The genome sequence of<i>Aloe vera</i>reveals adaptive evolution of drought tolerance mechanisms

Jaiswal, Shubham K.; Chakraborty, Abhisek; Mahajan, Shruti; Kumar, Sudhir; Sharma, Vineet K.

doi:10.1101/2020.05.29.122895

Cited by 3 publications

(1 citation statement)

References 94 publications

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“…Previous studies of long-lived or water/heat stress-adapted plants generally suggest that biotic and abiotic stress responses are positively selected for and play roles in the continuous arms race against the environment and pathogens [50][51][52] . Using GO enrichment to compare patterns of gene expression between young and older leaf sections separated by >6 years of growth 53 (Fig.…”

Section: Resultsmentioning

confidence: 99%

The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

et al. 2021

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The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant’s longevity and tolerance to temperature, nutrient and water stress.

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Section: Resultsmentioning

confidence: 99%

The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

et al. 2021

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High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl

Chakraborty

Mondal

Mahajan

et al. 2023

Preprint

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An intriguing example of differential adaptability is the case of two Asian peafowl species,Pavo cristatus(blue peafowl) andPavo muticus(green peafowl), where the former has a ″Least Concern″ conservation status and the latter is an ″Endangered″ species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of unique gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly ofP. cristatusconstructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time.

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Genome sequencing of Syzygium cumini (Jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

Chakraborty

Mahajan

Bisht

et al. 2023

Preprint

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Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequencedS. cuminigenome, which is the largest genome sequenced for the first time from the world's largest tree genusSyzygiumusing Oxford Nanopore and 10x Genomics sequencing technologies. The tetraploid and highly heterozygous draft genome ofS. cuminihad a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position ofS. cuminiwas established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy inS. cuminiwas evident from the higher number of coding genes and expanded gene families compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid inS. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.

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The genome sequence ofAloe verareveals adaptive evolution of drought tolerance mechanisms

Abstract: 18

Cited by 3 publications

References 94 publications

The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl

Genome sequencing of Syzygium cumini (Jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

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