Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny

Abstract

The loggerheadmarineturtle, Carettacaretta, isawidelydistributedand endangeredspeciesthatisfacingcriticalpopulationdecline,especiallyin Colombian Caribbeanrookeries.MitochondrialDNAsequencedataareof greatimportanceforthedescription,monitoring,andphylogeneticanalysesof migratoryturtlepopulations.Inthisstudy,thefirstfullmitochondrialgenomeofa loggerheadturtlenestingintheColombianCaribbeanwassequencedandanalyzed. This mitochondrialgenomeconsistsof16362bpwithanucleotidecompositionof T:25.7%,C:27%,A:35%andG:12%.Sequenceannotationoftheassembled molecule revealedanorganizationandnumberofcodingandfunctionalunits as reportedforothervertebratemitogenomes.ThisColombianloggerheadturtle (Cc-AO-C)showedanovelD-Loophaplotypeconsistingofthirteennewvariable sites,sharing99.2%sequenceidentitywiththepreviouslyreportedCaribbean loggerheadCC-A1D-Loophaplotype.All13protein-codinggenesintheCc-AO-C mitogenomewerecomparedandalignedwiththosefromfourotherloggerhead turtlesfromdifferentlocations(Florida,Greece,Peru,andHawaii).Elevenof thesegenespresentedmoderategeneticdiversitylevels,andgenesCOIIandND5 showedthehighestdiversity,withaveragenumbersofpair-wisedifferencesof16.6 and 25,respectively.Inaddition,thefirstapproachrelatedtot-RNAs2Dand3D structureanalysisinthismitogenomewasconducted,leadingtoobservedunique featuresintwotRNAs(tRNATrp and tRNALeu). Themarineturtlephylogeny wasrevisitedwiththenewlygenerateddata.Theentiremitogenomeprovided phylogeneticallyinformativedata,aswellasindividualgenesND5,ND4,and16S. In conclusion,thisstudyhighlightstheimportanceofcompletemitogenomedata in revealinggeneflowprocessesinnaturalloggerheadturtlepopulations,aswellas in understandingtheevolutionaryhistoryofmarineturtles.