RT Journal Article
SR Electronic
T1 The genome sequence of <em>Aloe vera</em> reveals adaptive evolution of drought tolerance mechanisms
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.29.122895
DO 10.1101/2020.05.29.122895
A1 Jaiswal, Shubham K.
A1 Chakraborty, Abhisek
A1 Mahajan, Shruti
A1 Kumar, Sudhir
A1 Sharma, Vineet K.
YR 2020
UL http://biorxiv.org/content/early/2020/05/31/2020.05.29.122895.abstract
AB 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 StatementThe authors have declared no competing interest.MSAMultiple signs of adaptive evolutionCAMCrassulacean acid metabolismCOGClusters of Orthologous GroupsKEGGKyoto Encyclopedia of Genes and GenomesGOGene ontologyBUSCOBenchmarking Universal Single-Copy OrthologsSIFTSorting Intolerant From TolerantFDRFalse discovery rateBLASTBasic Local Alignment Search ToolN50minimum contig length needed to cover 50% of the genomeABAAbscisic acidsnoRNAsmall nucleolar RNAsnRNAsmall nuclear RNAtRNAtransfer RNArRNAribosomal RNAsrpRNAsignal recognition particle RNAmiRNAmicro RNAMYBMyeloblastosisbHLHbasic helix–loop– helixCPPcysteine-rich polycomb-like proteinLBDLateral Organ Boundaries (LOB) DomainEMB3127Embryo Defective 3127PnsB3Photosynthetic NDH subcomplex B3TL29Thylakoid Lumen 29IRT3Iron regulated transporter 3PDV2Plastid Division2SIRBSirohydrochlorin ferrochelatase BG6PD5Glucose-6-phosphate dehydrogenase 5KAT2Potassium channel in Arabidopsis thaliana 2PHYBPhytochrome BELF3Early Flowering 3LHYLate Elongated HypocotylFTFlowering locus TPHYAPhytochrome AGIGiganteaFKF1Flavin-binding, Kelch repeat, F box 1SPA1Suppressor of PHYA-105 1HY5Elongated Hypocotyl5CHSChalcone synthaseCPACapping Protein APNC1Peroxisomal adenine nucleotide carrier 1PEX14Peroxin 14IRT3Iron regulated transporter 3NRAMP1Natural Resistance-Associated Macrophage Protein 1ALA1Aminophospholipid ATPase 1NAT8Nucleobase-Ascorbate Transporter 8NRT2.6High affinity Nitrate Transporter 2.6ppc-aL1aPhosphoenolpyruvate carboxylaseCENH3Centromeric histone H3NORKNodulation receptor kinasePPRPentatricopeptide RepeatPTS1Peroxisomal targeting signal 1PTS2Peroxisomal targeting signal 2LTR-RTLong terminal repeat RetrotransposonsESTExpressed sequence tag