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