Sunday, 9 June 2013

The White Tigers, the White Gorillas and the Green Turtle

We have been quite busy in the past weeks setting up our own NGS sequencing lab, but we haven't stop to look around for genomics news and new genomes!
Three articles have been published recently: the complete sequence of two species of turtle to get insight on the evolution of their peculiar body structure, the complete genome sequence of the only known exemplar of white gorilla; a large sequencing and genome wide association study to identify the cause of albinism in white tigers.

The first study appeared at the end of April on Nature Genetics (The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Wang et al.) describe the complete genome assembly of two kind of turtles (P. sinensis and C. mydas) and also reports interesting results from embryo studies and comparative developmental studies against chicken embryos. Taken together these data give a comprehensive picture on turtle evolution and new insight on the crucial factor driving their peculiar body structure. From extensive analysis of embryo gene expression and comparison with chicken, authors found that turtle development initially follows the common vertebrate pattern but then it differentiate from the stage TK11 and they were also able to identify a set of 233 genes that should be crucial for the specific turtle body plan.

"Taken together, these results suggest that turtles indeed conform to the developmental hourglass model (Supplementary Fig. 15) by first establishing an ancient vertebrate body plan and by developing turtle-specific characteristics thereafter. The above results suggest that turtle-specific global repatterning of gene regulation begins after TK11 or the phylotypic period. Although turtle and chicken express many shared developmental genes in the embryo during the putative phylotypic period (Fig. 4a and Supplementary Tables 27and 28) and have the fewest expanded or contracted gene family members expressed (Supplementary Fig. 16) at this stage, later stages showed increasing differences in their molecular patterns. We found 233 genes that showed turtle-specific increasing expression patterns after the phylotype (Fig. 4b). Considering that the chicken orthologs did not show this type of increasing expression (Supplementary Figs. 17 and 18), these 233 genes represent attractive candidates for clarifying the genomic nature of turtle-specific morphological oddities"

This paper combines different techniques and imply a lot of NGS experiments. First of all, the genome sequencing of the two specimens was conducted by paired-end sequencing on Illumina HiSeq 2000 using both short and long insert libraries for a median of 105X and 82X (estimated genome size of about 2.2 Gb). The complete set of turtle transcripts were assessed by computational analysis, but also supported by RNA-Seq data of the soft-shell turtle conducted with three different approach: Titanium sequencig, Illumina strand-specific and non strand-specific RNA-seq, for a total of about 37 Gb of sequencing. Finally, authors investigated miRNAs as well by sequencing small RNAs on Illumina platform. They then used computational tools and comparison with other species known miRNA to infer potential binding sites and conserved miRNA species.

The other two paper deals with some more "exotic" species, trying to dissect the molecular origin of albinism in a white gorilla known as Snowflake and in a family of white tigers raised in captivity. Oculocutaneous albinism in humans is knwon to be related to mutations in the SLC45A2 gene and the authors found that this is the case also in the two considered species.
Complete sequence of the white gorilla was published at the end of May on BMC Genomics (The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. Prado-Martinez et al.). Authors reported the 19X whole genome sequencing of the only known white gorilla and compared these data with the human reference genome and other two already sequenced gorilla genome searching for SNVs in albinism related genes. Data analysis lead to the identification of a missense mutation in SLC45A2 gene resulting in the G518R aminoacid substitution, which should alter the function of the protein channel thus leading to albinism in the white gorilla. Interestingly, it resulted that the genome of snowflake presented large ROH regions, suggesting that it defect may result from high rate of inbreeding.

The study on white tigers was published at the beginning of June on Current Biology (The genetic basis of white tigers. Xu et al.). The authors performed an extensive genomic analysis on a family of 16 white tigers raised in captivity to track down the molecular defect responsible for the albinism in this species. Applying a combined approach based on genome-wide association mapping with restriction-site-associated DNA sequencing (RAD-seq), followed by whole-genome sequencing (WGS) of the three parents, they identified the aminoacid substitution A477V in the SLC45A2 gene as the causative mutation. This finding was confirmed by validation in 130 unrelated tigers identified and three-dimensional homology modeling, suggesting that the substitution may partially block the transporter channel cavity.

No comments: