
カップアスのゲノム解読により、カカオとの高い相同性と独自の進化的特徴が明らかになった。これらの知見は、カップアスの育種と保全に役立つ重要な資源となる。


coremsg

Background Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon Basin, valued for its large fruits and seed-pulp, contributing notably to the Amazonian bioeconomy. The seed-pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere cupuassu genome, disclosing features of the genomic structure, evolution, and phylogenetic relationships within the Malvaceae.

Results The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in the ten chromosomes, and it exhibits approximately 65% gene synteny with the T. cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeats retrotransposons expansion at post-species divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed, tandem and proximal duplicated genes associated to general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, and impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species.

Conclusions Sequencing the cupuassu genome offers a foundational resource for both breeding and conservation efforts, yielding insights into the evolution and diversity within the genus Theobroma .

Core ideas 

AUTHOR SUMMARY Cupuassu, a fruit-bearing tree from the Amazon, is prized for its nutritious fruits and seeds, widely used in food and cosmetics. In this study, we sequenced the complete genome of cupuassu to understand its development, unique traits, and genetic relationship with cacao and other related species. The cupuassu genome shares a high similarity with cacao, but it also exhibits distinctive features. Notably, repetitive DNA elements have significantly influenced its genomic structure. Furthermore, specific genes responsible for its fruit and seed characteristics, as well as disease resistance, were identified. Overall, this research not only deepens our knowledge of cupuassu genetics but also illuminates broader aspects of plant evolution and diversity in the Amazon. It lays the groundwork for advanced breeding programs and promises to contribute significantly to the Amazonian bioeconomy. Ultimately, these findings have important implications for agriculture and conservation, highlighting the intricate processes of plant adaptation and evolution.

### Competing Interest Statement

The authors have declared no competing interest.

*   BUSCO
    :   Benchmarking Universal Single-Copy Orthologs
    CDS
    :   coding sequence
    CTAB
    :   Cetyltrimethylammonium Bromide
    FP
    :   Frosty pod
    GO
    :   Gene Ontology
    HiC
    :   Chromosome conformation capture techniques
    HMW
    :   High molecular weight
    Ka
    :   non-synonymous nucleotide substitutions
    Ks
    :   synonymous substitutions
    LAI
    :   LTR Assembly Index
    LARD
    :   Large Retrotransposon Derivatives
    lncRNAs
    :   long non-coding RNAs
    LTR-RT
    :   Long Terminal Repeat Retrotransposons
    miRNAs
    :   microRNAs
    mya
    :   million years ago
    QTL
    :   Quantitative trait locus
    rDNA
    :   ribosomal DNA
    snoRNAs
    :   small nucleolar RNAs
    snRNAs
    :   small nuclear RNAs
    sRNAs
    :   small RNAs
    T2T
    :   telomere-to-telomere
    TE
    :   Transposable Elements
    TRIM
    :   Terminal-repeat Retrotransposons in Miniature
    tRNAs
    :   transfer RNAs
    WBD
    :   Witches’ broom disease
    WGD
    :   Whole-genome duplication

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation

アマゾンのカップアスの染色体レベルでのゲノム解読-園芸革新のための進化的洞察


アマゾンのカップアスの染色体レベルでのゲノム解読:園芸革新のための進化的洞察


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大気CO2濃度上昇はシロイヌナズナの葉のイオノーム含量を全体的に減少させるが、遺伝的多様性により、この反応には大きな幅がある。遺伝解析により、CO2濃度上昇によるイオノーム変化に関与する多数の遺伝子が同定された。


The elevation of atmospheric CO2 leads to a decline in the plant mineral content, which might pose a significant threat to food security in the coming decades. To date, very few genes have been identified as having a role in the negative effect of elevated CO2 on plant mineral composition. Yet, several studies have shown a certain degree of diversity in the ionome’s response to elevated CO2, associated with genotypic variation. This suggests the existence of genetic factors controlling the effect of CO2 on ionome composition. However, no large-scale studies have been carried out to date to explore the genetic diversity of the ionome responses to elevated CO2. Here, we used six hundred Arabidopsis thaliana accessions, representing geographical distributions ranging from worldwide to regional and local environments, to analyze the natural genetic variation underlying the negative effect of elevated CO2 on the ionome composition in plants. We show that the growth under elevated CO2 leads to a global and important decrease of the ionome content whatever the geographic distribution of the population. We also observed a high range of genetic diversity in the response of the ionome composition to elevated CO2, and we identified sub-populations, showing effects on their ionome ranging from the most pronounced to resilience or even to a benefit in response to elevated CO2. Using genome-wide association mapping on the response of each mineral element to elevated CO2 or on integrative traits, we identified a large set of QTLs and genes associated with the ionome response to elevated CO2. Finally, we demonstrate that the function of one of these genes is associated to the negative effect of elevated CO2 on the plant mineral composition. This resource will contribute to understand the genetic mechanisms underlying the negative effect of elevated CO2 on plant mineral nutrition, and could help towards the development of crops adapted to a high-CO2 world.

### Competing Interest Statement

The authors have declared no competing interest.

Natural genetic variation underlying the negative effect of elevated CO2 on ionome composition in Arabidopsis thaliana

大気中co2濃度上昇がシロイヌナズナのイオノーム組成に及ぼす負の影響の遺伝的基盤


大気中CO2濃度上昇がシロイヌナズナのイオノーム組成に及ぼす負の影響の遺伝的基盤
