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

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

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.

Wild type Zebrafish: Whole Genome Sequence

Till date, the main genomics work has been focused on lab grown Zebrafish strains that functionally represent genetic clones; little or no true genetic diversity was captured in these initial genome studies. Therefore to address questions related to genomic variations, IGIB sequenced a Wild type Strain of Zebrafish caught directly from the water bodies in India.

Institute of Genomics and Integrative Biology (IGIB), which is a constituent laboratory of the Council of Scientific and Industrial Research (CSIR) has completed the whole genome sequencing of a Wild type Strain of Zebrafish (Danio rerio). This work marked India’s entry into the arena of whole genome sequencing of animals.

The Zebrafish genome is about half the size of the human genome, containing about 1700 million DNA base pairs. The research team at IGIB generated over 89 Gigabases of DNA sequences in two months time resulting in over 20X coverage of the Zebrafish genome. The Solexa / Illumina sequencing technology was employed for sequencing the Zebrafish Wildtype strain. This next-generation sequencing technology enables massively parallel sequencing of millions of genomic fragments ranging from 36 to 76 base pairs, which are then mapped back to the reference genome. This humongous exercise was made possible with the CSIR Supercomputing facility at IGIB. Mayo Clinic, Rochester, USA will join this CSIR led project for genome annotation.

Zebrafish, a four centimeter-long fish native to Indian rivers, has attracted considerable scientific interest worldwide primarily as a non-mammalian vertebrate model organism. Zebrafish  share many features of the human system. Using the new advancements in sequencing technologies alongside cutting-edge bioinformatics capabilities, Indian scientists explored genetic variation through comparing the genomes of single Wild type Strain Zebrafish parent and approximately 100 of its offsprings, which were bred and phenotyped at IGIB. The whole genome sequencing of approximately 100 of the offspring is expected to complete by 2012.