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

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dc.authoridMollman, Rachel/0000-0002-6873-6212
dc.authoridKuralay, Selim Can/0000-0002-8891-1575
dc.authoridCiftci, Almila/0000-0002-3406-3064
dc.authoridEROL, OSMAN/0000-0002-6310-1402
dc.authoridINAL, Behcet/0000-0003-2215-2710
dc.authoridCAY, SELAHATTIN BARIS/0000-0002-3144-606X
dc.authoridZararsiz, Gokmen/0000-0001-5801-1835
dc.authoridCinar, Yusuf Ulas/0000-0002-6554-6894
dc.contributor.authorCay, Selahattin Baris
dc.contributor.authorCinar, Yusuf Ulas
dc.contributor.authorKuralay, Selim Can
dc.contributor.authorInal, Behcet
dc.contributor.authorZararsiz, Gokmen
dc.contributor.authorCiftci, Almila
dc.contributor.authorMollman, Rachel
dc.date.accessioned2024-12-24T19:30:01Z
dc.date.available2024-12-24T19:30:01Z
dc.date.issued2022
dc.departmentSiirt Üniversitesi
dc.description.abstractCrocus istanbulensis (B.Mathew) Ruksans 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 lridaceae 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.
dc.description.sponsorshipScientific Research Projects Coordination Unit of Istanbul University [37223, 37723]; National Center for High Performance Computing of Turkey (UHeM) [5004732017]
dc.description.sponsorshipThis study was funded by Scientific Research Projects Coordination Unit of Istanbul University. Project number: 37223 and 37723. Computing resources used in this work were funded by the National Center for High Performance Computing of Turkey (UHeM) under grant number 5004732017. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
dc.identifier.doi10.1371/journal.pone.0269747
dc.identifier.issn1932-6203
dc.identifier.issue6
dc.identifier.pmid35704623
dc.identifier.scopus2-s2.0-85132082014
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.1371/journal.pone.0269747
dc.identifier.urihttps://hdl.handle.net/20.500.12604/7333
dc.identifier.volume17
dc.identifier.wosWOS:000843575700095
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherPublic Library Science
dc.relation.ispartofPlos One
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241222
dc.titleGenome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukans
dc.typeArticle

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