327885.1), Miichthys miiuy (GCA_001593715.1), Collichthys lucidus (GCA_004119915.1), Larimichthys polyactis (GETG00000000.1), and Larimichthys crocea (GCA_000972845.2). Meanwhile, the ecological characteristics of the 20 research species were obtained from the Fishbase website [22] and the research results of Xiao et al. (2016) [4], as shown in Table 1. Firstly, we obtained the assembly sequences from the National Center for Biotechnology Information (NCBI) database under the accession number. Additionally, a dataset of 1721 single-copy conserved nuclear coding sequences (> 200bp) was obtained by comparing and optimizing eight well-annotated model fish genomes: Lepisosteus oculatus, Anguilla anguilla, Danio rerio, Gadus morhua, Oryzias latipes, Oreochromis niloticus, Gasterosteus aculeatus, and Tetraodon nigroviridis [23]. Subsequently, we extracted the single-copy conserved nuclear coding sequences of each research species using the HMMER software (Version 3.1, Howard Hughes Medical Institute, Chevy Chase, MD, USA; [24]). Specifically, 1721 parameterized hidden Markov model (HMM) profiles were obtained based on 1721 sequence alignments using the ‘hmmbuild’ function of the HMMER software. Each HMM model was applied to search against each research species dataset using the nHMMER program within HMMER, with the resulting hits output as a table. We used Python scripts (available on Dryad; [23]) to retain the hits that were at least 70% as long as the shortest model fragment and had a bit score of at least 100, and de-redundancy was performed on these hits with 100% similarity by using the CD-HIT software [25]. The remaining high-quality single-copy conserved nuclear coding sequences of each research species were aligned and spliced into single nucleotide sequences using the MAFFT software [26]. Conserved sequences were extracted from each concatenated nucleotide sequence using Gblocks with parameter -t=c [27]. Finally, we performed 1000 nonparametric bootstrap replicates for the optimal GTRGAMMA substitution model of all concatenated nucleotide sequences in the MEGA (Version 6.0, National Institutes of Health, Bethesda, MD, USA; [28]) software, and then a complete neighbor-joining (NJ) tree of the abovementioned twenty species was reconstructed according to the branch lengths and bootstrap support values. Additionally, we also reconstructed the NJ trees based on the amino acid sequences and variation sites of concatenated nucleotide sequences. The iTol (Version 4.0, Beijing Institute of Genomics, Beijing, China; [29]) software was used to visualize the phylogenetic relationship. Finally, the estimated molecular clock data of L. polyactis and L. crocea (min and max differentiation times are 11.2 and 42.0 MYA) were obtained from the TimeTree database [30], and then the divergence times of the seven Sillago species were estimated using the r8s software [31].

2.5. Prediction of PSGs of Sillago Species

In the present study, the codeml program in the PAML (Version 4.9, University College London, London, UK; [32]) software was applied to identify the PSGs of Sillago species. Firstly, we constructed tree files for 20 research species (including the seven Sillago species and 13 outgroups) using each single-copy orthologous gene, respectively. Subsequently, the branch-site model (model = 2, Nsites = 2) in the codeml program was used to identify the PSGs of Sillago species, and a comparison was also conducted between the null and alternative models. The null model assumed that Sillago species were under purifying selection and that therefore those sites on the foreground branch evolved neutrally (non-synonymous (dN)/synonymous (dS) = 1, modelA1, fix_omega = 1, and omega = 1.5), and the alternative model assumed that those sites on the foreground branch were under positive selection (dN/dS > 1, modelA2, fix_omega = 0, and omega = 1.5). Then, a likelihood ratio test (LRT) was applied to calculate the log-likelihood values (2△ln) between the null model and alternative model of each single-copy orthologous gene. After a Chi-square statistical analysis, a gene was considered as a PSG of Sillago species if the FDR-adjusted p < 0.01. Finally, we used the Blast2GO [33] software to predict the functions of those PSGs.

3. Results

3.1. Illumina Sequencing and the De Novo Assembly of the Seven Sillago Species’ Transcriptomes

Illumina sequencing was carried out on muscle from the seven Sillago species. After cleaning and quality testing, we obtained 138.4 Gb of clean reads from the seven Sillago species, and the details of the data are listed in Table 2. All clean reads of the present study were uploaded to the SRA databases of NCBI under BioProject number PRJNA596307, with accession numbers of SRR10743279 to SRR10743285. The Trinity software was applied to the de novo assembly of the clean data, and 82,024, 58,102, 102,185, 69,748, 102,903, 63,807, and 85,990 unigenes were generated from S. aeolus, S. japonica, S. parvisquamis, S. sihama, S. sinica, S. sp.1, and S. sp.2, respectively. The assembly information of the seven Sillago species is shown in Table 3. Additionally, the BUSCO analysis results showed that 91.5%, 83.1%, 94.2%, 91.7%, 93.1%, 88.7%, and 89.1% of protein-coding genes were found in the unigenes of S. aeolus, S. japonica, S. parvisquamis, S. sihama, S. sinica, S. sp.1, and S. sp.2, respectively.

3.2. Orthologous Gene Identification and the Phylogenetic Structure of Sillago Species

Single-copy conserved nuclear coding sequences of these eight model species were applied to search for orthologous genes in 20 research species. Using the HMMER software, we identified a set of 140 orthologous exon markers longer than 200bp. Then, the concatenated alignment of 140 orthologous genes produced a data matrix with 82,833 bp for 20 research species. The NJ analyses of 20 concatenated nucleotide sequences, concatenated amino acid sequences, and concatenated variation sites were implemented in the MEGA package, and the phylogenetic structures of Sillago species are shown in Figure 2, Figure 3 and Figure 4. According to all phylogenetic analyses, fishes from the same family eventually cluster into one branch, except for C. hamatus and G. acuticeps. Seven Sillago species, including two suspected new species, were also clearly distinguished from other Perciformes. Additionally, the divergence time was estimated, and the results showed that the internal divergence time varied within the seven Sillago species due to the different kind of concatenated sequence used for analysis. Specifically, the internal divergence times of the seven Sillago species based on concatenated nucleotide sequences was between 161.29 and 27.80 MYA, and the internal divergence time based on the amino acid sequences was between 27.02 and 4.15 MYA, while that based on variation sites was between 24.13 and 3.46 MYA.

3.3. PSGs Representative of Sillago Species

We calculated the log-likelihood values (2△ln) between the null model and alternative model for 140 orthologous genes. After a Chi-square statistical analysis, a total of 44 genes with FDR-adjusted p < 0.05 were identified as PSGs and these genes were suspected to contribute to the specific adaptive evolution of Sillago fishes in the burrowing lifestyle. (Table 4). Combining nr (non-redundant protein sequence) database annotation information, we speculate that these adaptive genes are potentially related to the stress response, material (amino acid and lipid) and energy metabolism, growth and differentiation, embryogenesis, visual sense, and other things. Further gene function enrichment analysis indicated that these adaptive genes were involved in cellular process (GO: 0050794), metabolic process (GO: 0006006), cell parts (GO: 0044464), cells (GO: 0005623), catalytic activity (GO: 0003824), binding (GO: 0005488), and other things (Figure 5). Additionally, we identified the networks of molecular interactions in the cells and variants specific to particular organisms by comparing the adaptive genes to the KEGG database (Table 5). Results showed that these adaptive genes were significantly enriched for nicotinate and nicotinamide metabolism (map00760), carbon fixation pathways in prokaryotes (map00720), purine metabolism (map00230), C5-Branched dibasic acid metabolism (map00660), starch and sucrose metabolism (map00500), arginine biosynthesis (map00220), riboflavin metabolism (map00740), pantothenate and CoA biosynthesis (map00770), pyrimidine metabolism (map00240), the biosynthesis of antibiotics (map01130), the citrate cycle (map00020), propanoate metabolism (map00640), thiamine metabolism (map00730), and arginine and proline metabolism (map00330).

4. Discussion

As they are typical marine demersal fish, species differentiation of Sillago species is often disordered, which ultimately affects the accurate interpretation by taxonomists of their evolutionary processes. Meanwhile, more complex habitat environments caused by climate change and human activities can also have an impact on the survival of Sillago species. However, it is undeniable that unraveling their complete phylogenetic relationships and adaptive mechanisms can effectively solve the above problems. In order to gather this fundamental knowledge, we first sequenced and assembled the transcriptome of seven Sillago species. Then, we identified the orthologous genes of seven Sillago species and 13 other Perciformes species based on transcriptome data. Finally, the phylogenetic relationships were reconstructed and the PSGs of Sillago species were inferred based on orthologous genes. In brief, we believe that this research can provide new perspectives for protecting the Sillago fishery resource.

4.1. Transcriptome Data Processing

In the present study, we obtained 138.4 Gb of clean transcriptomic data from seven Sillago species. To our knowledge, this study may be the first systematic research of seven Sillago species’ transcriptomes by using high-throughput sequencing technology, except for S. japonica [34]. It is undeniable that the transcriptome assembly results of S. japonica, S. sp.1, and S. sp.2 are imperfect because their N50 lengths are less than 1000 bp. Meanwhile, the BUSCO results also found that the unigenes of S. japonica, S. sp.1, and S. sp.2 lacked integrity. This is the case because some of the reads contaminated by the sequencing process were removed. Additionally, the selection of the reference genome (the S. sinica genome was selected as the reference sequence in this study) and assembly strategy (software and parameters) can also influence the final assembly efficiency. However, we still believe that these data expand the currently available genomic resources for Sillago species.

4.2. More Accurately Determining the Phylogenetic Relationships of Seven Sillago Species

Knowledge of the phylogeny of Sillago species is insufficient due to their similar phenotypic and physiological characteristics. Additionally, the paucity of genomic resources has restricted the phylogenetic resolution of Sillago species relationships. Currently established high-throughput sequencing technologies enable systematists to acquire huge amounts of orthologous genes for phylogenetic relationship reconstruction for Sillago species [23]. It is well known that the differentiation of orthologous genes usually leads to the speciation of species [35]. Therefore, there is every reason to believe that we can more accurately determine the phylogenetic relationships of Sillago species based on hundreds to thousands of orthologous genes. Although more complete orthologous genes could be obtained based on whole-genome sequencing technology, their application in phylogenetic analysis is limited by the high sequencing cost and methodological challenges of big databases [13]. With this background, orthologous exon markers captured by transcriptome sequencing have been attempted to be used in phylogenetic studies [36]. In fact, Betancur-R et al. (2013) considered that exons can be translated to amino acids, and further, to reduce errors from base compositional biases in phylogenetic studies [37]. Therefore, we focused on orthologous exon markers to reconstruct the phylogenetic relationships between seven Sillago species in this study. Unfortunately, only 140 orthologous exon markers were obtained using the HMMER method, and we suspected it may be related to the imperfect assembly results for S. japonica, S. sp.1, and S. sp.2. Although the number of markers is small, their efficiency has been verified by Hughes et al. [23], thus we believed that these markers are suitable for subsequent phylogenetic relationship reconstruction. Unsurprisingly, the reconstructed phylogenetic structure based on 140 orthologous exon markers (nucleotide sequences, amino acid sequences, and variation sites) is significantly congruent with the prevailing morphological and molecular biological view of Perciformes species relationships, except for C. hamatus and G. acuticeps. In other words, fishes from the same family eventually cluster into one branch. The reconstructed phylogenetic relationships of seven Sillago species are consistent with the results based on the mitochondrial genome [38]. Our study also provided evidence to prove that S. sp.1 and S. sp.2 may belong to the cryptic species of Sillago. However, more detailed evidence, including ecological and morphological data, needs to be provided in the further definition of S. sp.1 and S. sp.2. Additionally, there is no denying the fact that we still need to supplement other Sillago transcriptome data to reconstruct a more comprehensive understanding of phylogenetic relationships. It is worth noting that C. hamatus and G. acuticeps belong to the family Channichthyidae and Bathydraconidae, respectively, but the two species were clustered into one branch in this study. We suspected that the accuracy of the data may have contributed to the divergence. Additionally, some markers that were used to construct phylogenetic relationships between C. hamatus and G. acuticeps may have genetic convergence [39], which eventually cause the two species to cluster into one branch. This also confirmed that the selection of genetic markers may influence the reconstruction results of phylogenetic relationships [40]. Further studies will need larger datasets to illustrate the divergence.
The evolutionary sequence of Sillago species was identified based on differentiation times. The evolutional sequence of the seven Sillago species was consistent with that in previous studies [38]. Previous studies suspected that incomplete or missing swim bladders may be an adaptive mechanism for Sillaginidae species to demersal life [2]. In addition, Xiao (2018) also deduced that the swim bladders of Sillaginidae ancestors were extremely simple, and then became more complex as they evolved [38]. It is worth noting that the swim bladder of S. aeolus is imperfect relative to that in the other six Sillago species. Therefore, the evolutionary sequence of seven Sillago species based on transcriptome data also seems to support the hypothesis about the evolution of swim bladders. However, when evaluating the differentiation time of Sillago species based on different sequence formats, the results are quite different. In fact, Schwarzhans considered that Sillaginidae species gradually evolved into different species at Miocene (23 MYA to 5.33 MYA) [41]. Additionally, Takahashi has found an otolith fossil of Sillago from Niigata Prefecture (Japan) that may have existed during the Pliocene (5.3 MYA to 2.58 MYA) [42]. In the present study, the differentiation times based on amino acid sequences and variation sites are consistent with those in previous studies, although there existed a significant bias when using nucleotide sequences. We suspect that the base compositional biases caused by high-throughput sequencing affects the subsequent differentiation time analysis. However, it is undeniable that the tolerance of amino acid sequences to degenerate bases can effectively reduce this deviation [37]. Future studies still need to verify whether amino acid sequences and variation sites are more suitable for estimating the evolutionary order of species. Surprisingly, we used branch length to predict the differentiation times with other Perciformes species that might be quite different from those in the time tree database. There are two probable reasons: (1) the divergence in differentiation time results may be influenced by the estimation strategies and the number of genes used; (2) the orthologous exon markers obtained from transcriptome data are mostly functional genes, and the convergent evolution of functional genes has an inevitable effect on the evaluation of the species differentiation time.
In brief, transcriptome data can provide hundreds to thousands of single-copy orthologous exon markers, and then be used to reconstruct a more complete view of Sillago species phylogenetic relationships. However, when using orthologous exon markers obtained from transcriptome data to reconstruct phylogenetic relationships, two recommendations are worth considering: (1) the amino acid sequences of orthologous exon markers can reduce errors caused by base compositional biases, so it is necessary for phylogenetic relationship reconstruction; (2) the accuracy of phylogenetic relationships may be positively correlated with the number of orthologous exon markers used, which is possibly because a large number of markers can eliminate the bias from a small number of convergent evolutionary genes.

4.3. Positively selected genes Might Contribute to the Ecological Adaptation of Sillago Species

Transcriptome-wide analysis of the rates of non-synonymous to synonymous orthologous nucleotide substitutions represents an effective approach to quantitatively measure the selection force [17,43]. To reveal the molecular mechanism underlying the ecological adaptation of Sillago species, we estimated the dN/dS to identify the PSGs of Sillago species. A total of 44 orthologous genes were identified to be positively selected and might be involved in many biological processes, including the stress response (LTV1 [44], SMO [45], PSA [46,47], ABCB7 [48], UBIAD1 [49], COPA [50], MED27 [51,52], MED28 [51,52], SF3A1 [53], SF3B5 [53], TFIP11 [54], NUDT6 [55], POLλ [56], and DEPDC5 [57]), energy metabolism (APF [58] and IMMT [59]), carbohydrate metabolism (SUCLG1 [60]), amino acid metabolism (GCN4 [61] and CPD [62]), lipid metabolism (HUWE1 [63] and FABZ [64]), visual sense (AP4B1 [65] and PRPF8 [66]), growth and differentiation (ABTB1 [67], UBE4A [68], DOHH [69], and GAB1 [70]), embryogenesis (SBDS [71], TAF5L [72], and SEC8 [73]), and others.
We suspected that the complexity (i.e., localized oxygen depletion, sulfide accumulation, and high turbidity) of the habitat environment may make Sillago species subject to multiple environmental stressors. Multiple environmental stressors might contribute to DNA damage and immunosuppression in Sillago species [74,75]. Meanwhile, the burrowing behavior of Sillago species may cause mechanical injuries to skin, and thus pathogens may enter the organism from the wound. Therefore, we suspected that those PSGs related to the stress response reflect the plasticity of Sillago species’ adaptation to multiple environmental stressors. A previous study has considered that the foraging probability and food-intake of Sillago species larvae may be limited by low light [76]. The inadequate intake can further affect all kinds of behaviors that necessitate high energy consumption, such as predation, reproduction, and others [77]. Therefore, it is a questionable whether the positive selection of material and metabolism-related genes related to material and energy metabolism could maintain the energy compensation of Sillago species. Interestingly, two vision genes were found to be positively selected in Sillago species. The positive selection of vision genes can enhance the visual acuity of Sillago species, which is useful for some behaviors (predation, reproduction, and others) in low light [78]. Meanwhile, the retina of Sillago species may have possessed a well-developed vascularization due to the positive selection of vision genes, possibly to overcome the hypoxic conditions [78]. A previous study has also considered that light can affect the foraging, growth, and reproductive behavior and the circadian rhythms of fishes [79]. It has been discussed above that multiple environmental stressors may affect the stress response, predation behavior, material and energy metabolism, and visual sensitivity of Sillago species, which may eventually limit the survival and development of Sillago species. Therefore, we suspected that Sillago species might positively select a battery of genes associated with growth, differentiation, and embryogenesis to maintain their effective population numbers under multiple environmental stressors.
All in all, these PSGs might contribute to the ecological adaptation of Sillago species to the multiple environmental stressors, and these PSGs are also crucial to the evolution of Sillago species. However, our current evidence only shows specific protein sequence mutation in Sillago species. Whether these PSGs lead to favorable mutations in the phenotype of fish is unknown. Meanwhile, future experiments are also needed to explore which ecological traits of fish might have evolved along with these PSGs.

5. Conclusions

This study is the first systematic report of the transcriptome resource of Sillago species, and these data enrich the genomic information for molecular studies of these species. Based on eight well-annotated model fish genomes, we obtained 140 orthologous exon markers shared in Sillago species and then reconstructed a more complete phylogenetic relationship. Through the rates of non-synonymous to synonymous orthologous nucleotide substitutions, we found positive selection traces in 44 genes, and these genes are potentially related to the stress response, material (carbohydrate, amino acid, and lipid) and energy metabolism, growth and differentiation, embryogenesis, visual sense, and other things. This suggests that multiple environmental stressors may have led to specific selection force towards key genes in Sillago species. However, further experiments are needed to determine the exact function of these PSGs in Sillago species. Taken together, our results reconstruct a more complete view of the phylogenetic relationships of Sillago species based on transcriptome resources. We also suspect that the capacity of Sillago species to thrive in multiple environmental stressors may be due to the positive selection of these adaptive genes. The present study only represents a first step in understanding the habitat adaptive mechanism of the fish family Sillaginidae at the molecular level; further studies are still needed to validate the results and hypotheses.

Author Contributions

Conceptualization, T.G.; methodology, F.L.; validation, F.L., N.S., Y.Z., D.J. and T.G.; formal analysis, F.L.; sampling, D.J.; writing—original draft preparation, F.L.; writing—review and editing, F.L., Y.Z., N.S., D.J. and T.G.; supervision, T.G.; project administration, T.G.; funding acquisition, T.G. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (41976083).

Acknowledgments

Sillago parvisquamis were provided by Hirotaka Nomura from Marine Ecology Research Institute (Chiba, Japan).

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

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Animals 10 00633 g001 550
Figure 1. The sampling location and standard length (SL) of each sequencing individual.
Figure 1. The sampling location and standard length (SL) of each sequencing individual.
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Animals 10 00633 g002 550
Figure 2. Inferred phylogenetic relationships and divergence times (data in the blue circles) of the seven Sillago species based on the concatenated nucleotide sequences.
Figure 2. Inferred phylogenetic relationships and divergence times (data in the blue circles) of the seven Sillago species based on the concatenated nucleotide sequences.
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Figure 3. Inferred phylogenetic relationships and divergence times (data in the blue circles) of the seven Sillago species based on the concatenated amino acid sequences.
Figure 3. Inferred phylogenetic relationships and divergence times (data in the blue circles) of the seven Sillago species based on the concatenated amino acid sequences.
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Animals 10 00633 g004 550
Figure 4. Inferred phylogenetic relationships and divergence times (data in the blue circles) of the seven Sillago species based on the concatenated variation sites.
Figure 4. Inferred phylogenetic relationships and divergence times (data in the blue circles) of the seven Sillago species based on the concatenated variation sites.
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Figure 5. GO enrichment analysis of representative positively selected genes.
Figure 5. GO enrichment analysis of representative positively selected genes.
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Table
Table 1. The ecological characteristics of 20 research species.
Table 1. The ecological characteristics of 20 research species.
SpeciesClassificationMilieuClimate ZoneDepth Range (M)Maturity Length (cm)Feeding HabitsType of Fish Eggs
E. fuscoguttatusSerranidaeMarine; brackish; reef-associatedTropical1–6050CarnivorousPelagic
E. coioidesSerranidaeMarine; brackish; reef-associatedSubtropical1–10025–30CarnivorousPelagic
P. fluviatilisPercidaeFreshwater; brackish; demersalTemperate1–3011–23.4CarnivorousAdhesive
C. hamatusChannichthyidaeMarine; demersalPolar4–60033–37CarnivorousPelagic
G. acuticepsBathydraconidaeMarine; demersalPolar0–550-CarnivorousPelagic
D. eleginoidesNototheniidaeMarine; demersalTemperate50–385038–60CarnivorousPelagic
T. bernacchiiNototheniidaeMarine; demersal;Polar0–70018CarnivorousPelagic
A. regiusSciaenidaeMarine; brackish; demersalSubtropical15–30080CarnivorousPelagic
N. albifloraSciaenidaeMarine; demersal; coastal waters with mudddy to sanddy-muddy bottomsTemperate25–80-CarnivorousPelagic
M. miiuySciaenidaeMarine; brackish; demersal; coastal waters with mudddy to sanddy-muddy bottomsTemperate15–100-CarnivorousPelagic
C. lucidusSciaenidaeMarine; demersal; coastal waters with mudddy to sanddy-muddy bottomsSubtropical0–9013CarnivorousPelagic
L. polyactisSciaenidaeMarine; demersal; sublittoral zone above 120 m with muddy to sanddy-muddy bottomsSubtropical0–12018.1CarnivorousPelagic
L. croceaSciaenidaeMarine; brackish; demersal; coastal waters and estuaries with muddy to muddy-sandy bottoms shallower than 120 m depthTemperate0–12017CarnivorousPelagic
S. aeolusSillaginidaeMarine; demersal; nearshore shallow and estuarine waters; burrowing life-styleTropical0–6012CarnivorousPelagic
S. japonicaSillaginidaeMarine; demersal; nearshore shallow and estuarine waters; burrowing life-styleSubtropical0–30-CarnivorousPelagic
S. parvisquamisSillaginidaeMarine; brackish; demersal; nearshore shallow and estuarine waters; burrowing life-styleSubtropical0–30-CarnivorousPelagic
S. sihamaSillaginidaeMarine; brackish; reef-associated; nearshore shallow and estuarine waters; burrowing life-styleTropical0–6013–19.1CarnivorousPelagic
S. sinicaSillaginidaeMarine; brackish; demersal; nearshore shallow and estuarine waters; burrowing life-styleTropical--CarnivorousPelagic
S. sp.1Sillaginidae------
S. sp.2Sillaginidae------
Note: “-” indicates that no statistics were found.
Table
Table 2. The clean transcriptomic reads of the seven Sillago species.
Table 2. The clean transcriptomic reads of the seven Sillago species.
Sillago SpeciesRead NumberGC%%≥Q30
S. aeolus78,709,24651.1492.37
S. japonica50,013,64153.0292.96
S. parvisquamis113,351,00852.8893.75
S. sihama87,050,70251.3492.63
S. sinica97,977,19952.1994.51
S. sp.151,710,08153.8693.74
S. sp.270,996,52653.5792.95
Table
Table 3. The transcriptome assembly information of the seven Sillago species.
Table 3. The transcriptome assembly information of the seven Sillago species.
Sillago SpeciesUnigene
NumberTotal Length (bp)Mean Length (bp)N50 Length (bp)
S. aeolus82,02451,896,226787.321,403
S. japonica58,10223,966,004428.99461
S. parvisquamis102,18579,280,2111,019.381,986
S. sihama69,74848,391,713815.811,369
S. sinica102,90378,264,349992.701,848
S. sp.163,80734,524,368588.49738
S. sp.285,99049,751,159652.68902
Table
Table 4. Representative positively selected genes in Sillago species.
Table 4. Representative positively selected genes in Sillago species.
Gene NameDescription×10-ValueFDR-Adjusted p-Value
Stress responseMED27mediator of RNA polymerase II transcription subunit 273.02 × 10−390.00
MED28mediator of RNA polymerase II transcription subunit 282.33 × 10−290.00
LTV1protein LTV1 homolog1.08 × 10−377.89 × 10−03
SMOSpermine oxidase2.21 × 10−221.27 × 10−14
PSApuromycin-sensitive aminopeptidase3.70 × 10−410.00
ABCB7ATP-binding cassette sub-family B member 7, mitochondrial5.54 × 10−310.00
COPAcoatomer subunit alpha4.99 × 10−450.00
SF3A1splicing factor 3A subunit 12.31 × 10−440.00
SF3B5splicing factor 3B subunit 58.30 × 10−600.00
DEPDC5GATOR complex protein DEPDC5 isoform X31.72 × 10−460.00
POLλDNA polymerase lambda1.48 × 10−800.00
TFIP11tuftelin-interacting protein 112.10 × 10−720.00
NUDT6Nucleoside diphosphate-linked moiety X motif 61.32 × 10−830.00
UBIAD1UbiA prenyltransferase domain-containing protein 17.59 × 10−960.00
Energy metabolismAPFbis(5′-nucleosyl)-tetraphosphatase [asymmetrical]5.30 × 10−640.00
IMMTMICOS complex subunit MIC60 isoform X21.66 × 10−1261.38 × 10−04
Carbohydrate metabolismSUCLG1succinate-CoA ligase [ADP/GDP−forming] subunit alpha, mitochondrial2.37 × 10−230.00
Amino acid metabolismGCN1eIF-2-alpha kinase activator GCN11.82 × 10−410.00
CPDCarboxypeptidase D6.74 × 10−460.00
Lipid metabolismHUWE1E3 ubiquitin-protein ligase HUWE1 isoform X13.95 × 10−351.15 × 10−03
HUWE1E3 ubiquitin-protein ligase HUWE1 isoform X14.55 × 10−240.00
HUWE1E3 ubiquitin-protein ligase HUWE1 isoform X18.49 × 10−547.85 × 10−03
HUWE1E3 ubiquitin-protein ligase HUWE1 isoform X11.31 × 10−380.00
HUWE1E3 ubiquitin-protein ligase HUWE1 isoform X11.48 × 10−400.00
HUWE1E3 ubiquitin-protein ligase HUWE1 isoform X11.40 × 10−410.00
FABZhydroxyacyl-thioester dehydratase type 2, mitochondrial7.36 × 10−800.00
HUWE1E3 ubiquitin-protein ligase HUWE1 isoform X12.11 × 10−1175.07 × 10−03
HUWE1E3 ubiquitin-protein ligase HUWE1 isoform X11.57 × 10−1170.00
Visual senseAP4B1AP-4 complex subunit beta-15.00 × 10−450.00
PRF8Pre-mRNA-processing-splicing factor 82.12 × 10−520.00
Growth and differentiationABTB1ankyrin repeat and BTB/POZ domain-containing protein 11.96 × 10−360.00
UBE4Aubiquitin conjugation factor E4 B isoform X21.31 × 10−291.11 × 10−12
GAB1GRB2-associated-binding protein 1 isoform X13.65 × 10−610.00
DOHHdeoxyhypusine hydroxylase2.66 × 10−640.00
EmbryogenesisSBDSribosome maturation protein SBDS2.55 × 10−390.00
SEC8exocyst complex component 81.38 × 10−900.00
TAF5LTAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L0.000.00
OthersCCDC25Coiled-coil domain-containing protein 259.63 × 10−170.00
PIGYphosphatidylinositol N-acetylglucosaminyltransferase subunit Y1.12 × 10−400.00
-fumarylacetoacetate hydrolase domain-containing protein 2-like isoform X26.37 × 10−430.00
USP24ubiquitin carboxyl-terminal hydrolase 24 isoform X25.15 × 10−310.00
RPN226S proteasome non-ATPase regulatory subunit 12.38 × 10−440.00
CXORF56UPF0428 protein CXorf56 homolog1.53 × 10−1360.00
TALINtalin rod domain-containing protein 10.003.81 × 10−06
Table
Table 5. KEGG pathway enrichment analysis of representative PSGs.
Table 5. KEGG pathway enrichment analysis of representative PSGs.
PathwayPathway_IDKey EnzymeGene Name
Nicotinate and nicotinamide metabolismmap00760diphosphataseAPF
Carbon fixation pathways in prokaryotesmap00720ligase (ADP-forming)SUCLG1
Purine metabolismmap00230adenylpyrophosphatase; diphosphatase; phosphataseABCB7, APF, ABCB7
C5-Branched dibasic acid metabolismmap00660ligase (ADP-forming)SUCLG1
Starch and sucrose metabolismmap00500diphosphataseAPF
Arginine biosynthesismap00220synthase (NADPH)UBIAD1
Riboflavin metabolismmap00740diphosphataseAPF
Pantothenate and CoA biosynthesismap00770diphosphataseAPF
Pyrimidine metabolismmap00240diphosphataseAPF
Biosynthesis of antibioticsmap01130synthase (NADPH); ligase (ADP-forming); ligase (GDP-forming)UBIAD1, SUCLG1, SUCLG1
Citrate cycle (TCA cycle)map00020ligase (ADP-forming); ligase (GDP-forming)SUCLG1, SUCLG1
Propanoate metabolismmap00640ligase (ADP-forming); ligase (GDP-forming)SUCLG1, SUCLG1
Thiamine metabolismmap00730PhosphataseABCB7
Arginine and proline metabolismmap00330synthase (NADPH)UBIAD1

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Lou, F.; Zhang, Y.; Song, N.; Ji, D.; Gao, T. Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of Sillago Species. Animals 2020, 10, 633. https://doi.org/10.3390/ani10040633

AMA Style

Lou F, Zhang Y, Song N, Ji D, Gao T. Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of Sillago Species. Animals. 2020; 10(4):633. https://doi.org/10.3390/ani10040633

Chicago/Turabian Style

Lou, Fangrui, Yuan Zhang, Na Song, Dongping Ji, and Tianxiang Gao. 2020. "Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of Sillago Species" Animals 10, no. 4: 633. https://doi.org/10.3390/ani10040633

APA Style

Lou, F., Zhang, Y., Song, N., Ji, D., & Gao, T. (2020). Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of Sillago Species. Animals, 10(4), 633. https://doi.org/10.3390/ani10040633

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