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The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms

Shubham K. Jaiswal, Abhisek Chakraborty, Shruti Mahajan, Sudhir Kumar, View ORCID ProfileVineet K. Sharma
doi: https://doi.org/10.1101/2020.05.29.122895
Shubham K. Jaiswal
1Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal
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Abhisek Chakraborty
1Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal
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Shruti Mahajan
1Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal
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Sudhir Kumar
1Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal
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Vineet K. Sharma
1Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal
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  • ORCID record for Vineet K. Sharma
  • For correspondence: vineetks@iiserb.ac.in
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ABSTRACT

Aloe vera is a species from Asphodelaceae plant family having unique characteristics such as drought resistance and also possesses numerous medicinal properties. However, the genetic basis of these phenotypes is yet unknown, primarily due to the unavailability of its genome sequence. In this study, we report the first Aloe vera draft genome sequence comprising of 13.83 Gbp and harboring 86,177 coding genes. It is also the first genome from the Asphodelaceae plant family and is the largest angiosperm genome sequenced and assembled till date. Further, we report the first genome-wide phylogeny of monocots with Aloe vera using 1,440 one-to-one orthologs that resolves the genome-wide phylogenetic position of Aloe vera with respect to the other monocots. The comprehensive comparative analysis of Aloe vera genome with the other available high-quality monocot genomes revealed adaptive evolution in several genes of the drought stress response, CAM pathway, and circadian rhythm in Aloe vera. Further, genes involved in DNA damage response, a key pathway in several biotic and abiotic stress response mechanisms, were found to be positively selected. This provides the genetic basis of the evolution of drought stress tolerance capabilities of Aloe vera. This also substantiates the previously suggested notion that the evolution of unique characters in this species is perhaps due to selection and adaptive evolution rather than the phylogenetic divergence or isolation.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Email addresses of authors: Shubham K. Jaiswal – shubhamj{at}iiserb.ac.in, Abhisek Chakraborty – abhisek18{at}iiserb.ac.in, Shruti Mahajan – shruti17{at}iiserb.ac.in, Sudhir Kumar – sudhir19{at}iiserb.ac.in, Vineet K. Sharma – vineetks{at}iiserb.ac.in

  • LIST OF ABBREVIATIONS

    MSA
    Multiple signs of adaptive evolution
    CAM
    Crassulacean acid metabolism
    COG
    Clusters of Orthologous Groups
    KEGG
    Kyoto Encyclopedia of Genes and Genomes
    GO
    Gene ontology
    BUSCO
    Benchmarking Universal Single-Copy Orthologs
    SIFT
    Sorting Intolerant From Tolerant
    FDR
    False discovery rate
    BLAST
    Basic Local Alignment Search Tool
    N50
    minimum contig length needed to cover 50% of the genome
    ABA
    Abscisic acid
    snoRNA
    small nucleolar RNA
    snRNA
    small nuclear RNA
    tRNA
    transfer RNA
    rRNA
    ribosomal RNA
    srpRNA
    signal recognition particle RNA
    miRNA
    micro RNA
    MYB
    Myeloblastosis
    bHLH
    basic helix–loop– helix
    CPP
    cysteine-rich polycomb-like protein
    LBD
    Lateral Organ Boundaries (LOB) Domain
    EMB3127
    Embryo Defective 3127
    PnsB3
    Photosynthetic NDH subcomplex B3
    TL29
    Thylakoid Lumen 29
    IRT3
    Iron regulated transporter 3
    PDV2
    Plastid Division2
    SIRB
    Sirohydrochlorin ferrochelatase B
    G6PD5
    Glucose-6-phosphate dehydrogenase 5
    KAT2
    Potassium channel in Arabidopsis thaliana 2
    PHYB
    Phytochrome B
    ELF3
    Early Flowering 3
    LHY
    Late Elongated Hypocotyl
    FT
    Flowering locus T
    PHYA
    Phytochrome A
    GI
    Gigantea
    FKF1
    Flavin-binding, Kelch repeat, F box 1
    SPA1
    Suppressor of PHYA-105 1
    HY5
    Elongated Hypocotyl5
    CHS
    Chalcone synthase
    CPA
    Capping Protein A
    PNC1
    Peroxisomal adenine nucleotide carrier 1
    PEX14
    Peroxin 14
    IRT3
    Iron regulated transporter 3
    NRAMP1
    Natural Resistance-Associated Macrophage Protein 1
    ALA1
    Aminophospholipid ATPase 1
    NAT8
    Nucleobase-Ascorbate Transporter 8
    NRT2.6
    High affinity Nitrate Transporter 2.6
    ppc-aL1a
    Phosphoenolpyruvate carboxylase
    CENH3
    Centromeric histone H3
    NORK
    Nodulation receptor kinase
    PPR
    Pentatricopeptide Repeat
    PTS1
    Peroxisomal targeting signal 1
    PTS2
    Peroxisomal targeting signal 2
    LTR-RT
    Long terminal repeat Retrotransposons
    EST
    Expressed sequence tag
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    Posted May 31, 2020.
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    The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms
    Shubham K. Jaiswal, Abhisek Chakraborty, Shruti Mahajan, Sudhir Kumar, Vineet K. Sharma
    bioRxiv 2020.05.29.122895; doi: https://doi.org/10.1101/2020.05.29.122895
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    The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms
    Shubham K. Jaiswal, Abhisek Chakraborty, Shruti Mahajan, Sudhir Kumar, Vineet K. Sharma
    bioRxiv 2020.05.29.122895; doi: https://doi.org/10.1101/2020.05.29.122895

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