RT Journal Article
SR Electronic
T1 Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.04.20.488802
DO 10.1101/2022.04.20.488802
A1 F.G. Çilingir
A1 L. A’Bear
A1 D. Hansen
A1 L.R. Davis
A1 N. Bunbury
A1 A. Ozgul
A1 D. Croll
A1 C. Grossen
YR 2022
UL http://biorxiv.org/content/early/2022/04/20/2022.04.20.488802.abstract
AB The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is considered vulnerable due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts focused on both wild and ex-situ populations. A high-quality genome would also open avenues to investigate the genetic basis of the exceptionally long lifespan. Here, we produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture (Hi-C). We produced a 2.37 Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNAseq-assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. We also performed a low-coverage re-sequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. The high-quality chromosome-level reference genome for A. gigantea is one of the most complete turtle genomes available. It is a powerful tool to assess the population structure in the wild population and reveal the geographic origins of ex-situ individuals relevant for genetic diversity management and rewilding efforts.Competing Interest StatementThe authors have declared no competing interest.μgmicrogramμlmicroliter°Cdegree CelciusAGATAnother Gtf/Gff Analysis ToolkitANGSDAnalysis of Next Generation Sequencing Databaqbase alignment qualitybpbase pairsBUSCOBenchmarking Universal Single-Copy OrthologsBWABurrows-Wheeler AlignerDNAdeoxyribonucleic acidcDNAcomplementary DNAdsDNAdouble-strand DNAEAZAEuropean Association of Zoos and AquariaETHSwiss Federal Institute of Technology in ZüCrichGAIAGenome-wide Alignment Including Adapter-trimmingGATKGenome Analysis ToolkitGbpgigabase pairsGCguanine and cytosineGCEGenomic Character EstimatorgDNAgenomic DNAHi-Cchromosome conformation captureHiFihigh-fidelityHMWhigh molecular weightIsoSeqisoform sequencingIUCNInternational Union for Conservation of NatureJBATJuicebox Assembly ToolsKATk-mer analysis toolkitLSliquid sampleMAFminor allele frequencyMbpmegabase pairsmgmilligramminminutemLmillilitermMmillimolarNCBINational Center for Biotechnology InformationNEBNew England BiolabsngnanogramNGSAdmixNext Generation Sequencing AdmixturengsLDNext Generation Sequencing Linkage DisequilibriumOrthoDBorthologous databasePacBioPacific BiosciencesPBSphosphate-buffered salinePCAprincipal component analysisPCRpolymerase chain reactionQUASTQuality Assessment ToolRefSeqreference sequenceRfamRNA familiesRNAribonucleic acidRNA-seqRNA sequencinfrpmrevolutions per minuteSauropsida_odb10sauropsids orthologous database 10SMRTsingle-molecule real-timeSNPsingle nucleotide polymorphismSRASequence Read ArchiveSTARSpliced Transcripts Alignment to a ReferenceSyRISynteny and Rearrangement IdentifiertRNAtransfer RNArRNAribosomal RNAsnRNAsmall nuclear RNAmiRNAmicro RNATSEBRATranscript Selector for BRAKERUniProtKBUniversal Protein KnowledgebaseVertebrata_odb10vertebrate orthologous database 10