A5055376683- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Ichthyology and Marine Biology
- Animal Genetics and Reproduction
- Developmental Biology and Gene Regulation
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- RNA Research and Splicing
- Aquaculture Nutrition and Growth
- Reproductive biology and impacts on aquatic species
- Aquaculture disease management and microbiota
- Genetic diversity and population structure
- Fish Biology and Ecology Studies
- Genomics and Chromatin Dynamics
- Aquatic life and conservation
- Physiological and biochemical adaptations
- RNA and protein synthesis mechanisms
- interferon and immune responses
- Fish biology, ecology, and behavior
- HER2/EGFR in Cancer Research
- RNA modifications and cancer
- Congenital heart defects research
- Neuroendocrine regulation and behavior
- Identification and Quantification in Food
- MicroRNA in disease regulation
- CRISPR and Genetic Engineering
Institute of Molecular and Cell Biology
2016-2025
Agency for Science, Technology and Research
2016-2025
National University of Singapore
2013-2022
University of Surrey
2020
Instituto de Ciencias Agrarias
2020
A*STAR Graduate Academy
2002-2019
Isfahan University of Medical Sciences
2019
Shahid Beheshti University of Medical Sciences
2019
Jinan University
2019
University of Jordan
2019
The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less one-sixth sequence, gene loci occupy about one-third genome. As with human are not evenly distributed, but clustered into sparse dense regions. Some “giant” genes were observed that had average coding sequence sizes spread genomic lengths significantly larger those their orthologs....
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand molecular mechanisms underlying cichlid phenotypic diversity, we sequenced genomes transcriptomes five lineages African cichlids: Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; four members lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent Malawi), Pundamilia nyererei (very recent...
The emergence of jawed vertebrates (gnathostomes) from jawless was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes bony vertebrates. Here we report whole-genome analysis a fish, elephant shark (Callorhinchus milii). We find that C. milii genome is slowest evolving all known vertebrates, including 'living fossil' coelacanth,...
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage lobe-finned fish thought to have become extinct 70 million years ago. modern looks remarkably similar many its ancient relatives, and evolutionary proximity our own ancestors provides glimpse the that first walked on land. Here we report genome sequence African coelacanth, Latimeria chalumnae. Through phylogenomic analysis, conclude lungfish, not is closest relative tetrapods. Coelacanth protein-coding...
Ingo Braasch, John Postlethwait and colleagues report the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before duplication. Their data provide insights into evolution genes involved in immunity, mineralization development facilitate comparison cis-regulatory elements between humans. To connect human biology to fish biomedical models, we sequenced teleost duplication (TGD). The slowly evolving has conserved content size many entire chromosomes bony...
Heterogametic sex chromosomes have evolved independently in various lineages of vertebrates. Such chromosome pairs often contain nonrecombining regions, with one the harboring a master sex-determining (SD) gene. It is hypothesized that these from pair autosomes diverged after acquiring SD By linkage and association mapping locus fugu (Takifugu rubripes), we show SNP (C/G) anti-Müllerian hormone receptor type II (Amhr2) gene only polymorphism associated phenotypic sex. This changes an amino...
The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs increase sequencing efficiency, with concomitant development improved annotation technology and, therefore, propose to create collection tissue DNA specimens 10 000 specifically designated the very near future. For this purpose, we, Genome 10K Community...
Significance Ray-finned fishes form the largest and most diverse group of vertebrates. Establishing their phylogenetic relationships is a critical step to explaining diversity. We compiled comparative genomic database that provides genome-scale support for previous results used it resolve further some contentious in fish phylogeny. A vetted set exon markers identified this study promising resource current sequencing approaches significantly increase genetic taxonomic coverage tree life all...
With about 24,000 extant species, teleosts are the largest group of vertebrates. They constitute more than 99% ray-finned fishes (Actinopterygii) that diverged from lobe-finned fish lineage (Sarcopterygii) 450 MYA. Although role genome duplication in evolution vertebrates is now established, its structuring teleost genomes has been controversial. At least two hypotheses have proposed: a whole-genome an ancient and independent gene duplications different lineages. These are, however, based on...
Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small the elephant shark, Callorhinchus milii, chimaera, makes it an attractive model fish whole-genome sequencing comparative analysis. Here, authors describe survey (1.4x coverage) analysis shark genome, one first genomes be sequenced this depth. Repetitive sequences, represented mainly by novel...
Seahorses have a specialized morphology that includes toothless tubular mouth, body covered with bony plates, male brood pouch, and the absence of caudal pelvic fins. Here we report sequencing de novo assembly genome tiger tail seahorse, Hippocampus comes. Comparative genomic analysis identifies higher protein nucleotide evolutionary rates in H. comes compared other teleost fish genomes. We identified an astacin metalloprotease gene family has undergone expansion is highly expressed pouch....
Highlights•A CRISPR-Cas9 and PiggyBac-based approach allows efficient correction of HD hiPSCs•The corrected hiPSCs can be differentiated into synaptically active neurons•Correction gene mutation reverses a number phenotypic abnormalities•Isogenic help distinguish from genetic background-related effectsSummaryHuntington disease (HD) is dominant neurodegenerative disorder caused by CAG repeat expansion in HTT. Here we report human induced pluripotent stem cells (hiPSCs) using piggyBac...
Abstract Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient their timing in relation to cyclostome-gnathostome divergence remained contentious. Here we generate de novo long-read-based chromosome-scale assemblies for Japanese lamprey elephant shark. Using these other representative genomes developing algorithms probabilistic macrosynteny model, reconstruct high-resolution...
With our increasing ability for generating whole-genome sequences, comparative analysis of whole genomes has become a powerful tool understanding the structure, function, and evolutionary history human other vertebrate genomes. By virtue their position basal to bony vertebrates, cartilaginous fishes (class Chondrichthyes) are valuable outgroup in studies vertebrates. Recently, holocephalan fish, elephant shark, Callorhinchus milii (Subclass Holocephali: Order Chimaeriformes), been proposed...
Although core mechanisms and machinery of premRNA splicing are conserved from yeast to human, the details intron recognition often differ, even between closely related organisms. For example, genes pufferfish Fugu rubripes generally contain one or more introns that not properly spliced in mouse cells. Exploiting available genome sequence data, a battery analysis techniques was used reach several conclusions about organization evolution regulatory elements vertebrate genes. The classical...
The evolutionary origin of spliceosomal introns has been the subject much controversy. Introns are proposed to have both lost and gained during evolution. If gain or loss unique events in evolution, they can serve as markers for phylogenetic analysis. We made an extensive survey distribution seven that present Fugu genes, but not their mammalian homologues; we show these were acquired by actinopterygian (ray-finned) fishes at various stages also investigated intron pattern rhodopsin gene...
Significance Lampreys and hagfishes (cyclostomes) are the only living group of jawless vertebrates therefore important for study vertebrate evolution. We have characterized Hox clusters in Japanese lamprey ( Lethenteron japonicum ), shown that it contains at least six as compared with four tetrapods. This suggests lineage has undergone an additional round genome duplication Several conserved noncoding elements (CNEs) were predicted lamprey, elephant shark, human. Transgenic assay CNEs...
The colonization of land by tetrapod ancestors is one the major questions in evolution vertebrates. Despite intense molecular phylogenetic research on this problem during last 15 years, there is, until now, no statistically supported answer to question whether coelacanths or lungfish are closest living relatives tetrapods. We determined DNA sequences nuclear-encoded recombination activating genes ( Rag1 and Rag2 ) from all three groups, Australian Neoceratodis forsteri , South American...
In humans, the claudin superfamily consists of 19 homologous proteins that commonly localize to tight junctions epithelial and endothelial cells. Besides being structural tight-junction components, claudins participate in cell–cell adhesion paracellular transport solutes. Here, we identify annotate genes whole-genome teleost fish, Fugu rubripes ( ), determine their phylogenetic relationships those mammals. Our analysis reveals extensive gene duplications lineage, leading 56 . A total 35 can...
Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers elucidate the molecular mechanisms underlying these adaptations. We discover an expansion innate immune system genes in may provide defence against terrestrial pathogens. Several ammonia excretion pathway gills experienced positive selection, suggesting important roles mudskippers'...