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Aquaculture omics: An update on the current status of research and data

analysis
Article in Marine Genomics · August 2022

DOI: 10.1016/j.margen.2022.100967
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Marine Genomics 64 (2022) 100967
Contents lists available at ScienceDirect
Marine Genomics
journal homepage: www.elsevier.com/locate/margen
Review
Aquaculture omics: An update on the current status of research and

data analysis
Jitendra Kumar Sundaray a, Sangita Dixit b, Ashraf Rather c, Kiran D. Rasal d, Lakshman Sahoo a, *
a
ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India
b
Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan University (Deemed to be University), Bhubaneswar 751003, Odisha, India
c
Division of Fish Genetics and Biotechnology, College of Fisheries, Sher-e- Kashmir University of Agricultural Science and Technology, Rangil-Ganderbal 190006, Jammu
and Kashmir, India
d
Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400 061, Maharastra, India
A R T I C L E I N F O A B S T R A C T
Keywords: Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein
Transcriptomics nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as
NGS capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of
miRNAs
genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of
Metagenomics
SNPs
quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the
Aquaculture continuous development of high throughput sequencing technology has revolutionized the biological sciences
and provided necessary tools. Application of ‘omics’ in aquaculture research have been successfully used to
resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date,
high quality draft genomes of over fifty fish species have been generated and successfully used to develop large
number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in
several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aqua
culture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in
reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a
promising scientific tool to analyze the complex genomes contained within microbial communities. Meta
genomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, anti
biotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In
the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.
1. Introduction employment and animal protein nutritional security it is not free from
obstacles. One of the major obstacles of aquaculture growth is lack of
Fish is the cheapest source of quality animal protein and can meet the availability of elite germplasm. Another challenging problem in aqua
growing demand for animal protein. It is one of the sustainable sources culture is fish diseases caused by several pathogens, such as bacteria,
of essential amino acids, proteins, vitamins and omega-3 fatty acids etc. viruses, and fungi, showing high economic losses, and in turn, aqua
Teleosts are the largest group of vertebrates comprising more than culture results in environmental problems (Schwitzguébel and Wang,
32000 of species spreading across marine to freshwater habitat (Nelson 2007). To make the aquaculture sector sustainable and profitable, it is
et al., 2016), however till today only four hundred species are cultured essential to solve these problems using novel ideas and technologies.
(Gjedrem and Robinson, 2014). Currently, aquaculture is an emerging During the last decade technological advancement accelerated fish
and increasingly growing agriculture sector (FAO, 2016). Globally, India genome sequencing enabling development of protocols/methods facili
ranks second for fisheries production, and China produces 1/3rd of the tate to study the global alteration of genes, proteins and metabolites
total fish harvested and 2/3rd of the fish cultivated (FAO, 2016). expression level (Zampiga et al., 2018). The genome information of an
Though aquaculture has the potential to provide livelihood, rural organism remains unchanged during its entire period of life, however
* Corresponding author at: Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002,
India.
E-mail address: [email protected] (L. Sahoo).
https://doi.org/10.1016/j.margen.2022.100967
Received 17 June 2021; Received in revised form 26 May 2022; Accepted 15 June 2022
1874-7787/© 2022 Elsevier B.V. All rights reserved.
J.K. Sundaray et al. Marine Genomics 64 (2022) 100967
Table 1
Comparative account of NGS platforms.
Generation of sequencing Sequencing Technology NGS platform Accuracy Read per Run GB per Time per Run Cost (USD)
technology (%) (Bases) Run
2nd generation Illumina iSeq >99.9% 2*150 0.3-1.2 1-10 days ~20,000
MiniSeq >99.9% 2*150 1.7-7.5 1-10 days ~50,000
MiSeq >99% 2*300 0.3-15 1-10 days ~100,000
NextSeq 80%-99% 2*150 10-120 NA 250,000
HiSeq 90%-99% 2150 10-1000 24hrs 650,000
Thermo Fisher PGM 87.5% 400 0.08-2.0 72 hrs 80,000
S5 >99% 400 0.6-1.5 NA 60,000
Proton >99% 200 10-15 NA 149,000
3rd generation Pacific Bioscience PacBio RSII 90% 60,000 0.5-1.0 30 minutes to 2 750,000
hrs
Sequel 99.9% 60,000 5-10 2 hrs 350,000
Oxford Nanopore Technology MinIon 99.3% 100,000+ 10-20 6hrs 1000
GridIon 99.3% 100,000+ 50-100 72hrs 2400
PromethIon 98%-99.1% 100,000+ 480-960 72hrs 25,000
Intelligent Biosystems 2*100bp NA NA Upto 80GB 40hrs 120,000
(Qiagen)
Table 2
Genome sequences of some aquaculture species
Species Sequencing platform Total size Contig N50 Scaffold N50 Percentages of References
(Mb) (Kb) (Mb) genome
Stickleback 9.0X Sanger 463 83.2 10.8 86.9 (Jones et al., 2012)
Catfish Illumina, PacBio 783 77.2 7.73 97.2 (Liu et al., 2016)
Grass carp 132X Illumina 900.5 40.8 6.46 64.0 (Wang et al., 2015)
Seabass 30X 675.4 53.2 5.09 86.0 (Tine et al., 2014)
(Venkatesh et al.,
Shark 454, Sanger 937 46.6 4.5 -
2014)
Turbot Illumina 544 31.2 4.3 - (Figueras et al., 2016)
Tilapia 269X Illumina 1 010 29.3 2.80 70.9 (Brawand et al., 2014)
(McGaugh et al.,
Cavefish 94X Illumina 964 14.7 1.78 -
2014)
Zebrafish 7.5X Sanger, Illumina 1 410 25.0 1.55 96.5 (Howe et al., 2013)
Medaka 10.6X Sanger 700.4 9.8 1.41 89.7 (Kasahara et al., 2007)
Platy fish 454, Illumina 669 22.0 1.1 90.2 (Schartl et al., 2013)
Common carp 454, Illumina, SOLiD 1690 68.4 1.0 51.8 (Xu et al., 2014a)
Tetraodon 8.3X Sanger 342.4 16.0 0.98 64.6 (Jaillon et al., 2004)
(Amemiya et al.,
Coelacanth Illumina 2 860 12.7 0.92 -
2013)
Sole Illumina 477 26.5 0.87 93.3 (Chen et al., 2014)
Cod 454 753 7.1 0.69 44.1 (Star et al., 2011)
Yellow
76X Illumina 644 25.7 0.50 - (Wu et al., 2014)
croacker
Rainbow trout 70X Illumina 1 900 7.7 0.38 54. 0 (Berthelot et al., 2014)
Lamprey Sanger 816 - 0.17 - (Smith et al., 2013)
Fugu 5.6X Sanger 332.5 16.5 0.05-0.1 - (Aparicio et al., 2002)
Rohu Illumina, Ion torrent, Roche 454 and PacBio 1480 30.6 1.95 98 (Das et al., 2020)
Catla Illumina and Nanopore 1010 - 0.7 (Sahoo et al., 2020)
Illumina, Ion torrent, Roche 454, Nanopore and (Kushwaha et al.,
Indian catfish 941 - 1.3 94
PacBio 2021)
the resultant product of gene i.e the proteins or metabolites are subject response and host immune response (Qian et al., 2014). The functional
to change at expression level in a rapid and dynamic way. Technological classification of gene expression data is represented as matrices, and
advancement allowed analysis of transcriptome data, and the resulting microarray data analysis mainly involves statistical analysis, classifica
technology is known as RNA sequencing technology (RNA-seq technol tion, and clustering approaches (Can, 2014).
ogy) (Qian et al., 2014). RNA-seq technology overcomes many limita In this review, we first summarized the high-throughput sequencing
tions of other transcriptomic methods, such as the microarray and tag- technologies. We then reviewed the recent advances of whole-genome
based sequencing method. Although RNA-seq methods have been sequencing, transcriptomics, metagenome sequencing, miRNAs and
available for a relatively short period, studies using the RNA-seq method single nucleotide polymorphisms (SNPs) and their applications in
have entirely reformed our perspective of the range and depth of aquaculture sectors.
eukaryotic transcriptomes. In applying the transcriptomics technology
of the aquaculture sector, both model and non-model fish species have 2. Whole-genome sequencing in aquaculture species
benefited from these sequencing methods and have undergone
tremendous progress over the past several years. RNA-seq has helped to The availability of genome sequences is crucial for understanding a
map and annotate fish transcriptomes, such as gene expression, gene species’ biology and serves as a roadmap to facilitate the development of
regulatory networks, metabolic pathways, and protein-protein interac technologies to achieve sustainable production. Aquaculture genomics
tion networks, and has also provided an understanding of many bio started in the 1990s in the USA, Europe, China and other countries,
logical processes in fish, such as adaptive evolution, development, stress although genome research started before the 1980s. The First
2
Fig. 1. Illustration of application of high throughput sequencing in fish genomics and genetics.
Aquaculture Genomics Workshop was held in 1977 at Dartmouth, European seabass, grass carp, rohu, catla and Indian catfish, have been
Massachusetts, in the United States of America (https://www.globalse sequenced and published (Table 2).
afood.org). For genome research, four species, catfish, salmonids, stri The pyrosequencing was the first NGS technology available in the
ped bass and tilapia, were the focus of the above mentioned genomics market and the Atlantic cod (Gadus morhua, cold-water marine fish)
workshop. Through advanced sequencing technologies and the devel genome was sequenced employing this NGS platform only (shotgun and
opment of next-generation sequencing (NGS) platforms, rapid growth is paired end library sequencing), and the genome size was estimated to be
presently made in the whole-genome sequencing of aquaculture species 830 Mb, with 13,000 contigs and more than 3800 scaffolds with N50
(Kumar and Kocour, 2017). To decipher the genome sequences of the scaffold size of 488,312 Kb. Genome annotation identified 22,154
aquaculture species, several sequencing technologies were used, such as protein-coding genes (Star et al., 2011). The Pacific oyster (Crassostrea
Sanger sequencing, pyrosequencing (454 GS-FLX, Roche, Basel, gigas) is an essential marine shellfish species having high percentages of
Switzerland), sequencing by ligation (SOLiD, Life Technologies, Cali repetitive sequences was sequenced using hybrid approach ie short read
fornia, USA), sequencing by synthesis (Illumina, California, USA), ion sequencing in combination with fosmid-pooling. The assembled genome
semiconductor (Ion Tor-rent), and single-molecule real-time sequencing was observed to be 559 Mb and 90 % of it was covered by the longest
(Pac-Bio). A comparative account of different NGS platforms with 1670 scaffolds with N50 size of 401 kb (Zhang et al., 2012). The whole-
output parameters is provided in Table 1. Before 2005, the output of genome sequence of tetraploid common carp (Cyprinus carpio) has been
NGS platforms was less than one Gb/run; after 2005, the production of completed in recent years (2014) by adopting multiplatform sequencing
these platforms increased to ~1500 GB/run, and in 2016, the cost of strategy ie Illumina, SOLiD and Roche 454 platform at the Chinese
sequencing was reduced 1000-fold/per base pair, and the bioinformatics Academy of Fishery Sciences using both single-end and paired-end or
analysis pipelines improved. Thus, the utility of whole-genome mate-pair libraries of various insert size ranging from 250 bp to 8 kb and
sequencing is ever-expanding in aquaculture species. In the recent scaffold N50 length was observed to be 1.0 Mb (Xu et al., 2014a). The
past, whole-genome sequencing projects started with several different draft genome size is 1.69 Gb, contains 52,610 protein-coding genes, and
aquaculture species in various states of assembly. Currently, scientists 2503 scaffolds contributed to 90% of the assembly (Xu et al., 2014b).
are using single-molecule real-time (SMRT) sequencing, which means Another important freshwater species is Nile tilapia (Oreochromis nilo
more short-read sequencing (SRS) in combination with very long-read ticus), which has been cultured in more than 100 countries with over 6
sequencing (Vij et al., 2016; Roberts et al., 2013). The draft genome million tons of annual production. Its genome was sequenced with four
sequences of twenty-seven species, Pacific oyster, common carp, other species (Neolamprologus brichardi/pulcher, Metriaclima zebra,
3
Table 3 Table 5
Transcriptome profiling in aquaculture species; purpose, targeted tissues and List of unique miRNAs identified and their functional role
references Species miRNAs Function References
Transcriptome Tissue Species References
Rainbow trout let-7, miR-10, miR- Cell (Ma et al.,
analysis in
(Oncorhynchus 21, miR- 24, miR-25, differentiation 2012)
Reproduction Brain, Melanogrammusaeglefinus, (Das et al., 2020; mykis) miR-30, miR-143,
and Gonads, Salmo salar, Gadusmorhua, Roy et al., 2018), miR-146, miR-148,
development Liver, Silurusmeridionalis, (Sahu et al., and miR-202
Pituitary Silurusasotus, Labeorohita 2015), ( Nile tilapia let-7b, c,j, miR-1, Growth (Huang et al.,
Gasterosteus aculeatus, Kushwaha et al., (Oreochromis miR-15a, miR-22a, regulation 2012)
Anguilla japonica, 2021; Jin et al., niloticus) miR-27a, miR-30b,
Oreochromis niloticus, Danio 2015), (Avarre miR-34, miR-125b,
rerio, Gobiocyprisrarus et al., 2014) miR-133a,miR-140,
Immunity and Spleen, Rainbow trout, (Chapman et al., miR-152, miR-192,
disease Kidney, Ctenopharyngodon Idella, 2014; Sudhagar miR-193a, miR-199,
Brain, Atlantic Salmon, Danio riror, et al., 2018) ( miR-204, miR-206,
Muscle, Latescalcarifer, Syahputra et al., miR-214, miR-218a,
Intestine, Nototheniacoriiceps, Brown 2019; Dang b
Heart, Skin trout, Salmo trutta et al., 2016; Zebra Fish (Danio mir-430, mir-427, Regulates mRNAs (Giraldez et al.,
Maekawa et al., rerio) mir-520, mir-93, overexpression 2006)
2019; mir-20, mir-17
Stockhammer Teleost fish mir-462, mir-731, Immune response (Andreassen
et al., 2009; Kim mir-146, mir-21,mir- and Høyheim,
et al., 2019) 181, mir-155, mir- 2017)
Toxicology and Embryos, Snout bream, Zebrafish, (Zheng et al., 221, mir-1388, mir-
stress Liver, Larimichthyscrocea, Nile 2018; Asker 100, mir-99
Testis, tilapia, Aristihthysnobilis, et al., 2013), (Xu Rohu miR-22, miR-122, carbohydrate (Rasal et al.,
Gills, Cyprinus carpio, et al., 2015; (Labeorohita) miR-365, miR-200, metabolism 2020)
Intestine, Gobicyprisrarus, Brown Miao et al., and miR-146, miR-
Swim Trout, European flounder 2018), (Wang 216, miR-130, miR-
bladder, et al., 2016; 456, miR-20, miR-
Muscle Zhang et al., 23, miR-29, miR-
2017b) 200, miR-139, miR-
Growth and Brain, Rainbow trout, Atlantic (Danzmann 1338, miR-199, miR-
nutrition Pituitary, salmon, Dicentrarchuslabrax, et al., 2016; 22, miR-100
Liver, Danio rerio, Atlantic cod, Geay et al., Bata (Labeobata) miR-202, miR-133, Liver specific (Rasal et al.,
Muscle, Atlantic salmon, Sparus 2011; De Santis miR-132, and miR- 2019)
Gut/ aurata, Aliivibriowodanis et al., 2015), ( 29, miR-202, miR-
Intestine Hjerde et al., 132, and let-7, mir-
2015; Morrison 132,mir-29
and Wright, Triploid Fish miR-101a, miR-99, Testicular (Tao et al.,
2005) miR-101a, miR-100, development 2018)
miR-22a, miR-146a,
miR-21, and miR-7a,
mir-143
Table 4 Zebra Fish (Danio miR-148, mir-152, Heart (Klett et al.,
List of currently available gene prediction software packages rerio) mir-144, mir-16c, regeneration 2018)
mir-29b, mir-26,
Sl. No. Name Links mir-133, mir-19,
1 AUGUSTUS http://augustus.gobics.de/ mir-152, mir-218,
2 CRITICA http://www.ttaxus.com/software.html mir-101
3 ChemGenome http://bgf.genomics.org.cn/
4 DNA SUBWAY http://dnasubway.iplantcollaborative.org/
5 BGF http://bgf.genomics.org.cn/ L. catla, and Clarias magur have been sequenced (Das et al., 2020; Sahoo
6 EUGENE http://eugene.toulouse.inra.fr/ et al., 2020; Kushwaha et al., 2021). A multiplatform sequencing
7 FGENESH http://linux1.softberry.com/berry.phtml?
approach was adopted to sequence these genomes. Illumina short read
topic=fgenesh&group=programs&
subgroup=gfind and 454 pyrosequencing was used to decipher the L. rohita genome with
8 FRAMED http://tata.toulouse.inra.fr/apps/FrameD/ scaffold N50 values of 1.95Mb and assembled genome size of 1.49 Gb.
FD Similarly, the L. catla genome was sequenced using a combination of
9 GeneID http://genome.crg.es/software/geneid/geneid.html short read sequencing (Illumina) and long read sequencing (Oxford
10 GeneMark http://topaz.gatech.edu/GeneMark
Nanopore) resulting an assembled size of 1.01 Gb with scaffold N50
11 GeneTack http://topaz.gatech.edu/GeneTack
value 0.7 Mb. Whereas a combination of Illumina, Iontorrent, 454 and
Oxford Nanopre sequencing technology was used to decipher the
Pundamilia nyererei, and Astatotilapia burtoni) using sequencing by syn genome sequence of C. magur. The assembled genome of C. magur was
thesis (SBS) technology. The assembled genome contained 77,578 con found to be 941 Mb with scaffold N50 values of 1.3 Mb and 23,748
tigs with a 29.5 kb N50 value and 13,517 scaffolds with a 2.8 Mb of N50 estimated protein coding genes. The assembled genomes of other spe
value. The genome length of the Nile tilapia (Oreochromis niloticus) is cies, e.g., trobut, salmon, catfish and tilapia etc. are available in the
815.7 Mb, containing 21,437 protein-coding genes, 22 pseudogenes, NCBI SRA resources database. Still, the whole genome sequence of many
and 821 non-coding RNAs (Brawand et al., 2014). Additionally, whole- aquaculture species is not accessible for public use. Hopefully, all
genome sequencing of goldfish was completed in 2019 using SMRT reference genomes will be available in the public domain in the coming
sequencing technology and found that the genome size was 1.6-2.08 pg. years. The availability of high-quality reference genomes will lead to an
The assembled genome contained 9415 contigs with an N50 of 817 kbp in-depth understanding of aquaculture species’ production and repro
and 1246 scaffolds (Chen et al., 2019). Similarly, the genome sequences ductive biology, thereby enhancing aquaculture production.
of commercially important indigenous fish species such as Labeo rohita,
4
Table 7 transcriptome data analysis is provided in Fig. 1. In the recent past,

List of miRNA prediction tools/packages transcriptome analysis has been widely used in the aquaculture sector
Tool Application Description Online Portal for effective identification and expression study of candidate/target
genes involved in reproduction, growth, immunity, development, stress,
MiRscan Web server A classic miRNA http://genes.mit.edu/
prediction server mirscan/ disease, and toxicology (Garg et al., 2011). Recently, a project widely
microPred Packages A tool to classify pre- http://www.cs.ox.ac. known as Fish-T1K was initiated to profile transcripts of 1000 fishes
miRNAs from pseudo uk/people/manohara. (Sun et al., 2016). Large numbers of transcripts, including novel tran
hairpins and other rukshan.batuwita/ scripts, have been successfully identified in various organisms, including
ncRNAs microPred.htm
miRAbela Web server A tool to predict if a http://www.mirz.
model and non-model aquaculture species, using high-throughput RNA
sequence contains unibas.ch/ sequencing technology (RNA-seq), such as channel catfish (Ictalurus
miRNA-like structures punctatus) (Sun et al., 2016; Liu et al., 2016), zebrafish (Danio rerio)
miRNAFold Web server Ab initio miRNA http://evryrna.ibisc. (Collins et al., 2012), European sea bass (Dicentrarchus labrax) (Sarro
prediction in genomes univ-evry.fr/m
poulou et al., 2019), and rainbow trout (Oncorhynchus mykiss) (Palstra
iRNAFold/
MirEval Web server A tool for evaluating http://mimirna.centen et al., 2013). In addition, liver-specific transcripts corresponding to
sequences for possible ary.org.au/mireval/ various conditions have been identified in the liver (Liu et al., 2014;
miRNA-like properties Qian et al., 2016; Zhang et al., 2017a; Yadetie et al., 2018; Dai et al.,
CID- Web server Identification of https://github.co 2021).
miRNA and package miRNAs from a single m/alito/CIDmiRNA
sequence or complete
Similarly, transcripts having a profound role in fish reproduction
genome have been identified in several species (Reading et al., 2012; Cardoso
miRanda Web server 7 nt base pairing and http://cbio.mskcc.org/ et al., 2018; Yang et al., 2018; Tian et al., 2019; Saaristo et al., 2021). In
weighted seed match, microrna_data/ addition, the regulation of glucose metabolism has been recently iden
Energy calculation
tified and demonstrated to have similar regulation patterns and activity
RNAhybrid Web service Finds minimum free https://bibiserv2.ce
energy (MFE) of bitec.unibielefeld.de/ in model zebrafish and mammals (Zhang et al., 2018). Although the
hybridization of long rnahybrid application of transcriptome analysis in the aquaculture sector is chal
and short RNA lenging, the literature search at PubMed/Google with the keyword fish
TargetScan Web server 6–7 nucleotide (nt) base http://www.target and RNA-seq indicates that the publication percentages in the aqua
pairing, Z-score (Energy scan.org/
culture field (particularly in fish) have increased considerably in the past
3-4 years. Some target tissues for transcriptome sequencing analysis of
3. Transcriptome study and data analysis in aquaculture species various fish are listed in Table 3.
High-throughput technology (RNA-seq) is also used to identify novel
Transcriptomics is the technique used to study an organism at the transcript regions in the genome. RNA-seq results found a large number
transcript level under particular conditions. Transcriptome data analysis of unknown transcribed regions in all fish species, including rohu carp
gives a brief idea of molecular function and cellular processes that are (Robinson et al., 2012; Sahu et al., 2015), zebrafish (Pauli et al., 2012)
active and dormant. Transcriptome analysis is used from a specific tissue and rainbow trout (Palstra et al., 2013). Among them, many ncRNAs are
(Li et al., 2014), a whole individual (Rodríguez-Celma et al., 2013), or a essential due to their crucial roles in various biological functions (BFs)
pool of individuals (Helm et al., 2013). The current progress in NGS and cellular processes (CCs), such as gene regulation, genome defense,
technologies and advancement in computational tools have facilitated translation and RNA splicing (Mattick and Makunin, 2006). For
understanding the function/regulation of known/new genes at a example, more than 500 unique long-strand ncRNAs were found in
genome-wide scale (Chaitankar et al., 2016). Transcriptome analysis zebrafish embryos (Ulitsky et al., 2011). In addition, 19,015 unique
workflow includes RNA isolation and purification methods involving genes were observed in the ovarian tissue of crucian carp (Wang et al.,
TRIzol (phenol-chloroform), silica gel columns, and oligo dT-based ap 2019), 940 reproduction-related genes involving 184 reproduction, 223
proaches (Tan and Yiap, 2009). High-quality RNA with sufficient hormone-activity, and receptorbinding genes, 178 receptor-activity
integrity (between 9 and 10) was taken for library preparation and genes, and 355 embryonic-development-related proteins were identi
sequencing purposes. Impure or degraded RNA will perform poorly in fied in Labeo rohita (Hamilton) (Sahu et al., 2015). Nearly 809
enzymatic applications. A graphical representation of the workflow for reproduction-related genes were identified in Cyprinus carpio (Anitha
et al., 2019). These newly identified transcripts will help further
Table 6
Metagenome information of some aquaculture species
Species Tissue Host microbes Genus OTUs References
Sea Cucumber Intestine Bacteroidetes, Rhodobacterales, Vibro, Rhodobacteraceae, >90% (Zhang et al., 2019)
Flavobacteriaceae,
Freshwater Fish Intestine Fusobacteria Serratia, Bacteroides, Cetobacterium, 94% (Tsuchiya et al., 2008; Tang et al.,
Clostridium, Bifidobacterium, Lactobacillus, 2019)
Streptococcus
Common carps, Asian Gut and Proteobacteria, Firmicutes, Fusobacteria Cetobacterium, Aeromonas, Acinetobacter, 95% (Ni et al., 2014; Ye et al., 2014), (
carp, Prussian carp Intestine and Cyanobacteria Clostridium, Streptococcus, Streptophyte Li et al., 2015; Kashinskaya et al.,
2015)
Nile tilapia Gut Proteobacteria Fusobacteria, Firmicutes, Cetobacterium, Aquaspirillum, Edwardsiella 92% (Zhang et al., 2017c; Adeoye
Actinobacteria, Bacteroidets and Plesiomonas et al., 2016)
European eels Skin mucus Gamma proteobacteria, Flavobacteria, Vibrio, Pseudomonas, Stenotrophomonas, 30 (Carda Diéguez et al., 2014)
Betaproteobacteria, Achromobactin, Agrobacterium, Xanthomonas -95%
Alphaproteobacteria
Common crap, Skin–mucus Proteobacteria, Fusobacteria Lysobacter, Amylibacter, Methylobacterium, 96% (Li et al., 2013; Llewellyn et al.,
Atlantic salmon Burkholderia, Ratstonia 2017)
Thresher shark Skin–mucus Proteobacteria, Bacteroidets, Pseudoalteromonas, Erythrobaacteria, 91- (Doane et al., 2017)
Cyanobacteria Marinobacteria,Psudomonas,Sphingopyxi, 79%
Alteromonas
5
Fig. 2. Steps for SNP mining.
annotation and functional analysis of the sequenced genome. Paralichthys olivaceus (20), and Hippoglossus hippoglossus (40) (Hsu et al.,
2014), have been documented.
4. MicroRNA discovery and data analysis in aquaculture species Kloosterman and coworkers identified 66 novel and 139 known
miRNAs from 5-day-old Danio rerio larvae. They suggested that out of
MicroRNAs (miRNAs) are small noncoding endogenous single- 205 miRNAs, miR-153 regulates snap25 during synaptic transmission
stranded RNAs of 19–25 nucleotides in length that play an essential and motor neuron development and that miR-27 targets ptk2.2 to
role in developmental biology by gene modulation via post regulate pharyngeal arch morphogenesis in zebrafish (Kloosterman
transcriptional gene regulation during acclimatization and adaptation in et al., 2007). Tozzini and coworkers studied an annual fish (Notho
the case of adverse conditions or climate change (Rasal et al., 2016). branchius furzeri) and identified 165 conserved miRNAs in the brain,
MicroRNAs are present in the 3’ untranslated region (UTR) of the gene whereas 17–92 microRNAs were mainly associated with brain neuro
(Kaeuferle et al., 2014) and have substantial contributions to regulatory genesis (Terzibasi Tozzini et al., 2014). Recently, 138 conserved and 161
networks of development and adaptive plasticity in fishes (Rasal et al., novel miRNAs were identified in the liver tissue of Labeo rohita and
2016). High-throughput sequencing technology has been widely used to Labeo bata and revealed that miR-200, miR-22, miR-365, miR-122, and
discover miRNAs in several organisms (Salem et al., 2010; Zhu and miR-146 are mainly involved in the carbohydrate metabolism pathway
Leung, 2015). Changes in miRNA expression in animals have been (Rasal et al., 2019; Rasal et al., 2020). Evidence is increasing daily in
shown during larval and juvenile growth (Campos et al., 2014), during support of the critical role of miRNAs regulating various biological
larval ontogeny (Bizuayehu et al., 2015), in eggs (Ma et al., 2012), and processes in aquaculture species.
in skin pigmentation (Yan et al., 2013). The miRNA data were gener
ated/discovered using marker discovery, gene discovery, variant iden 5. Metagenome profiling and data analysis in aquaculture
tification, and miRNA identification processes. miRNA function was species
predicted by using bioinformatics tools. Some target gene prediction
tools and their online web portals are shown in Table 4. Huang et al. Microbes play an essential role in various ecosystems; however, not
(Huang et al., 2015) studied miRNAs in 11 different fishes and predicted all the microbes present in an environment have been characterized. The
43 miRNAs belonging to 38 miRNA families with their target genes metagenomics approach provides detailed information about the
through expressed sequence tags (EST) and genome sequence surveys microbiome structure present in a particular environment (Simon and
(GSSs). Then, some selected miRNAs were validated through real-time Daniel, 2011; Larsen et al., 2014). It is commonly used in microbial
PCR. These findings suggested that computational methods are more ecology to study microbial communities in more detail, including many
convenient for screening miRNAs and their target genes/proteins/ microbes/strains that cannot be cultivated in the laboratory. Previously,
pathways from non-model fishes. Juanchich et al. (Juanchich et al., scientists used traditional disease control methods such as antibiotics
2016) found 2946 miRNAs in 16 different tissues of rainbow trout using and vaccines to control the pathogen. However, rising public pressures
high-throughput sequencing technology. We have presented informa against antibiotics in animals and aquaculture shifted the focus from
tion about some individual miRNAs and their functions in Table 5. killing pathogens to promoting beneficial microbes. Therefore, studies
Recently, mature miRNAs of some fish species, such as Danio rerio (346), on the effects of prebiotics on fish and associated microbiomes have
Salmo salar (371), Takifugu rubripes (175), Cyprinus carpio (134), Tet been published in the last decade. Recently, sequencing and bioinfor
raodon nigroviridis (132), Oryzias latipes (168), Ictalurus punctatus (281), matics analyses have made it possible to mine massive metagenomic
6
Table 8
SNPs identified in aquatic animals.
Species Sequencing Platform Nos of SNP discovered Computational tools Validation methodology References
used used
Chinook salmon (Oncorhynchus Sanger sequencing 40 tagRepeats.perl Taqman (Smith et al.,

tshawytscha) 2005)
Chum salmon (O. keta) Sanger sequencing 155 tagRepeats.perl Taqman (Smith et al.,
2005)
Sockeye salmon (O.nerka) Sanger sequencing 114 tagRepeats.perl Taqman (Smith et al.,
2005)
Atlantic salmon (Salmo salar) Sanger sequencing 19 Phred/Phrap/ Sanger sequencing (Ryynanen and
PolyPhred series of Primmer, 2006)
base-calling
Brown trout (Salmo trutta) Sanger sequencing 15 Phred/Phrap/ Sanger sequencing (Ryynanen and
base-calling
Arctic char (Salvelinusalpinus) Sanger sequencing 2 Phred/Phrap/ Sanger Sequencing (Ryynanen and
base-calling
Atlantic cod (Gadusmorhua) Sanger sequencing 724 Phred/Phrap/ MassARRAY Sequenome (Moen et al.,
PolyBayes series of 2008)
base-calling
Rainbow trout (O.mykiss) 454 13140–24 627 ssahaSNP program Golden Gate Assay (Sanchez et al.,
2009)
Lake whitefish (Coregonus spp.) 454 6042 ssahaSNP program SNPplex (Renaut et al.,
2010)
Rainbow trout (O. Mykiss) 454 GSFLX titanium 58000 ssahaSNP program Golden Gate Assay (Sanchez et al.,
2011)
Common carp (C. carpio) Illumina Hiseq2000 712,042 Intra-strain SNPs (483,276 BWA and SAMtools Sanger sequencing and (Xu et al., 2012)
SNPs mirror carp, 486,629 SNPs PCR amplification
purse red carp, 478,028 SNPs for
Xingguo red carp and 488,281 SNPs
for Yellow River carp
European anchovy (E.encrasicolus) 454 and Illumina 2317 SAMtools Taqman genotyping assay (Montes et al.,
2013)
Indo-pacific dolphin Illumina 3681 SOAPsnp NA (Gui et al., 2013)
Pufferfish (Takifugurubripes) Illumina 62270 BWA and SAMtools PCR amplification and (Cui et al., 2014)
direct sequencing
Bay scallop (Argopectenirradians) Illumina 32,206 and 23,312 SNPs for northern SOAPsnp (Du et al., 2014)
and southern bay scallops.
Channel Catfish (I. punctatus) Illumina 407,861 SAMtools Not done (Sun et al., 2014)
Half-smooth Tongue sole 454 21234 ssahaSNP program Not done (Wang et al.,
(C. semilaevis) 2014)
White Shrimp (L. Vannamei) Illumina Hiseq2000 96040 BWA and SAMtools Sanger sequencing and (Yu et al., 2014)
PCR amplification
Olive Flounder (P. olivaceus) EST seq 514 SNPs EST-EST alignment Taqman (Kim et al., 2014)
Zebrafish (D. rerio) Illumina 164 CLCBio workbench SequenomMassARRAY (Ulloa et al.,
2015)
Pacu (Piaractusmesopotamicus) Illumina 32 BWA and SAMtools PCR (Mastrochirico-
Filho et al., 2016)
Rainbow trout (Oncorhynchus Illumina 59,112, 87,066 SAMtools and GATK Sanger sequencing and (Al-Tobasei et al.,
mykiss) tool PCR amplification 2017)
southern catfish (Silurus Restriction site- 26 714 SOAPsnp tool PCR (Xie et al., 2018)
meridionalis) associated DNA
(RAD) sequencing
Tilapia species (Oreochromis Double digested 57 species-specific SNP markers Stacks v1.46 PCR-based KASP assays (Syaifudin et al.,
niloticus, O. aureus, O. restriction-site 2019)
mossambicus, O. u. hornorum) associated DNA
(ddRAD) sequencing
Pacific oyster (Crassostrea gigas) RAD 21,499 Xiom Analysis Suite PCR (Vendrami et al.,
(version 3.1, 2019)
Affymetrix),
FreeMapTools
Large yellow croaker (Larimichthys double-digest 5,261 SNP JoinMap4.1 PCR amplification and (Kong et al.,
crocea) restriction-site direct sequencing 2019)
associated DNA
(ddRAD)
datasets and discover general patterns that govern microbial ecosys RAST (Keegan et al., 2016), EBI Metagenomics (Hunter et al., 2013),
tems. High-throughput sequencing technology has been widely used for and some computational pipelines, such as MEGAN (Huson et al., 2007),
making thousands of microbial genome information at a low cost. These Mothur (Neves et al., 2017), and QIIME (Siegwald et al., 2017), without
data have been produced using two approaches: shotgun and (16S ri command-line operations or solid computational knowledge (Table 7).
bosomal RNA [rRNA] gene) amplicon metagenomic sequencing Metagenome sequencing has been documented in some fish species,
methods, which identify functional genes at a large scale. For analyzing such as zebrafish (Semova et al., 2012), Atlantic salmon (Zarkasi et al.,
and visualizing the amplicon and metagenomic data, several tools/on 2016), Seabream (Kormas et al., 2014), rainbow trout (Wong et al.,
line servers have been used, such as IMG/M (Chen et al., 2017), MG- 2013), grass carp (Ni et al., 2014), Antarctic peninsula (Cowart et al.,
7
2018), Malaysian mahseer (Tan et al., 2019) and Arctic charr (Nyman needs to be explored in commercially important aquaculture species.
et al., 2017). Bacterial community profiles in the fish microbiota were Transcriptome profiling and differential gene expression analysis tech
observed in response to various factors affecting the host, including nology must be employed to identify further vital transcripts/genes
variations in temperature, stress, salinity, digestive physiology, devel involved in growth, disease resistance, and immunity. The identification
opmental stage, climate change, and feeding strategy. Information of miRNAs, essential production and reproductive trait regulators, is
regarding the fish species and their common microbes is shown in underused in aquaculture species. Metagenomics has great potential to
Table 6. However, metagenomics has also shed light on community identify key microbial pathways and metabolites responsible for
function when backed up with metatranscriptomic data (RNA-seq of important physiological and biological processes in aquaculture species.
environmental samples), providing information regarding essential mi Furthermore, it has enormous potential to determine the importance of
crobial survival in a particular condition. This dual approach has novel species-specific probiotics of aquaculture. In summary, applica
revealed that some groups of archaea, generally known as ammonia tion of NGS technology and other techniques/tools will significantly
oxidizers, have the physiological machinery to digest proteins, carbo impact aquaculture production in the coming decades.
hydrates, and lipids (Li et al., 2015), prompting a complete rethinking of
the carbon cycle in aquaculture environments. Declaration of Competing Interest
6. Current status of single nucleotide polymorphism (SNP) The authors have no conflict of interest.
analysis in aquaculture species
Acknowledgements
Single nucleotide polymorphism (SNP) markers are considered
decisive genetic markers. They signify the most acceptable resolve Preparation of this review was supported by the Centre for Agricul
possible for a marker map (at the single nucleotide level), are codomi tural Bioinformatics (CABin), IASRI, New Delhi (Grant ID:1004469/
nant, biallelic and commonly plentiful in populations with a low mu 2020) and the authors are thankful to Director, ICAR-Central Institute of
tation rate. However, the DNA sequencing approach is the gold standard Freshwater Aquaculture, Bhubaneswar, India for the support and
of SNP detection. Various techniques/tools have been used for SNP encouragement.
discovery. Scanning for changes in targeted sites in the genome was the
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Aquaculture omics: An update on the current status of research and data

Article in Marine Genomics · August 2022

J.K. Sundaray Sangita Dixit

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Aquaculture omics: An update on the current status of research and

Table 7 transcriptome data analysis is provided in Fig. 1. In the recent past,

Fig. 2. Steps for SNP mining.

Chinook salmon (Oncorhynchus Sanger sequencing 40 tagRepeats.perl Taqman (Smith et al.,

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