African coelacanth: Whole Genome Sequence

An international team of scientists has sequenced and analyzed the genome of the African coelacanth, Latimeria chalumnae. Ancient lobe fins were the first vertebrates to brave the land, and the coelacanth genome is expected to reveal much about the origins of tetrapods, the evolutionary line that gave rise to amphibians, reptiles, birds, and mammals. Coelacanths have fleshy, lobed fins, that were believed to live during cretaceous period, when dinosaurs still roamed earth.  Ancient lobe fins were the first vertebrates to brave the land. Coelacanth genome is expected to reveal much about the origins of tetrapods, the evolutionary line that gave rise to amphibians, reptiles, birds and mammals.

The findings were published in the magazine Nature, April 17, 2013.

http://www.scientificamerican.com/article.cfm?id=slow-evolving-lobe-finned-coelacanth-genome-unlocked&page=2

Custom gene editing rewrites zebrafish DNA

Researchers led by Stephen Ekker, a molecular biologist at the Mayo Clinic in Rochester, Minnesota, have for the first time made custom changes to parts of the zebrafish (Danio rerio) genome, using artificial enzymes to cut portions of DNA out of targeted positions in a gene sequence, and replace them with synthetic DNA. The work is published in Nature. Ekker and his colleagues are the first to use artificial TALENs for genome editing in live zebra fish larvae. TALENs have the potential to work on any DNA sequence and cause permanent modifications. They also allow faster analysis of induced mutations — in some cases, the team found, it is possible to observe effects in the injected larvae immediately.

Read more: Nature-doi:10.1038/nature.2012.11463

Intronless genes in teleost fish genomes

A recent study made by German scientists revealed that Takifugu rubripes, Tetraodon nigroviridis, Oryzias latipes, Gasterosteus aculeatus and Danio rerio genomes are respectively comprised of 2.83%, 3.42%, 4.49%, 4.35% and 4.02% single exon genes (SEGs). These SEGs encode for a variety of family proteins including claudins, olfactory receptors and histones that are essential for various biological functions. Annotation features of three Dicentrarchus labrax chromosomes revealed 78 (5.30%) intronless genes, comparisons with G. aculeatus showed that SEG composition and their order varied significantly among corresponding chromosomes, even for those with nearly complete synteny. More than half of SEGs identified in most of the species have at least one ortholog multiple exon gene in the same genome, which provides insight to their possible origin by retrotransposition. In spite of the fact that they belong to the same lineage, the fraction of predicted SEGs varied significantly between the genomes analyzed, and only a low fraction of proteins (4.1%) is conserved between all five species. Furthermore, the inter-specific distribution of SEGs as well as the functional categories shared by species did not reflect their phylogenetic relationships. These results indicate that new SEGs are continuously and independently generated after species divergence over evolutionary time as evidenced by the phylogenetic results of single exon claudins genes. Results of this study provide strong support for the idea that retrotransposition followed by tandem duplications is the most probable event that can explain the expansion of SEGs in eukaryotic organisms.

Study was published in Marine Genomics. 2011 4(2):109-19.

First non-avian reptile whole genome sequence unveiled: Anolis carolinensis

Amniotes, the first truly terrestrial vertebrates, diverged from other animals some 320 million years ago to form the mammalian and reptilian lineages. Until now, however, the only representatives of the reptile branch to be sequenced were birds-the chicken, the turkey and the zebra finch.

Scientists from USA, UK and Sweden, recently reported the genome sequence of the North American green anole lizard, Anolis carolinensis. They found that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

The genome sequence of A. carolinensis allows a deeper understanding of amniote evolution. Filling this important reptilian node with a sequenced genome has revealed derived states in each major amniote branch and has helped to illuminate the amniote ancestor.

The research is published in latest issue of Nature

Whole genome sequence: Anolis carolinensis lizard

Scientist found Anolis to have the most compositionally homogeneous genome of all amniotes sequenced thus far, a homogeneity exceeding that for the frog Xenopus. Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. GC-rich isochores, with shorter introns and higher gene density are reported in all genomes sequenced till date, but disappeared from the Anolis genome. Using genic GC as a proxy for isochore structure so as to compare with other vertebrates, researchers found that GC content has substantially decreased in the lineage leading to Anolis since diverging from the common ancestor of Reptilia ∼275 MYA, perhaps reflecting weakened or reversed GC-biased gene conversion, a non-adaptive substitution process that is thought to be important in the maintenance and trajectory of isochore evolution.

Results demonstrate that GC composition in Anolis is not associated with important features of genome structure, including gene density and intron size, in contrast to patterns seen in mammal and bird genomes.

Findings are published in the latest issue of Genome Biology and Evolution

Alternative Splicing Switch

Adapted from Cell doi:10.1016/j.cell.2011.08.023

Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. Scientists from Canada and USA identified an evolutionarily conserved embryonic stem cell (ESC)-specific AS event that changes the DNA-binding preference of the forkhead family transcription factor FOXP1. An ESC-specific splicing switch in FOXP1 transcripts produces the FOXP1-ES isoform. FOXP1-ES has distinct DNA-binding properties compared to the canonical FOXP1 isoform. FOXP1-ES stimulates key pluripotency genes and represses many differentiation genes. FOXP1-ES is required for ESC pluripotency and efficient induced pluripotent stem cells (iPSC) reprogramming.

These results reveal a pivotal role for an AS event in the regulation of pluripotency through the control of critical ESC-specific transcriptional programs.

The findings are published in the recent issue of Cell

Mouse genomic variation

Adapted from Nature 477, 289-294.

Recently Scientist from USA, UK and Germany reported the genomic variation in mouse and its effect on phenotypes and gene regulation. They reported genome sequences of 17 inbred strains of laboratory mice and identified almost ten times more variants than previously known. By identifying candidate functional variants at 718 quantitative trait loci, scientists showed that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism.

Research outcomes are published in latest issue of Nature

Whole genome Sequence of Atlantic Cod

Recently, scientists from Norway have investigated and present the genome sequence of Atlantic cod (Gadus morhua). The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. Genome sequence provided evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are conserved  feature of the adaptive immune system of jawed vertebrates and, are essential for the function of this pathway. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.

The study is published in the latest issue of Nature

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10342.html#/affil-auth

Medaka Hd-rR: Whole Genome Sequencing Project

Sequencing of the medaka genome was started at the Academia Sequencing Center of the National Institute of Genetics (NIG) in mid 2002. The project was supported by group grant Genome Science (Grant-in-Aid for Scientific Research on Priority Areas supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan).

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The sequencing was conducted by the whole-genome shotgun strategy using southern inbred strain, Hd-rR. The genome was assembled from 13.8 million reads, obtained from the whole genome shotgun plasmid, fosmid, and bacterial artificial chromosome (BAC) libraries. The total size of the assembled contigs was 700.4 megabases (Mb). 50% of nucleotides are covered in scaffolds (or contigs) of length 1.41Mb (9.8 kilobases) that are called N50 values. This contiguity is sufficient to characterize the genomic structures of genes.

Four versions of the medaka genome sequence data named 200406, 200506, version 0.9, and version 1.0  have been released to the public to provide users with timely information. The former two versions had shorter scaffolds that were not anchored on the medaka chromosomes because they were built in 2004 and 2005, before genetics markers were available. Versions 0.9 and 1.0 created in 2006, when comprehensive genetic markers were available, so that about 90% of their scaffolds and ultracontigs were located on the twenty-four medaka chromosomes. Versions 0.9 and 1.0 were built from the identical contigs and scaffolds, but the assembly of version 1.0 is longer than that of version 0.9 because more genetic markers could be used to generate version 1.0. Version 0.9 is left open to the public because most of the data analysis in the medaka genome paper published in Nature (2007) was based on version 0.9.

The University of Tokyo Medaka Genome Browser (UTGB Medaka) a web-based genome database browser, which provides various information related to medaka genomes, including assembly sequences, genes, clones, homologus genome sequences to other species, etc.