A high-quality genome assembly of the Laotian shad (Tenualosa thibaudeaui), an endemic species of the Mekong River Basin.

The Laotian shad (Tenualosa thibaudeaui) belongs to the family Clupeidae and is mainly distributed across Lao PRD, Cambodia, and northern Thailand. Due to overfishing and dam reconstruction, the Laotian shad is on the verge of extinction and currently listed as vulnerable by the IUCN. Nanopore and Illumina sequencing data were integrated to generate the first high-quality genome assembly for T. thibaudeaui. The assembled genome was 638 Mb in size, including 228 scaffolds with a N50 value of 16.6 Mb. BUSCO analysis revealed the completeness of the assembly to be more than 96%. A total of 24,810 protein-coding genes were predicted. According to the pairwise sequentially Markovian coalescent analysis, the effective population size of the Laotian shad sharply declined from 3 Mya to 20 Kya. We found a significant ratio in contraction of gene families that may reflect secondary gene loss. Our high-quality genome assembly of the Laotian shad will provide a valuable resource for future research in conservation genetics, as well as for investigating the phylogenetics and comparative genomics of shads.

First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima.

OBJECTIVES: American shad (Alosa sapidissima) is an important migratory fish under Alosinae and has long been valued for its economic, nutritional and cultural attributes. Overfishing and barriers across the passage made it vulnerable to sustain. To protect this valuable species, aquaculture action plans have been taken though there are no published genetic resources prevailing yet. Here, we reported the first de novo assembled and annotated transcriptome of A. sapidissima using blood and brain tissues. DATA DESCRIPTION: We generated 160,481 and 129,040 non-redundant transcripts from brain and blood tissues. The entire work strategy involved RNA extraction, library preparation, sequencing, de novo assembly, filtering, annotation and validation. Both coding and non-coding transcripts were annotated against Swissprot and Pfam datasets. Nearly, 83% coding transcripts were functionally assigned. Protein clustering with clupeiform and non-clupeiform taxa revealed ~ 82% coding transcripts retained the orthologue relationship which improved confidence over annotation procedure. This study will serve as a useful resource in future for the research community to elucidate molecular mechanisms for several key traits like migration which is fascinating in clupeiform shads.

A high-resolution genome of an euryhaline and eurythermal rhinogoby (Rhinogobius similis Gill 1895).

Rhinogobius similis is distributed in East and Southeast Asia. It is an amphidromous species found mostly in freshwater and sometimes brackish waters. We have obtained a high-resolution assembly of the R. similis genome using nanopore sequencing, high-throughput chromosome conformation capture (Hi-C), and transcriptomic data. The assembled genome was 890.10 Mb in size and 40.15% in GC content. Including 1373 contigs with contig N50 is 1.54 Mb, and scaffold N50 is 41.51 Mb. All of the 1373 contigs were anchored on 22 pairs of chromosomes. The BUSCO evaluation score was 93.02% indicating high quality of genome assembly. The repeat sequences accounted for 34.92% of the whole genome, with retroelements (30.13%), DNA transposons (1.64%), simple repeats (2.34%), and so forth. A total of 31,089 protein-coding genes were predicted in the genome and functionally annotated using Maker, of those genes, 26,893 (86.50%) were found in InterProScan5. There were 1910 gene families expanded in R. similis, 1171 gene families contracted and 170 gene families rapidly evolving. We have compared one rapidly change gene family (PF05970) commonly found in four species (Boleophthalmus pectinirostris, Neogobius melanostomus, Periophthalmus magnuspinnatus, and R. similis), which was found probably related to the lifespan of those species. During 400-10 Ka, the period of the Guxiang Ice Age, the population of R. similis decreased drastically, and then increased gradually following the last interglacial period. A high-resolution genome of R. similis should be useful to study taxonomy, biogeography, comparative genomics, and adaptive evolution of the most speciose freshwater goby genus, Rhinogobius.

Cross-species gene enrichment revealed a single population of Hilsa shad (Tenualosa ilisha) with low genetic variation in Bangladesh waters.

Tenualosa ilisha is a popular anadromous and significant trans-boundary fish. For sustainable management and conservation of this fish, drawing an appropriate picture reflecting population status of this species is very essential based on their all-strategic habitats in Bangladesh. In this study, 139 samples from 18 sites were collected and cross-species gene enrichment method was applied. Like most of the Clupeiforms, nucleotide diversity of this shad was very low (0.001245-0.006612). Population differences between most of the locations were low and not significant (P > 0.05). However, P values of a few locations were significant (P < 0.05) but their pairwise FST values were very poor (0.0042-0.0993), which is inadequate to recognize any local populations. Our study revealed that the presence of a single population in the Bangladesh waters with some admixtured individuals, which may contain partial genes from other populations. Most of the individuals were admixed without showing any precise grouping in the ML IQtree and Network, which might due to their highly migratory nature. Fishes from haors and small coastal rivers were not unique and no genetic differences between migratory cohorts. The hilsa shad fishery should be managed considering it as a single panmictic population in Bangladesh with low genetic diversity.

Health risk estimation of metals bioaccumulated in commercial fish from coastal areas and rivers in Bangladesh.

Metal contaminations in commercial fish have become a great public health concern worldwide including Bangladesh. The current study was conducted to provide preliminary evidence of nine metals in three commercially significant fish namely Pampus argenteus, Sardinella longiceps and Tenualosa ilisha collected from four coastal stations- Kuakata, Pathorghata, Cox's Bazar, and Pirojpur, and eight stations of five rivers- Padma, Meghna, Jamuna, Katcha, and Nobogonga in Bangladesh. High magnitudes of Pb (0.74-4.59 mg/kg ww), Cd (0.07-0.24 mg/kg ww), and Mn (0.45-2.03 mg/kg ww) were recorded in the sampling stations that exceeded the maximum permissible limits (MPL) proposed by different recognized organizations. Significant mean differences of metal concentrations were observed (p < 0.05) between species and stations. In fish samples, excessive metals accumulations were recorded from Kuakata (St.1) at the coastal area, and Nobogonga (St. 12) among the rivers. The health risk assessment (HRA) was carried out comprehensively via the estimated daily intake (EDI), target hazard quotient (THQ), hazard index (HI), and target cancer risk (TR) calculations. The outcomes of EDI, THQ, and HI suggest that chronic exposure to towering Pb content might pose potential health threats to inhabitants particularly living in highly polluted stations of the coastal area. In addition, the massive TR values of Cd intake through fish consumption from the coastal area might create cancer risks. Accordingly, the ingestion of metals contaminated fish portends chronic as well as acute health risks to Bangladeshi people living both at home and abroad.

Ecological risk and source apportionment of heavy metals in surface water and sediments on Saint Martin's Island in the Bay of Bengal.

The study aimed to determine eight hazardous heavy metals in surface water and sediment samples collected from the Naf River, Shah Porir Dwip (estuary), and mostly around Saint Martin's Island in the Bay of Bengal. The results of heavy metals in water samples were ranged as Pb 14.7-313.0, Cd 33.0-70.0, Cr < 11.0-37.0, Cu 38.0-57.0, Zn 26.8-69.2, Ni 102.0-285.0, and Hg 0.3-1.6 µg L-1. The concentrations of metals in sediment samples were ranged as Pb < 10.0-37.5, Cd 0.2-1.0, Cr < 5.0-30.1, Cu < 3.0-30.9, Zn 24.1-88.0, Ni < 4.0-48.3, As 0.1-7.3, and Hg < 0.01-0.08 mg kg-1 dw. Ni and Cr were strongly correlated, suggesting that this pair of metals might diffuse from a common origin. The contamination factor (Cif) demonstrated that sediment samples were mostly contaminated by Cd and slightly contaminated by Pb and Zn. The geoaccumulation index (Igeo) revealed considerable values for Cd on Saint Martin's Island. Cd as a single regulator posed moderate to considerable risk frequently among the sampling stations. Pollution load index (PLI) values remained below 1 (< 1), which indicated a decrease from baseline pollution value among all stations. However, potential ecological risk (PER) was graded for two stations (St1 and St13) with a moderate-risk zone due to the Cd contribution. However, shipping emission and lithogenic sources were the most predominant for heavy metals in the sediment, which were determined by applying the principal component analysis-absolute principal component score (PCA-APCS). Graphical abstract.