Population genomics of apricots unravels domestication history and adaptive events

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Июнь 25, 2021

Abstract Among crop fruit trees, the apricot ( Prunus armeniaca ) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca genomes four high-quality assemblies anchored on genetic maps. Chinese European apricots form two differentiated gene pools with high diversity, resulting from independent domestication events distinct wild Central Asian populations, subsequent flow. A relatively low proportion of genome is affected by selection. Different genomic regions show footprints selection in cultivated apricots, despite convergent phenotypic traits, predicted functions both groups involved perennial life cycle, quality disease resistance. Selection appear more abundant a hotspot chromosome 4, while admixture pervasive apricots. Our clues biology selected traits targets for tree research breeding.

Язык: Английский

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Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective

International Journal of Molecular Sciences, Год журнала: 2020, Номер 22(1), С. 333 - 333

Опубликована: Дек. 30, 2020

In plants, fruit ripening is a coordinated developmental process that requires the change in expression of hundreds to thousands genes modify many biochemical and physiological signal cascades such as carbohydrate organic acid metabolism, cell wall restructuring, ethylene production, stress response, organoleptic compound formation. Prunus species (including peaches, apricots, plums, cherries), leads breakdown complex carbohydrates into sugars, firmness reductions (softening by degradation cuticle properties alteration), color changes (loss green chlorophylls increase non-photosynthetic pigments like anthocyanins carotenoids), acidity decreases, aroma increases (the production release volatile compounds). Actually, level information molecular events at transcriptional, biochemical, hormonal, metabolite levels underlying fruits has increased considerably. However, we still poorly understand switch occurs during transition from unripe ripe fruits. The objective this review was analyze bases quality through an integrated metabolic, genomic, transcriptomic, epigenetic approach better involved with important consequences breeding point view.

Язык: Английский

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GreeNC 2.0: a comprehensive database of plant long non-coding RNAs

Nucleic Acids Research, Год журнала: 2021, Номер 50(D1), С. D1442 - D1447

Опубликована: Окт. 13, 2021

Abstract The Green Non-Coding Database (GreeNC) is one of the reference databases for study plant long non-coding RNAs (lncRNAs). Here we present our most recent update where 16 species have been updated, while 78 added, resulting in annotation more than 495 000 lncRNAs. Moreover, sequence clustering was applied providing information about conservation and gene families. current version database available at: http://greenc.sequentiabiotech.com/wiki2/Main_Page.

Язык: Английский

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Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

Methods in molecular biology, Год журнала: 2022, Номер unknown, С. 101 - 131

Опубликована: Янв. 1, 2022

Язык: Английский

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Transposable element evolution in plant genome ecosystems

Current Opinion in Plant Biology, Год журнала: 2023, Номер 75, С. 102418 - 102418

Опубликована: Июль 15, 2023

The relationship of transposable elements (TEs) with their host genomes has usually been seen as an arms race between TEs and genomes. Consequently, are supposed to amplify by bursts transposition, when the TE escapes surveillance, followed long periods quiescence efficient control. Recent data obtained from increasing number assembled plant resequencing population datasets show that dynamics is more complex varies among families This variation ranges large accommodate populations very active in elimination, inconspicuous low activity high transposition elimination rates. each family results a history interaction genome populated many other families, much like evolving ecosystem.

Язык: Английский

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Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness

Horticulture Research, Год журнала: 2024, Номер 11(7)

Опубликована: Июнь 21, 2024

Chinese cherry (

Язык: Английский

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Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae

Annual Review of Plant Biology, Год журнала: 2020, Номер 71(1), С. 547 - 573

Опубликована: Апрель 29, 2020

Rosaceae (the rose family) is an economically important family that includes species prized for high-value fruits and ornamentals. The also exhibits diverse fruit types, including drupe (peach), pome (apple), drupetum (raspberry), achenetum (strawberry). Phylogenetic analysis ancestral fruit-type reconstruction suggest independent evolutionary paths of multiple fleshy types from dry fruits. A recent whole genome duplication in the Maleae/Pyreae tribe (with apple, pear, hawthorn, close relatives; referred to as Maleae here) may have contributed evolution fruit. MADS-box genes, known regulate floral organ identity, are emerging regulators development. differential competence organs respond fertilization signals explain different abilities form Future comparative genomics functional studies closely related with distinct will test hypotheses provide insights into mechanisms diversity. These efforts be facilitated by wealth data resources Rosaceae.

Язык: Английский

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Chromosome-level draft genome of a diploid plum (Prunus salicina)

GigaScience, Год журнала: 2020, Номер 9(12)

Опубликована: Дек. 1, 2020

Plums are one of the most economically important Rosaceae fruit crops and comprise dozens species distributed across world. Until now, only limited genomic information has been available for genetic studies breeding programs plums. Prunus salicina, an diploid plum species, plays a predominant role in modern commercial production. Here we selected P. salicina whole-genome sequencing present chromosome-level genome assembly through combination Pacific Biosciences sequencing, Illumina Hi-C technology.The had total size 284.2 Mb, with contig N50 1.78 Mb scaffold 32.32 Mb. A 96.56% assembled sequences were anchored onto 8 pseudochromosomes, 24,448 protein-coding genes identified. Phylogenetic analysis showed that close relationship mume armeniaca, diverging from their common ancestor ∼9.05 million years ago. During evolution 146 gene families expanded, some cell wall-related GO terms significantly enriched. It was noteworthy members DUF579 family, new class involved xylan biosynthesis, expanded which provided insight into metabolism plums.We constructed first high-quality using Biosciences, Illumina, technologies. This work provides valuable resource facilitating studying diversity mechanisms plums species.

Язык: Английский

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Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees

Current Biology, Год журнала: 2021, Номер 31(17), С. 3848 - 3860.e8

Опубликована: Июль 26, 2021

The Great Himalayan Mountains and their foothills are believed to be the place of origin development many plant species. genetic basis adaptation high plateaus is a fascinating topic that poorly understood at population level. We comprehensively collected sequenced 377 accessions Prunus germplasm along altitude gradients ranging from 2,067 4,492 m in Himalayas. de novo assembled three high-quality genomes Tibetan A comparative analysis indicated remarkable expansion SINE retrotransposons occurred observed differentiation between peaches low altitudes genes associated with light stress signaling, especially UV were enriched differentiated regions. By profiling metabolomes peach fruit, we determined 379 metabolites had significant correlations particular phenylpropanoids positively correlated altitudes. identified 62 peach-specific SINEs colocalized differentially accumualted relative cultivated peach. demonstrated two inserted locus controlling accumulation 3-O-feruloyl quinic acid. SINE1 was specific SINE2 predominant These genomic metabolic data for populations native region indicate helped species adapt harsh environment plateau by promoting beneficial metabolites.

Язык: Английский

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Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance

BMC Biology, Год журнала: 2022, Номер 20(1)

Опубликована: Июнь 13, 2022

Abstract Background Peach ( Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated temperate subtropical regions, emerging as excellent material to study the interaction between plant environment. During its genus, there are four wild species of peach, all living harsh environments. For example, one species, P. mira , originates from Qinghai-Tibet Plateau (QTP) exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses gene discovery quality-related traits peach using previous assembled genome were obtained, genomic basis response these different geographical environments remains unclear. Results To uncover key genes regulating adaptability analyze role genetic variations resistance formation, we performed de novo assembling relatives persica ), davidiana kansuensis ferganensis resequenced 175 varieties. The phylogenetic tree showed that divergence time other was 11.5 million years ago, which consistent with drastic crustal movement QTP. Abundant identified when compared results plant-pathogen pathways enriched containing small insertions deletions copy number peach. Then, data used identify new resistance. presence/absence result a hybridization event occurred dulcis enhanced their putative hybrid, . Using bulked segregant analysis, located nematode locus chromosome 2. Within mapping region, deletion promoter NBS-LRR found involve by expression. Furthermore, combined RNA-seq selective sweeps proposed CBF essential for high-altitude adaptation through increasing low temperature. Conclusions In general, reference genomes facilitate our understanding mechanism perennial crops, provide valuable resources future breeding improvement.

Язык: Английский

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