Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea (Pisum sp.)

Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.Peer reviewe

Simple enough, but not simpler : reconsidering additive logratio coordinates in compositional analysis

Compositional data, multivariate observations carrying relative information, are popularly expressed in additive logratio coordinates which are easily interpretable as they use one of the components as ratioing part to produce pairwise logratios. These coordinates are however oblique and they lead to issues when applying multivariate methods on them, including widely-used techniques such as principal component analysis and linear regression. In this paper we propose a way to redefine alr coordinates with respect to an orthonormal system and we also extend the idea to the case of compositional tables. The new approach is demonstrated in an application to movement behavior data