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

IF 11.8 2区 生物学 Q1 MULTIDISCIPLINARY SCIENCES
Rafael Moysés Alves, Vinicius A C de Abreu, Rafaely Pantoja Oliveira, João Victor Dos Anjos Almeida, Mauro de Medeiros de Oliveira, Saura R Silva, Alexandre R Paschoal, Sintia S de Almeida, Pedro A F de Souza, Jesus A Ferro, Vitor F O Miranda, Antonio Figueira, Douglas S Domingues, Alessandro M Varani
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引用次数: 0

Abstract

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 genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family.

Findings: The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies 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 with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as 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: The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.

在染色体尺度上对大叶猴面包树(cupuassu)进行基因组解码:从进化角度看园艺创新。
背景:大叶可可树(锦葵科),又称 "杯果",是亚马逊盆地的一种本土树种,因其果实大、籽浆多而珍贵,对亚马逊生物经济的贡献巨大。种子果肉可用于甜点和饮料,种子黄油可用于化妆品。在这里,我们展示了从端粒到端粒的cupuassu基因组测序结果,揭示了其基因组结构、进化特征以及在锦葵科中的系统发育关系:可可巴豆基因组跨度达 423 Mb,编码 31,381 个基因,分布在 10 条染色体上,与可可巴豆基因组的基因同源性约为 65%,反映了其进化史的保守性,尽管其中也有独特的基因组变异。主要变化表现在物种分化后出现的长端重复反转座子、反转座基因和单基因,以及基因家族呈现出独特的扩张和收缩模式。此外,正选择基因也很明显,特别是在保留和分散的串联基因和近端重复基因中,这些基因与果实和种子的一般性状以及防御机制有关,支持了复制后可能出现的亚功能化和新功能化的假说,以及不同驯化过程的影响。这些基因组变异可能是所观察到的巴西莓与其他锦葵科植物在果实和种子形态、成熟和抗病性方面的差异的基础:杯果基因组为育种改良和保护生物学提供了基础资源,有助于深入了解可可巴豆属的进化和多样性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
GigaScience
GigaScience MULTIDISCIPLINARY SCIENCES-
CiteScore
15.50
自引率
1.10%
发文量
119
审稿时长
1 weeks
期刊介绍: GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.
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