Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukšāns

Abstract

Crocus istanbulensis (B.Mathew) Rukšāns is one of the most endangered Crocus species in the world and has an extremely limited distribution range in Istanbul. Our recent field work indicates that no more than one hundred individuals remain in the wild. In the present study, we used genome skimming to determine the complete chloroplast (cp) genome sequences of six C. istanbulensis individuals collected from the locus classicus. The cp genome of C. istanbulensis has 151,199 base pairs (bp), with a large single-copy (LSC) (81,197 bp), small single copy (SSC) (17,524 bp) and two inverted repeat (IR) regions of 26,236 bp each. The cp genome contains 132 genes, of which 86 are protein-coding (PCGs), 8 are rRNA and 38 are tRNA genes. Most of the repeats are found in intergenic spacers of Crocus species. Mononucleotide repeats were most abundant, accounting for over 80% of total repeats. The cp genome contained four palindrome repeats and one forward repeat. Comparative analyses among other Iridaceae species identified one inversion in the terminal positions of LSC region and three different gene (psbA, rps3 and rpl22) arrangements in C. istanbulensis that were not reported previously. To measure selective pressure in the exons of chloroplast coding sequences, we performed a sequence analysis of plastome-encoded genes. A total of seven genes (accD, rpoC2, psbK, rps12, ccsA, clpP and ycf2) were detected under positive selection in the cp genome. Alignment-free sequence comparison showed an extremely low sequence diversity across naturally occurring C. istanbulensis specimens. All six sequenced individuals shared the same cp haplotype. In summary, this study will aid further research on the molecular evolution and development of ex situ conservation strategies of C. istanbulensis.

Complete chloroplast genome sequencing and comparative analysis of threatened dragon trees Dracaena serrulata and Dracaena cinnabari

“…2). Similar results were reported previously in other angiosperms [57][58][59] . Among the protein-coding genes 12 genes (rps11, 12,14,15,16,18,2,3,4,7,7,8) code for small ribosomal subunits, 9 genes (rpl14, 16, 2, 0, 22,23,32,33,36) for large ribosomal subunits, 44 genes (Table 2) photosynthesis related proteins, 4 (rpoA, rpoB, rpoC1, rpoC2) DNA dependent RNA polymerase, and 8 genes (accD, ccsA, cemA, matK, ycf1, ycf2, ycf3, ycf4) code for other proteins (Table 2).…”

The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

“…Additionally, several codon sites with significant posterior probabilities were found in rpo genes ( rpoB , rpoC1 , and rpoC2 ). The rpoB gene encodes the β-subunit of RNA Polymerase in plastomes [ 68 ], and the rpoC2 gene encodes another subunit of RNA Polymerase which is responsible for the expression of photosynthetic genes [ 69 ]. The previous research indicated that RNA polymerase could not only keep the essential metabolic process to survive, but also regulate the process of gene transcription and expression, for facilitating species to respond to the changing environment conditions [ 70 , 71 ].…”

Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris

“…Similar results were found in the wild chickpea species belonging to Fabaceae family and in the L. ervoides cp genome 20 , 50 , 51 . SSRs have been identified in various organelle genomes and have great application potential for studies on the molecular evolution of plant population genetics and crop breeding 52 .…”