실용적인-피아노-악보-광학-음악-인식을-위한-종단-간-접근법

verbesserung-der-ganganalyse-von-videos-bei-neurodegenerativen-erkrankungen-durch-wissensanreicherung-in-einem-vision-sprach-modell

recovering-3d-scene-representation-from-a-single-snapshot-compressive-image-using-neural-radiance-fields

praktische-end-to-end-optische-musikerkennung-für-klaviermusik

자율주행-차량과-드론의-만남-악천후-환경에서의-소스-프리-도메인-적응을-위한-하이퍼볼릭-연합-학습

a-hybrid-feature-selection-approach-for-accurate-sale-price-prediction

비디오-데이터를-활용한-강화학습을-위한-원칙적인-표현-학습

gemeinsames-lernen-von-autos-und-drohnen-für-robuste-bildverarbeitung-bei-widrigen-wetterbedingungen


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


title_rewrite

カップアスの進化的特性と園芸的特性