Sunday, October 2, 2011

'Orthology' matters in all fields of molecular biology

It is not a maniac lingo of the field of molecular phylogenetics any more. The idea of 'orthology' has spread throughout molecular biology, and has been a basis of comparative approaches of analyzing molecular sequences, although not fully recognized sometimes.

The journal Briefings in Bioinformatics, whose latest impact factor is 9.283, published a special issue titled 'Orthology and Applications'. This issue includes an obituary for Walter M. Fitch who passed away in March this year, focusing on his milestone of providing the idea of orthology and paralogy for the first time in his paper in 1970 (see below).

The 1st page of the paper by Fitch (1970) introducing the concept of orthology and paralogy (Systematic Zoology. 19: 99-113)
I also contributed a research paper based on a collaborative study to this special issue. This article reports an approach to scaffold separate coding regions of the same protein-coding gene split into multiple sequence segments with an aid of molecular phylogenetic information. In particular, my team provided a set of predicted peptide sequences on the low-coverage genome assembly of the ghost shark (aka, elephant shark, Callorhinchus milii). This gene prediction was achieved with the utility of the setting for gene prediction program, Augustus, trained for this species also by my team (also introduced here). I had tight communication with Christophe Dessimoz, the first author (and also the guest editor of this special journal issue) to examine the performance of the algorithm ESPRIT introduced in this article. It was a big excitement to work with him for the paper and to be part of this special issue.

(please also another obituary for W.M. Fitch in Science)