Shubha Vij

Republic Polytechnic · School of Applied Sciences

A reduction in daily caloric or nutrient intake has been observed to promote health benefits in mammals and other vertebrates. Feed Restriction (FR), whereby the overall food intake of the organism is reduced, has been explored as a method to improve metabolic and immune health, as well as to optimize productivity in farming. However, less is known...

Asian seabass (or commonly known as barramundi), Lates calcarifer, is a bony euryhaline teleost from the Family Latidae, inhabiting nearshore, estuarine, and marine connected freshwaters throughout the tropical Indo-West Pacific region. The species is catadromous, whereby adults spawn in salinities between 28 and 34 ppt at the mouth of estuaries, w...

The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microd...

[This corrects the article DOI: 10.1371/journal.pgen.1005954.].

The Asian seabass is an important marine food fish that has been cultured for several decades in Asia Pacific. However, the lack of a high quality reference genome has hampered efforts to improve its selective breeding. A 3D BAC pool set generated in this study was screened using 22 SSR markers located on linkage group 2 which contains a growth-rel...

Asian seabass (Lates calcarifer) is a food fish of increasing aquaculture importance. In order to improve our understanding on the digestive system and feeding of this species, morphological and histological features of the gut were studied. Morphologically, the Asian seabass gut is defined by a short and muscular esophagus, well-developed stomach...

Glycoprotein histochemistry of the Asian seabass digestive tract

The gut histology of Asian seabass subjected to repeated salinity challenge was similar to those of controls. The fishes were subjected to a simple salinity challenge through a transfer from full seawater (30–32 ppt salinity) to freshwater (0 ppt) and grown for three weeks before sampling, whereas the controls were grown in seawater all along (A–E)...

Raw data for Table 2, Fig. 8 and Fig. 2

Flow chart outlining the experimental setup for the salinity stress experiment. From each of the four groups (A, B, C, D), 6 mid intestine samples were collected for histological analyses. ASB: Asian seabass, dph: day post hatching.

Author We describe the genome assembly of Asian seabass (Lates calcarifer), a marine teleost with aquaculture relevance. Though >500 eukaryotic genome sequences are available in public repositories, the majority are highly fragmented with incomplete assemblies, which explains why considerable effort and resources are often spent to improve their q...

Observed k-mer distribution and modeling results. k-mer frequency counting analyses was done for the Illumina genomic reads. Jellyfish [74] was used with the following parameters and commands: jellyfish count -m 21 -s 100000000 -t 5 -o output -C InputFile (counting 21-mer frequencies), jellyfish merge -o output.jf output_* (merging multiple output...

Pipeline for Asian seabass population data analyses. The flowchart outlines the steps taken for analyses of Asian seabass genome sequence information from 62 fishes collected from 13 regions across its geographic range. (TIF)

Asian seabass tandem repeat consensus sequences. (DOCX)

The number of contigs in the primary Asian seabass genome assembly (v1; 3,917 contigs) compared to those of published fish genome assemblies (see S23 Table for more details). (TIF)

Evaluation of the Asian seabass scaffolded genome assembly (v2) by mapping Illumina PE Genome reads to assembly for linear insert size libraries in the size range of 500 bp (A) and 750 bp (B). The 80X Illumina paired-end HiSeq genome sequence data was mapped to the PacBio-based assembled genome using the CLC Genomics Workbench version 8.5.1 mapping...

A screenshot of the Asian seabass genome assembly (v1) showing a location wherein a ~15 kb region missed by short reads has been captured using long reads from PacBio sequencing. (TIF)

The Asian seabass genome assembly contains a more continuous cluster of MHC-class I genes compared to the well-assembled G. aculeatus genome. The L. calcarifer MHC-class I genes were found to be located on eight contigs/scaffolds, four of which were placed onto linkage group 3 (LG3). Four of these eight contigs/scaffolds were also >1Mb in length. T...

Tandem repeats with highest coverage of 23-mer HiSeq reads. (XLSX)

Summary of transposable elements identified in the Asian seabass genome. (XLSX)

Placement of genome sequences ≥40kb on assembled Maptigs. (XLSX)

Inventory of 247 overlaps between ends of neighbouring contigs that were closed during scaffolding of the Asian seabass genome. (XLSX)

Read statistics for B chromosome-derived sequences. (XLSX)

Assembly of B chromosome-derived fragment statistics. (XLSX)

Functional annotation of Asian seabass protein-coding genes. The number of genes in top ten entries for A) Interpro B) KEGG pathways and C) GO. (TIF)

PCA plots of Asian seabass populations using SNPs. A total of 64,634 SNPs were used for PCA analyses. The results at different percentages of explained variation are shown in A) and B). (TIF)

De novo assembly of Single Molecule Restriction Maps. (XLSX)

Statistics of sequence placement (only sequences ≥40kb) on assembled Maptigs. (XLSX)

Inventory of potentially misassembled sequences identified by the optical map data. (XLSX)

Summary of synteny blocks shared between L. calcarifer and D. labrax. (XLSX)

Summary of synteny blocks shared between L. calcarifer and G. aculeatus. (XLSX)

Sample collection details for Asian seabass whole genome resequencing effort. (XLSX)

Summary of sequenced fish genomes. (XLSX)

Comparison of GC content of Asian seabass genome assembly (v2)with few selected fish genomes (A), with representatives from the different classes of vertebrates (B) and comparison of GC content with genome size of selected fishes (C). The GC-content of genomes of interest were calculated using a 20 kb sliding window (BedTools utilities [145]). In a...

Maximum likelihood (ML) tree constructed using 123,594 SNPs from Lates calcarifer with Indian region (red), S-E Asia/Philippines (green) and Australia/Papua New Guinea (blue). (TIF)

Map of the tropical Asia Pacific region showing the sampling locations for Asian seabass across its native range. India-Western coast (orange), India-Eastern coast (brown), Cambodia (red), Thailand-Eastern Coast (purple), Vietnam (pink), Singapore (black), Philippines (yellow), Indonesia-South Jakarta (green), Indonesia-Kalimantan (dark green), Ind...

RepeatMasker output file tabulating the masking results for vertebrate repeat sequences (A)* and for Asian seabass-specific repeat sequences (B)^. (XLSX)

In silico enzyme selection for optical mapping. (XLSX)

Three evaluated MapCards for optical mapping. (XLSX)

Whole genome MapCard collection summary for optical mapping. (XLSX)

Details of Asian seabass whole genome resequencing effort. (XLSX)

Truss morphometric analyses of Asian seabass individuals from the three regions. (XLSX)

Functions over-represented in duplicated genes of the Asian seabass. (XLSX)

Cross-validation error analyses to identify the number of Ks which explain variation in the Asian seabass species complex. Cross-validation methodology was used to find number of Ks (clusters/population) which better explain observed variation. The best model was obtained at K = 3, with the lowest error level. (TIF)

The Asian seabass genome assembly (v2; blue bars) anchored to the 24 linkage groups (white bars) using 772 markers [21]. Regions indicated in red represent positions of contig/scaffold containing Lca_217 (peri-centromeric sequences). (TIF)

Truss morphometric analyses of Asian seabass individuals collected from three regions. Purple and green lines represent truss measurements with blue circles indicating the landmark regions. The descriptions for the landmarks are, 1—tip of the snout, 2—point on dorsal surface of fish that is exactly perpendicular to the base of pectoral fin, 3—anter...

Metrics of the Asian seabass genome assemblies. (XLSX)

Percentage of repeats in the Asian seabass genome obtained by various tools. (XLSX)

Details of microsatellites identified in the Asian seabass genome assembly (v2). (XLSX)

Asian seabass repeat libraries. (XLSX)

Statistics of tRNAs identified in the Asian seabass genome assembly. (XLSX)

Chromosome-level assembly of the Asian seabass genome (v3). (XLSX)

Summary statistics of synteny analyses. (XLSX)

Comparison of annotation statistics across a few fish genomes. (XLSX)

Functional classification of the Asian seabass gene set. (XLSX)

Comparison of SNP distribution across the exons, introns, intergenic and UTR regions. (XLSX)

Functions depleted in duplicated genes of the Asian seabass. (XLSX)

The Asian seabass (or barramundi; Lates calcarifer) is a marine teleost and a popular food fish in Southeast Asia and Australia. To date, comprehensive genome and transcriptome sequence information has not been available for this species in public repositories. Here, we report a comprehensive de novo transcriptome assembly of the Asian seabass. The...

In vertebrates, establishment of left-right (LR) asymmetry is dependent on cilia-driven fluid flow within the LR organizer. Mutations in CCDC11 disrupt LR asymmetry in humans, but how the gene functions in LR patterning is presently unknown. We describe a patient with situs inversus totalis carrying homozygous loss-of-function mutations in CCDC11....

Asian seabass or barramundi (Lates calcarifer) is an important food fish with commercial value and a wide geographic distribution. Though some reports based on molecular and/or morphological data exist, a comprehensive effort to establish species identity across its range is lacking. In order to address this issue and especially to ascertain whethe...

Asian seabass or barramundi (Lates calcarifer) is an important food fish with commercial value and a wide geographic distribution. Though some reports based on molecular and/or morphological data exist, a comprehensive effort to establish species identity across its range is lacking. In order to address this issue and especially to ascertain whethe...

Key Message OsiSAP1, an A20/AN1 zinc-finger protein, confers water-deficit stress tolerance at different stages of growth by affecting expression of several endogenous genes in transgenic rice. Abstract Transgenic lines have been generated from rice constitutively expressing OsiSAP1, an A20/AN1 zinc-finger containing stress-associated protein ge...

Lates calcarifer (Asian seabass/barramundi) is a carnivorous, marine teleost belonging to the order Perciformes. It is an important fish species from an aquaculture perspective, its farming initiated in the 1970s in Thailand followed by a rapid spread to a large number of countries extending beyond its native range. The Asian seabass is euryhaline...

Lates calcarifer (Asian seabass/barramundi) is an important food fish species belonging to the order Perciformes. The Asian seabass has a wide geographic distribution stretching from Northern Australia to at least the Western part of India. A comprehensive analysis of the identity of Asian seabass is, however, lacking. Therefore, in order to ascert...

Lates calcarifer (Asian seabass/Barramundi) is a carnivorous, marine teleost belonging to the order Perciformes, the largest order of vertebrates, containing ~40% of all bony fishes. It is an important fish species from an aquaculture perspective, its farming initiated in the 1970s in Thailand followed by a rapid spread to a large number of countri...

The organization of centromere sequences based on various families of satellite DNA (satDNA) in the vertebrates will be discussed as part of genome and centromere annotation of Asian seabass genome project. The sequencing of the Asian seabass genome was done using the Illumina HiSeq platform for linear insert libraries in two size ranges: 475-525 b...

The body of most fishes is fully covered by scales that typically form tight, partially overlapping rows. While some of the genes controlling the formation and growth of fish scales have been studied, very little is known about the genetic mechanisms regulating scale pattern formation. Although the existence of two genes with two pairs of alleles (...

The Asian seabass (Lates calcarifer) is an economically important food fish with a wide geographic distribution ranging from the Indo-West Pacific region to Northern Australia. It has an estimated genome size of ~700Mb and a poorly represented transcriptome in GenBank. The main aim of the project is to use next generation sequencing (NGS) platforms...

Stress associated proteins (SAPs), novel A20/AN1 zinc-finger domain-containing proteins, are fast emerging as potential candidates for biotechnological approaches in order to improve abiotic stress tolerance in plants - the ultimate aim of which is crop-yield protection. Until relatively recently, such proteins had only been identified in humans, w...

Our previous work with the zebrafish embryo had uncovered a master regulatory role for the winged-helix transcription factor FoxJ1 in motile ciliogenesis. In humans, dysfunction of motile cilia leads to Primary Ciliary Dyski-nesia (PCD). Mutations in only a few genes have thus far been associated with PCD. To identify new genes that are required fo...

List of organisms in which FoxJ1 orthologs were searched using the full-length human FoxJ1 protein sequence. (XLSX)

List of organisms in which FoxJ1 could not be identified either by reverse BLAST or phylogenetic analyses. (XLSX)

Normal motility in wild-type and foxJ1-1(RNAi) worms compared to the inchworming gait observed in worms with foxJ1-4(RNAi) and ift172(RNAi). (MOV)

Expression levels of invertebrate FoxJ1 proteins in zebrafish embryos. Western blot showing roughly equivalent levels of the zebrafish and sea urchin FoxJ1 proteins, but lower levels of expression of placozoan FoxJ1. Tubulin levels were measured as loading control. (JPG)

It is generally believed that the last eukaryotic common ancestor (LECA) was a unicellular organism with motile cilia. In the vertebrates, the winged-helix transcription factor FoxJ1 functions as the master regulator of motile cilia biogenesis. Despite the antiquity of cilia, their highly conserved structure, and their mechanism of motility, the ev...