Genomes Published in 2012

From time to time, we reported about publication of various genome papers in 2012 (e.g. pacific oyster). Readers may enjoy learning about all genomes published in 2012 from a full list posted in nextgenseek blog. Kromozome blog provided nice comparison of bioinformatic approaches and major discoveries. Twelve genomes were mentioned in Kromozome table - goat, pig, bat, owl, rice, wheat, tomato, banana, pacific oyster, gorilla bonobo and Neanderthal.

Interesting observations from a quick scan of the table

1. Three groups used SOAPdenovo for assembly. Two others used Newbler. Also, Phusion, Cortex, Velvet, ABySS, Celera were mentioned once.

2. 20K-30K protein-coding genes were found in each genome, except in bread wheat genome containing 94K genes !!

3. Sanger and 454 sequencing are still popular.

4. The finding from bat genome appears the most interesting.

Genes in DNA damage checkpoint/DNA repair pathway found to be under positive selection. So are COL3A1 (skin elasticity) CACNA2D1 (muscle contraction). Entire locus of PYHIN gene family (sensing microbial DNA) is lost.

We need to read all 12 papers to make better reporting of point (4) above instead of commenting based on another blog’s perspective. Unfortunately, by the time we finish reading all 12 papers, another twelve genomes will come out !!