Table-1.

Classification of fish diversity in Saudi Arabia using multiple methodologies.

Samples	Marker types	Outcomes	Locations	References
Conventional morphological identification
Schindleria parva	n/a	It is distinguished by a lack of pigmentation on the body, an inconspicuous gas bladder, and short teeth on the premaxillae. The holotype is a female of 11-mm standard length (11.9 mm total length), while the paratype is a male of 9-mm SL. Dorsal fin rays 10 (9), anal fin rays 9 (7). The body depth at the pectoral-fin origin is 5% (4%) of SL, the depth at the anal-fin origin is 8% (7%) of SL, the predorsal length is 63% (65%) of SL, the preanal length is 72% (72%), and the first anal-fin ray is located below the fourth dorsal-fin ray, for a total of 23+16 myomeres.	Red Sea, Jeddah, Saudi Arabia	[154]
Ophichthus olivaceus		It is distinguished from its congeners by the following combination of characters: Vertebrae 141–145; tail moderately short (2.15 in TL); head short (9.6–11.1 in TL); uniserial teeth in jaws and on vomer; pectoral fins slightly elongate, not lanceolate, with upper rays longer than lower; dorsal fin origin above middle of pectoral fin; and a generally uniform, dark tan body with an olivaceous hue shading to tan or pale orange ventrally, with two pale yellow blotches above the pectoral-fin base, snout and lower jaw dark brown, and olivaceous median fins.	Jizan, Red Sea coast of southern Saudi Arabia	[155]
Priolepis melanops		Priolepis melanops stands out from its congeners with the following characteristics: The species has unbranched dorsal-fin rays VI+I, 9, no elongated spines in the first dorsal fin, unbranched anal-fin rays I, 8, and pectoral-fin rays 14–15. The longitudinal scale series is 25, and there are no scales on the head or predorsal midline, but the sides of the nape are scaled. The sensory papillae below the eye have a developed transverse pattern. The fifth pelvic-fin ray is unbranched and 47% longer than the fourth ray. The body and most of the head are reddish-orange and coated with melanophores. The snout, mouth, chin, and chest are black, and the iris is black. The fins are translucent, with a faint black stripe down the base of each dorsal fin.	Al Lith, the coast of the Red Sea, Saudi Arabia	[159]
Next-generation sequencing
Oreochromis spilurus saudii	Antimicrobial peptides (AMPs)	The genome assembly of the newly cultured marine subspecies O. spilurus (0.76 Gb) has been completed for the first time. These predicted peptides are involved in major cellular processes and aid in diagnosing various fish ailments. Furthermore, 262 potential AMPs were discovered, which could aid in practical molecular breeding and combating emerging bacterial and viral illnesses. This subspecies can easily survive in the Red Sea in Saudi Arabia (salinity 42 ppt), indicating that this tilapia has a high salt tolerance gene.	Seawater ponds at the Jeddah Fisheries Center on the Red Sea, Saudi Arabia	[75]
Chaetodon austriacus	Genomic DNA	Using existing bony fish (superclass Osteichthyes) genomes as a reference, 28,926 high-quality protein-coding genes were predicted from 13967 assembled scaffolds. The quality and completeness of the C. austriacus draft genome indicate that it has the potential to serve as a resource for studies on the co-evolution of reef fish adaptations to the unique Red Sea environment, as well as a comparison of gene sequences between closely related congeneric butterflyfish species distributed more broadly across the tropical Indo-Pacific.	Near Ablo Island, Saudi Arabia	[160]
		The authors used double-digest restriction site-associated DNA sequencing (RAD-Seq) data to discover single nucleotide polymorphism (SNP) markers and their related functions with and without our reference genome to investigate if it improves the quality of RAD-Seq. Our analyses show a modest difference in the number of no annotated versus annotated SNPs across all species, highlighting the benefit of using genomic resources for closely related but not distantly related butterflyfish species based on the ability to assign putative gene function to SNPs and an enrichment of genes related to calcium transmembrane transport and binding among sister butterfly-fish taxa.	Red Sea and Arabian Sea	[161]
DNA barcoding
Garra tibanica	Cytochrome b gene	The clusters, inside groups, were supported by high bootstrap values and revealed that G. tibanica and Garra sahilia are related lineages in the same clade with 98.69% identity, and it is also consistent with traditional morphologically-based inferences.	Wadi Kadrah, Medina province, Saudi Arabia	[162]
Epinephelus tauvina	Genomic DNA from caudal fin	These findings could considerably impact grouper conservation and genetic improvement efforts. Intersimple sequence repeat (ISSR) and microsatellite (SSR) markers were beneficial for studying grouper species’ genetic diversity and structure.	Khafji, Al-Jubail, Al-Qatif, and Salwa, Saudi Arabia	[163]
Epinephelus coioides
Epinephelus malabaricus
Epinephelus bleekeri
Epinephelus areolatus
Genera from Cyprinion	Cytochrome b gene	The first cytochrome b gene sequences of Cyprinion acinaces acinases and Carasobarbus aponesis were identified and deposited in the public Gene Data Bank. The phylogenetic tree separated the species into two primary clusters, each with four sub-clusters. The evolutionary study validates the early taxonomic categorization and confirms that Cyprinion acinaes hijazi is a subspecies of Cyprinion acinaces acinaces. The phylogenetic tree built from the cytochrome b sequence also showed that Carasobarbus apoensis found in Saudi Arabia, is genetically closely linked to Carasobarbus luteus .	Wadi Khadrah and Ain Al-Jamma in Khyber, Medina Region, Saudi Arabia	[164]
Genera from Carasobarbus
Chlorurus sordidus	Genomic DNA	The current study found that C oxidase subunit I (COI) outperformed ISSR and start codon-targeted (SCoT) markers for discriminating across parrotfish species. Furthermore, ISSR outperformed SCoT since it could distinguish three unique groups in principal component analysis. This investigation also established the presence of three unique parrotfish species, providing insight into their diversity.	Farasan Islands on the Jeddah Coast, Saudi Arabia
Cheilinus trilobatus
Cheilinus quinquecinctus
Oreochromis niloticus	Randomly amplified polymorphic DNA	i) O. niloticus harvested from H1, H2, and H3 showed the maximum genetic variation (99.99) caused by OPA-02, OPA-05, and OPA-08. ii) The maximum and minimum polymorphism was recorded as 99.99 and 63.40% by OPA-05 and OPA-09. iii) The authors recorded the highest genetic variation in O. niloticus collected from the H4 location and the lowest from H1, which indicates that fish from H4 have more heterozygous genotypes. iv) Genetic distance ranged between 0.0005 and 0.0996. The highest and lowest genetics were recorded in the fish stocks obtained from H1 and H2, respectively.	Wadi Hanefah, Riyadh, Saudi Arabia	[156]
COI sequences (DNA barcoding)
Siganus rivulatus	Genomic DNA	The results for the SSR markers revealed seventy polymorphic alleles, with an average of 5.83 alleles per locus. Furthermore, the interpopulation genetic diversity was 0.063. The nucleotide content of the MT-COI sequences showed significant differences between the two examined populations. Phylogenetic analysis revealed that Red Sea samples were more flexible than Mediterranean Sea samples. The results suggested that the mtDNA of S. rivulatus is quite variable and a species-sensitive marker to detect probable genetic alterations, which could be part of the ecological adaptation and important to the success of the migrant S. rivulatus in the Mediterranean Sea.	Red Sea and the Mediterranean Sea	[157]
Ophichthus olivaceus	Mitochondrial COI	This finding highlights the benefit of combining all available sequence data for mitochondrial COI from Ophichthinae. This approach provides a comprehensive picture of evolutionary diversity at the species level. It allows for identifying close phylogenetic relationships, even when species IDs are uncertain due to barcoding data. The phylogenetic analysis identified Ophichthus lithinus as the closest relative of Ophichthus olivaceus spp. nov. among the 90 Ophichthinae species analyzed in this study. Bootstrapped studies revealed that the novel Red Sea species and O. lithinus formed reciprocally monophyletic clades.	Jizan, Red Sea coast of southern Saudi Arabia	[155]
Environmental DNA (eDNA)
Fish from the Labridae family	DNA from seawater	The authors discovered a wide range of prominent, cryptobenthic, and commercially important reef fish at the genus level, with specific genera in the Labridae family over-represented. Our method, however, failed to capture a significant fraction of the fish fauna known to inhabit the Red Sea, which we ascribe to insufficient spatial sampling, amplification stochasticity, and an apparent lack of sequencing depth. Given the growth in fish species descriptions, the completeness of taxonomic checklists, and the improvement in species-level assignment using bespoke genetic databases demonstrated here, we believe the Red Sea region is excellent for further testing of the eDNA technique.	Arabian Sea and Oman Sea	[158]
Marine finfish	n/a	The authors explore using RNA-guided immunity to combat Chillodonella protozoan and nervous necrosis virus in marine finfish. In addition, they also emphasize the immunological application of CRISPR-Cas against bacterial illnesses in channel catfish	n/a	[166]
Channel catfish