The complete chloroplast genome of <i>Theobroma grandiflorum</i>, an important tropical crop

Niu, Ying-Feng; Ni, Shu-Bang; Jin, Liu

doi:10.1080/23802359.2019.1693291

Cited by 9 publications

(5 citation statements)

References 11 publications

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“… 2018 ), Firmiana simplex NC041438, Theobroma grandiflorum NC054233 (Niu et al. 2019 ), Grewia biloba NC058214 (Xu et al. 2021 ), Colona floribunda NC054164 (Wang et al.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome of Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (Malvaceae)

Hou

Men

Bian

et al. 2023

Mitochondrial DNA Part B

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Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (1933), a shrub or small tree, is native to northern and southern China. It is an excellent relief and medicinal plant. The complete chloroplast genome is 158,043 bp in length, with a large single-copy region of 86,957 bp, a small single-copy region of 20,138 bp, two inverted repeat regions of 25,474 bp each, and a GC content of 37.4%. There were 129 genes annotated, including 84 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic trees are constructed using plastome data from 38 species and the maximum-likelihood method. The results of the chloroplast genome-wide analysis and the phylogenetic tree show the taxonomic phylogeny of the G. biloba var. parviflora in relation to other species, increasing the accuracy of the phylogenetic classification of the plant.

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“… 2018 ), Firmiana simplex NC041438, Theobroma grandiflorum NC054233 (Niu et al. 2019 ), Grewia biloba NC058214 (Xu et al. 2021 ), Colona floribunda NC054164 (Wang et al.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome of Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (Malvaceae)

Hou

Men

Bian

et al. 2023

Mitochondrial DNA Part B

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“…The testing phase is crucial since the best structures for the dataset studied herein may not be the best for a distinct dataset, in a completely different context. Allying sophisticated statistical genetic methods with classical breeding strategies, and employing the new molecular tools that are being developed for the species (Falcão et al., 2022; Mournet et al., 2020; Niu et al., 2019; Santos et al., 2022), will guide T. grandiflorum breeding programme towards the future.…”

Section: Discussionmentioning

confidence: 99%

Analysis of repeated measures data through mixed models: An application in Theobroma grandiflorum breeding

et al. 2023

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Theobroma grandiflorum is a perennial fruit tree native to the Amazon region. As a perennial species with continuous production throughout the years, breeders should seek well‐conducted trials, accurate phenotyping and adequate statistical models for genetic evaluation and selection that can leverage the information provided by the repeated measures. We evaluated 13 models with different covariance structures for genetic and residual effects for T. grandiflorum evaluation, using an unbalanced dataset with 34 hybrids from the triple‐crossing of nine parents, planted in a randomized complete block design. For nine consecutive years, the fruit yield of these hybrids was evaluated. Each model had its goodness‐of‐fit tested by the Akaike information criterion. The most adequate model for estimating the variance components and the breeding values were modelled with the first‐order heterogeneous autoregressive for residual effects and third‐order factor analytic for genetic effects. From this model, we used the factor analytic selection tools for selecting the top 10 families, providing a genetic gain of 10.42%. These results are important not only for T. grandiflorum breeding but also to show that in any repeated measures' data from fruit‐bearing perennial species the modelling of genetic and residual effects should not be neglected.

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“…In parallel, recent investigations have delved into the genomic architecture of T. grandiflorum , ranging from developing the first genetic map [ 18 ], the chloroplast and mitochondrial genomes [ 19 , 20 ], and in comparative transcriptomics [ 10 , 21 ]. These latter studies shed light on the interaction between cupuassu and M. perniciosa , setting the groundwork for breeding programs and transgenic approaches.…”

Section: Contextmentioning

confidence: 99%

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

Alves,

de Abreu,

Oliveira

et al. 2024

GigaScience

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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.

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The complete chloroplast genome of Theobroma grandiflorum, an important tropical crop

Cited by 9 publications

References 11 publications

The complete chloroplast genome of Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (Malvaceae)

The complete chloroplast genome of Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (Malvaceae)

Analysis of repeated measures data through mixed models: An application in Theobroma grandiflorum breeding

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

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