Bogdanova V.S., Mglinets A.V., Shatskaya N.V., Kosterin O.E., Solovyev V.I., Vasiliev G.V. Cryptic divergences in the genus Pisum L. (peas), as revealed by phylogenetic analysis of plastid genomes

Organellar genomes may shed light on complicated patterns of plant evolution at inter- and intraspecies level. Primary structure of plastid genomes sequenced in this study and taken from databases were characterised and compared in 21 diverse, mostly wild representatives of the genus Pisum (peas). Phylogenetic trees reconstructed via Bayesian approach on the basis of entire plastid genomes resembled those reconstructed on the basis of a nuclear gene His5 coding for a minor histone H1 subtype and corresponded to the taxonomic system of the genus. However, positions of two accessions, classified as P. sativum subsp. elatius (the wild subspecies of the common pea), appeared quite unexpected. On the entire plastid genome tree, an accession from the Black Sea area of Turkey, clustered with representatives of another species, P. fulvum, while the other, from Greece, was the first divergence of the P. sativum branch. In fact, plastid genomes of these two accessions were closer to those of P. fulvum in terms of nucleotide differences. We suppose the plastid genomes of these accessions to be ancient lineages ascending to a 'missing link' between P. fulvum and P. sativum. This could occur through occasional crossing of diverged pea lines in the past and biparental plastid inheritance, both events being possible in peas. A sequenced plastid genome also helped to clarify a complicated origin of a pea line VIR320 from Vavilov's collection associated with an unusual case of nuclear-cytoplasmic conflict.