Comparative chloroplast genomes analysis of nine Limonium (Plumbaginaceae) species, including two endangered species from the island of Malta

We present the first two complete plastomes from the centre of diversity of the genus Limonium which is the Mediterranean Sea; L. melitense (154139 bp) and L. zeraphae (154142 bp) are endangered, endemic species from the Maltese Archipelago. These de novo assembled plastomes are compared to each other and to those of seven other species from the Irano-Turanian and the Chinese Japanese region. They range in size from 150515 to 170033 bp. We attribute the expansion and contraction of these plastomes to variable copy number genes in the Inverted Repeats and difference is the number of repeats. We also identify high nucleotide diversity in the genes: ndhF, ycf1 and rpl32; the intergenic regions: rpl32-trnL_TAG, ndhF, rpl32, trnM_CAT-rps14, ndhH-rps15 and psbI-trnS_GCT and the second intron of the ycf3 gene. These can serve as molecular markers. Additionally 382 simple sequence repeats are identified. The main differences in the plastomes of the Maltese endemics include the number of functional genes with L. zeraphae having a pseudogenized copy of the rpl22 gene, difference in the boundaries of the quadripartite plastome, differences in repeat sequences and point mutations. Plastome pairwise genetic distance unambigously identifies each of the species. Six genes are undergoing strong positive selection and rapid evolution, namely ccsA, rpl22, rpoA, rps8, ycf1 and ycf2. The phylogenomic tree reflects geographical distribution and infrageneric classification up to Section level in the monophylatic genus Limonium. This work is linked to previous research on Limonium species and deepens our understanding of the characteristics and phylogenetic relationships of the genus.