Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei.

Pangasiidae (catfish order: Siluriformes) comprises 30 valid catfish species in four genera: Pangasius, Pangasianodon, Helicophagus, and Pseudolais. Their systematics are frequently revised due to the addition of newly described species. Although Pangasiidae is known to be a monophyletic family, the generic and phylogenetic relationships among the taxa are poorly resolved. This study characterized three newly obtained complete mitogenomes of Mekong River catfishes from Vietnam (Pangasius mekongensis, Pangasius krempfi, and Pangasianodon hypophthalmus), as well as the inter-and intrafamilial relationships of the Pangasiidae and catfish families in Siluroidei. The genomic features of their mitogenomes were similar to those of previously reported pangasiids, including all regulatory elements, extended terminal associated sequences (ETAS), and conserved sequence blocks (CSBs) (CSB-1, CSB-2, CSB-3, and CSBs, A to F) in the control region. A comprehensive phylogeny constructed from datasets of multiple 13 PCG sequences from 117 complete mitogenomes of 32 recognized siluriform families established Pangasiidae as monophyletic and a sister group of Austroglanididae. The [Pangasiidae + Austroglanididae] + (Ictaluridae + Cranoglanididae) + Ariidae] clade is a sister to the "Big Africa" major clade of Siluriformes. Furthermore, both phylogenies constructed from the single barcodes (83 partial cox1 and 80 partial cytB, respectively) clearly indicate genus relationships within Pangasiidae. Pangasianodon was monophyletic and a sister to the (Pangasius + Helicophagus + Pseudolais) group. Within the genus Pangasius, P. mekongensis was placed as a sister taxon to P. pangasius. Pangasius sanitwongsei was found to be related to and grouped with Pangasianodon, but in single-gene phylogenies, it was assigned to the Pangasius + Helicophagus + Pseudolais group. The datasets in this study are useful for studying pangasiid systematics, taxonomy and evolution.

Individual-based analyses reveal effects of behavioral and demographic variables associated with multi-annual reproductive success of male and female lake sturgeon.

Quantifying effects of individual attributes and population demographic characteristics that affect inter- and intrasexual interactions and adult reproductive success, and the spatial and temporal contexts in which they are expressed is important to effective species management. Multi-year individual-based analyses using genetically determined parentage allowed the examination of variables associated with the reproductive success of male and female lake sturgeon (Acipenser fulvescens) in the well-studied population in Black Lake, Michigan, USA. Spawning lake sturgeon (a total of 599 individuals where many were captured more than once based on 1024 total captures) and larvae (N = 3436) were genotyped during each of seven consecutive years (2001-2007). Factors associated with individual reproductive success differed between sexes and varied among spawning groups within a year and among years depending on spawning date (higher reproductive success earlier in the season for females) and spawning locations (higher reproductive success in upstream spawning zones for females). Female reproductive success increased nonlinearly with increasing body size. Male reproductive success increased with increasing residence time in spawning areas and, to a modest degree, with increasing body size in a nonlinear fashion. Fixed effects of repeatability in spawn timing and location across years led to consistently higher or lower reproductive success for females. Results identified factors, including time spent at spawning areas by males and intersexual encounters and mate number, that contributed to higher interindividual variance in reproductive success and affected population levels of recruitment, the degree of subpopulation genetic structure (lack of isolation by time), and effective population size.

Sexual dimorphism and reproductive biology of Cephalocassis borneensis (Siluriformes: Ariidae), a paternal mouth-brooding fish in the Mekong River.

Information on the reproductive biology of fish species is essential for fisheries management, conservation and culture potential assessment. Therefore, this study aimed to understand the sex-based morphological differences and reproductive characteristics of Cephalocassis borneensis, an ariid species with a rapid decline of wild populations. Fish samples were collected monthly from local fishermen (n = 1092) in the Vietnamese Mekong River over a year. Morphological analyses revealed that sexual dimorphism was observed in mature, but not immature, fish. The length at first maturity (Lm ) was smaller for males (11.5 cm) than for females (12.5 cm). Mature males had larger head length and pre-pectoral distance than mature females, increasing the space for oral incubation of fertilized eggs and larvae in males. Conversely, females were larger in three head parameters (head angle, head width and head depth) and three abdomen parameters (body deep, ventral fin length and distance between pectoral and ventral fin) involved in ovary development. Paternal mouth-brooding behaviour is an important reproductive strategy in C. borneensis to increase offspring survival. Monthly variations in gonado-somatic index and condition factor (K) and the presence of maturation stages indicated that C. borneensis spawns year-round, mainly in the rainy season from June to October. This species' fecundity was relatively low, from 10 to 31 eggs per female of quite large sizes (about 7.30 ± 0.68 mm in diameter). Besides, non-functional oocytes (hyaline eggs) of smaller size (<3 mm) were found in the females' ovaries. Low fecundity with large eggs and paternal care indicated that the species is an equilibrium strategist. These characteristics are critical in developing ariid species conservation plans, such as setting the time and mesh-size for fishing, and domestication programmes in artificial conditions.

Multiple genetic lineages of anadromous migratory Mekong catfish Pangasius krempfi revealed by mtDNA control region and cytochrome b.

Population genetic structure of migratory fishes can reflect ecological and evolutionary processes. Pangasius krempfi is a critically important anadromous catfish in the Mekong River, and its migration pathways and genetic structure have attracted much interest. To investigate, we quantified the genetic diversity of this species using the control region (D-loop) and Cytochrome b (Cytb) of the mitochondrial genome. Fish were sampled (n = 91) along the Mekong tributaries from upstream to estuaries and coastal areas in the Mekong Delta and compared to three samples from Pakse (Laos). The D-loop haplotype (0.941 ± 0.014) and nucleotide diversity (0.0083 ± 0.0005) were high in all populations, but that of Cytb was low (0.331 ± 0.059 and 0.00063 ± 0.00011, respectively). No genetic difference was detected between populations, indicating strong gene flow and confirming a long migration distance for this species. Pangasius krempfi was not genetically structured according to geographical populations but was delineated into three haplogroups, suggesting multiple genetic lineages. The presence of haplogroups in each sampling location implies that migration downstream is random but parallel when the fish enter two river tributaries bifurcating from the main Mekong River. Individuals can also migrate along the coast, far from the estuaries, suggesting a longer migration path than previously reported, which is crucial for maintaining diverse genetic origin and migration pathways for P. krempfi.

A Current Update on the Distribution, Morphological Features, and Genetic Identity of the Southeast Asian Mahseers, Tor Species.

The king of rivers or mahseer comprises three genera: Tor, Neolissochilus, and Naziritor, under the Cyprinidae family. The Tor genus has been classified as the true mahseer due to the presence of a median lobe among the three genera. The Tor species are widely distributed across Southeast (SE) Asia, and 13 Tor species have been reported previously: Tor ater, Tor dongnaiensis, Tor douronensis, Tor laterivittatus, Tor mosal, Tor mekongensis, Tor putitora, Tor sinensis, Tor soro, Tor tambra, Tor tambroides, Tor tor and Tor yingjiangensis. However, the exact number of valid Tor species remains debatable. Different and unstandardized approaches of applying genetic markers in taxonomic identification and morphology variation within the same species have further widened the gap and ameliorated the instability of Tor species taxonomy. Therefore, synchronized and strategized research among Tor species researchers is urgently required to improve and fill the knowledge gap. This review is a current update of SE Asia's Tor species, outlining their distribution, morphology, and genetic identification. In addition, the present review proposes that there are ten valid Tor species in the SE Asian region. This list will serve as a template and standard to improve the taxonomy of the SE Asian Tor species, which could serve as a basis to open new directions in Tor research.

Comparative Genomic and Transcriptomic Analyses Revealed Twenty-Six Candidate Genes Involved in the Air-Breathing Development and Function of the Bighead Catfish Clarias macrocephalus.

The bighead catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater species in the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air-breathing organ (ABO), while I. punctatus does not possess such an organ, and cannot breathe in air, providing an excellent model for studying the molecular basis of ABO development in teleost fish. To investigate the critical time window for the development of air-breathing function, seven development stages were selected based on hypoxia challenge results, and RNA-seq was performed upon C. macrocephalus to compare with the non-air-breathing I. punctatus. Five-hundred million reads were generated and 25,239 expressed genes were annotated in C. macrocephalus. Among those, 8675 genes were differentially expressed across developmental stages. Comparative genomic analysis identified 1458 C. macrocephalus specific genes, which were absent in I. punctatus. Gene network and protein-protein interaction analyses identified 26 key hub genes involved in the air-breathing function. Three top candidate genes, mb, ngb, hbae, are mainly associated with oxygen carrying, oxygen binding, and heme binding activities. Our study provides a rich data set for exploring the genomic basis of air-breathing function in C. macrocephalus and offers insights into the adaption to hypoxic environments.

Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish (Ictalurus punctatus).

The transition from fertilized egg to larva in fish is accompanied with various biological processes. We selected seven early developmental stages in channel catfish, Ictalurus punctatus, for transcriptome analysis, and covered 22,635 genes with 590 million high-quality RNA-sequencing (seq) reads. Differential expression analysis between neighboring developmental timepoints revealed significantly enriched biological categories associated with growth, development and morphogenesis, which was most evident at 2 vs. 5 days post fertilization (dpf) and 5 vs. 6 dpf. A gene co-expression network was constructed using the Weighted Gene Co-expression Network Analysis (WGCNA) approach and four critical modules were identified. Among candidate hub genes, GDF10, FOXA2, HCEA and SYCE3 were involved in head formation, egg development and the transverse central element of synaptonemal complexes. CK1, OAZ2, DARS1 and UBE2V2 were mainly associated with regulation of cell cycle, growth, brain development, differentiation and proliferation of enterocytes. IFI44L and ZIP10 were critical for the regulation of immune activity and ion transport. Additionally, TCK1 and TGFB1 were related to phosphate transport and regulating cell proliferation. All these genes play vital roles in embryogenesis and regulation of early development. These results serve as a rich dataset for functional genomic studies. Our work reveals new insights of the underlying mechanisms in channel catfish early development.

Dataset for genome sequencing and de novo assembly of the Vietnamese bighead catfish (Clarias macrocephalus Günther, 1864).

Freshwater catfish of the genus Clarias, known as the airbreathing catfish, are widespread and important for food security through small scale inland fisheries and aquaculture. Limited genomic data are available for this important group of fishes. The bighead catfish (Clarias macrocephalus) is a commercial aquaculture species in southeast Asia used for aquaculture and threatened in its natural environment through habitat destruction, over-exploitation and competition from other introduced species of Clarias. Despite its commercial importance and threats to natural populations, public databases do not include any genomic data for C. macrocephalus. We present the first genomic data for the bighead catfish from Illumina sequencing. A total of 128 Gb of sequence data in paired-end 150 bp reads were assembled de novo, generating a final assembly of 883 Mbp contained in 27,833 scaffolds (N50 length: 80.8 kbp) with BUSCO completeness assessments of 96.3% and 87.6% based on metazoan and Actinopterygii ortholog datasets, respectively. Annotation of the genome predicted 21,124 gene sequences, which were assigned putative functions based on homology to existing protein sequences in public databases. Raw fastq reads and the final version of the genome assembly have been deposited in the NCBI (BioProject: PRJNA604477, WGS: JAAGKR000000000, SRA: SRR11188453). The complete C. macrocephalus mitochondrial genome was also recovered from the same sequence read dataset and is available on NCBI (accession: MT109097), representing the first mitogenome for this species. Lastly, we find an expansion of the mb and ora1 genes thought to be associated with adaptations to air-breathing and a semi-terrestrial life style in this genus of catfish.

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation.

Tra catfish (Pangasianodon hypophthalmus), also known as striped catfish, is a facultative air-breather that uses its swim bladder as an air-breathing organ (ABO). A related species in the same order (Siluriformes), channel catfish (Ictalurus punctatus), does not possess an ABO and thus cannot breathe in the air. Tra and channel catfish serve as great comparative models for investigating possible genetic underpinnings of aquatic to land transitions, as well as for understanding genes that are crucial for the development of the swim bladder and the function of air-breathing in tra catfish. In this study, hypoxia challenge and microtomy experiments collectively revealed critical time points for the development of the air-breathing function and swim bladder in tra catfish. Seven developmental stages in tra catfish were selected for RNA-seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated, and a total of 21,448 unique genes were detected. A comparative genomic analysis between channel catfish and tra catfish revealed 76 genes that were present in tra catfish, but absent from channel catfish. In order to further narrow down the list of these candidate genes, gene expression analysis was performed for these tra catfish-specific genes. Fourteen genes were inferred to be important for air-breathing. Of these, HRG, GRP, and CX3CL1 were identified to be the most likely genes related to air-breathing ability in tra catfish. This study provides a foundational data resource for functional genomic studies in air-breathing function in tra catfish and sheds light on the adaptation of aquatic organisms to the terrestrial environment.

Exploring hidden diversity in Southeast Asia's Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding.

Members of the freshwater halfbeak genus Dermogenys are hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples of Dermogenys spp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidase c subunit I (COI) gene. Analysis was able to successfully differentiate the three species: D. collettei, D. siamensis, D. sumatrana; reveal the presence of a new putative species, Dermogenys sp., that was sampled in sympatry with D. collettei at three locations; as well as uncovering two genetic lineages of a fifth species, D. bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiating Dermogenys species, and the potential thereof in species discovery.

Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens).

Quantifying interannual variation in effective adult breeding number (N(b)) and relationships between N(b), effective population size (N(e)), adult census size (N) and population demographic characteristics are important to predict genetic changes in populations of conservation concern. Such relationships are rarely available for long-lived iteroparous species like lake sturgeon (Acipenser fulvescens). We estimated annual N(b) and generational N(e) using genotypes from 12 microsatellite loci for lake sturgeon adults (n = 796) captured during ten spawning seasons and offspring (n = 3925) collected during larval dispersal in a closed population over 8 years. Inbreeding and variance N(b) estimated using mean and variance in individual reproductive success derived from genetically identified parentage and using linkage disequilibrium (LD) were similar within and among years (interannual range of N(b) across estimators: 41-205). Variance in reproductive success and unequal sex ratios reduced N(b) relative to N on average 36.8% and 16.3%, respectively. Interannual variation in N(b)/N ratios (0.27-0.86) resulted from stable N and low standardized variance in reproductive success due to high proportions of adults breeding and the species' polygamous mating system, despite a 40-fold difference in annual larval production across years (437-16 417). Results indicated environmental conditions and features of the species' reproductive ecology interact to affect demographic parameters and N(b)/N. Estimates of N(e) based on three single-sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of N(b). Findings have important implications concerning applications of genetic monitoring in conservation planning for lake sturgeon and other species with similar life histories and mating systems.