Plastid and nuclear genomic resources of a relict and endangered plant species: Chamaedaphne calyculata (L.) Moench (Ericaceae)

Authors: MONIKA SZCZECINSKA, ANGELIKA GOMOLINSKA, PIOTR SZKUDLARZ, JAKUB SAWICKI

Abstract: Chamaedaphne calyculata, one of the largest shrubs in the family Ericaceae, is native to boreal zones of the northern hemisphere. The complete nucleotide sequence of the Chamaedaphne plastid genome was determined in the present study. The genome is a circular double-stranded DNA molecule 176,744 bp in length, that includes the typical large single-copy (LSC), small single-copy, and 2 inverted repeats (IR) regions. The C. calyculata plastid genome contains 113 genes, excluding the second IR region. A comparative analysis revealed that the plastid genome organization of the Chamaedaphne plastome is almost identical to that of Vaccinium macrocarpon, the first sequenced chloroplast genome from the family Ericaceae. The most profound changes were observed in regions IRa and IRb, which additionally contain rpl23 and rps14 genes and duplications of trnfM-CAU and trnG-UCC in LSC. Pairwise identity of chloroplast sequences in C. calyculata and V. macrocarpon was 79.6% and the p-distance was 0.032. A large number of nuclear and plastid microsatellites that could be useful for population genetics studies and phylogeographic research were also identified in the study.

Keywords: Plastid genome, sequencing by synthesis, Ericaceae, Chamaedaphne, SSR markers, comparative genomics

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