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Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

View ORCID ProfileF.G. Çilingir, L. A’Bear, D. Hansen, L.R. Davis, N. Bunbury, A. Ozgul, View ORCID ProfileD. Croll, C. Grossen
doi: https://doi.org/10.1101/2022.04.20.488802
F.G. Çilingir
1Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
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  • ORCID record for F.G. Çilingir
  • For correspondence: fgcilingir@gmail.com
L. A’Bear
2Seychelles Islands Foundation, PO Box 853, Victoria, Republic of Seychelles
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D. Hansen
3Zoological Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
4Indian Ocean Tortoise Alliance, Ile Cerf, Victoria, Republic of Seychelles
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L.R. Davis
5Zoo Zürich, Zürichbergstrasse 221, 8044 Zurich, Switzerland
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N. Bunbury
2Seychelles Islands Foundation, PO Box 853, Victoria, Republic of Seychelles
6Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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A. Ozgul
1Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
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D. Croll
7Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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  • ORCID record for D. Croll
C. Grossen
1Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
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Abstract

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 Statement

The authors have declared no competing interest.

  • Abbreviations

    μg
    microgram
    μl
    microliter
    °C
    degree Celcius
    AGAT
    Another Gtf/Gff Analysis Toolkit
    ANGSD
    Analysis of Next Generation Sequencing Data
    baq
    base alignment quality
    bp
    base pairs
    BUSCO
    Benchmarking Universal Single-Copy Orthologs
    BWA
    Burrows-Wheeler Aligner
    DNA
    deoxyribonucleic acid
    cDNA
    complementary DNA
    dsDNA
    double-strand DNA
    EAZA
    European Association of Zoos and Aquaria
    ETH
    Swiss Federal Institute of Technology in ZüCrich
    GAIA
    Genome-wide Alignment Including Adapter-trimming
    GATK
    Genome Analysis Toolkit
    Gbp
    gigabase pairs
    GC
    guanine and cytosine
    GCE
    Genomic Character Estimator
    gDNA
    genomic DNA
    Hi-C
    chromosome conformation capture
    HiFi
    high-fidelity
    HMW
    high molecular weight
    IsoSeq
    isoform sequencing
    IUCN
    International Union for Conservation of Nature
    JBAT
    Juicebox Assembly Tools
    KAT
    k-mer analysis toolkit
    LS
    liquid sample
    MAF
    minor allele frequency
    Mbp
    megabase pairs
    mg
    milligram
    min
    minute
    mL
    milliliter
    mM
    millimolar
    NCBI
    National Center for Biotechnology Information
    NEB
    New England Biolabs
    ng
    nanogram
    NGSAdmix
    Next Generation Sequencing Admixture
    ngsLD
    Next Generation Sequencing Linkage Disequilibrium
    OrthoDB
    orthologous database
    PacBio
    Pacific Biosciences
    PBS
    phosphate-buffered saline
    PCA
    principal component analysis
    PCR
    polymerase chain reaction
    QUAST
    Quality Assessment Tool
    RefSeq
    reference sequence
    Rfam
    RNA families
    RNA
    ribonucleic acid
    RNA-seq
    RNA sequencinf
    rpm
    revolutions per minute
    Sauropsida_odb10
    sauropsids orthologous database 10
    SMRT
    single-molecule real-time
    SNP
    single nucleotide polymorphism
    SRA
    Sequence Read Archive
    STAR
    Spliced Transcripts Alignment to a Reference
    SyRI
    Synteny and Rearrangement Identifier
    tRNA
    transfer RNA
    rRNA
    ribosomal RNA
    snRNA
    small nuclear RNA
    miRNA
    micro RNA
    TSEBRA
    Transcript Selector for BRAKER
    UniProtKB
    Universal Protein Knowledgebase
    Vertebrata_odb10
    vertebrate orthologous database 10
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    Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population
    F.G. Çilingir, L. A’Bear, D. Hansen, L.R. Davis, N. Bunbury, A. Ozgul, D. Croll, C. Grossen
    bioRxiv 2022.04.20.488802; doi: https://doi.org/10.1101/2022.04.20.488802
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    Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population
    F.G. Çilingir, L. A’Bear, D. Hansen, L.R. Davis, N. Bunbury, A. Ozgul, D. Croll, C. Grossen
    bioRxiv 2022.04.20.488802; doi: https://doi.org/10.1101/2022.04.20.488802

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