Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence

The Plant Journal, Journal Year: 2019, Volume and Issue: 101(2), P. 455 - 472

Published: Sept. 17, 2019

Summary We sequenced the genome of highly heterozygous almond Prunus dulcis cv. Texas combining short‐ and long‐read sequencing. obtained a assembly totaling 227.6 Mb estimated size 238 Mb, which 91% is anchored to eight pseudomolecules corresponding its haploid chromosome complement, annotated 27 969 protein‐coding genes 6747 non‐coding transcripts. By phylogenomic comparison with genomes 16 additional close distant species we that peach ( persica ) diverged around 5.88 million years ago. These two are syntenic show high degree sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit number presence/absence variants, many attributable movement transposable elements (TEs). Transposable have generated an important variants between peach, recent history TE seems markedly different them. may be at origin phenotypic differences both species, in particular for sweet kernel phenotype, key agronomic domestication character almond. Here cultivars, methylated insertions surround gene involved biosynthesis amygdalin, whose reduced expression has been correlated phenotype. Altogether, our results suggest role TEs diversification relative peach.

Language: Английский

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Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing

Horticulture Research, Journal Year: 2020, Volume and Issue: 7(1)

Published: Aug. 1, 2020

Abstract Sweet cherry ( Prunus avium ) is an economically significant fruit species in the genus . However, contrast to other important trees this genus, only one draft genome assembly available for sweet cherry, which was assembled using Illumina short-read sequences. The incompleteness and low quality of current limit its use genetic genomic studies. A high-quality chromosome-scale reference therefore needed. total 65.05 Gb Oxford Nanopore long reads 46.24 short were generated, representing ~190x 136x coverage, respectively, genome. final de novo resulted a phased haplotype 344.29 Mb with contig N50 3.25 Mb. Hi-C scaffolding eight pseudochromosomes containing 99.59% bases Genome annotation revealed that more than half (59.40%) composed repetitive sequences, 40,338 protein-coding genes predicted, 75.40% functionally annotated. With assembly, we gene duplication events contributed expansion families salicylic acid/jasmonic acid carboxyl methyltransferase ankyrin repeat-containing proteins cherry. Four auxin-responsive (two GH3s two SAURs) induced late stage development, indicating auxin crucial ripening process. In addition, 772 resistance identified predicted obtained study will provide valuable resources improvement molecular breeding.

Language: Английский

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Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: Jan. 5, 2021

Abstract Background Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic yet the impacts SVs remain largely unexplored in crops. Results Here, we generate high-quality de novo genome assembly for flat-fruit peach cultivar and produce comprehensive SV map peach, as high proportion sequence is occupied by heterozygous genome. We conduct population-level analyses that indicate undergone strong purifying selection during domestication, find evidence positive selection, with significant preference upstream intronic regions later improvement. perform SV-based GWAS identifies large 1.67-Mb inversion segregates perfectly shape. Mechanistically, this derived allele alters expression PpOFP2 gene positioned near proximal breakpoint inversion, confirm transgenic tomatoes causal Conclusions Thus, beyond introducing new genomics resources research, our study illustrates how focusing data drive basic functional discoveries plant science.

Language: 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, Journal Year: 2020, Volume and Issue: 22(1), P. 333 - 333

Published: Dec. 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.

Language: Английский

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Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities

Theoretical and Applied Genetics, Journal Year: 2022, Volume and Issue: 135(11), P. 3961 - 3985

Published: April 20, 2022

Language: Английский

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Marker-Assisted Selection in Breeding for Fruit Trait Improvement: A Review

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(10), P. 8984 - 8984

Published: May 19, 2023

Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst to work with in terms of genetics breeding. Most characterized by large trees, long juvenile periods, intensive agricultural practice, environmental variability plays an important role heritability evaluations every single trait. Although vegetative propagation allows for production a significant number clonal replicates evaluation effects genotype × environment interactions, spaces required plant cultivation intensity necessary phenotypic surveys slow down researchers. Fruit breeders very often interested traits: size, weight, sugar acid content, ripening time, storability, post-harvest practices, among other traits relevant each individual species. The translation trait loci whole-genome sequences into diagnostic genetic markers that effective affordable use breeders, who must choose genetically superior parents subsequently individuals their progeny, one most difficult tasks still facing tree geneticists. availability updated sequencing techniques powerful software tools offered opportunity mine tens genomes find out sequence variants potentially useful as molecular markers. This review devoted analysing what has been assisting selection processes, emphasis on crops which examples trustworthy have developed, such MDo.chr9.4 marker red skin colour apples, CCD4-based CPRFC1, LG3_13.146 flesh peaches, papayas, cherries, respectively.

Language: Английский

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Stone Fruit as Biofactories of Phytochemicals With Potential Roles in Human Nutrition and Health

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: Sept. 2, 2020

Phytochemicals or secondary metabolites present in fruit are key components contributing to sensory attributes like aroma, taste and color. In addition, these compounds improve human nutrition health. Stone an important source of array that may reduce the risk different diseases. The first part this review is dedicated description main organic found plants which include (a) phenolic compounds, (b) terpenoids/isoprenoids (c) nitrogen sulfur containing compounds; their principal biosynthetic pathways regulation stone fruit. Then, type levels bioactive fruits Rosaceae family such as peach (Prunus persica), plum (P. domestica, P. salicina cerasifera), sweet cherries avium), almond kernels dulcis, syn. amygdalus) apricot armeniaca); presented. last encompasses pre- postharvest treatments affecting phytochemical composition Appropriate management factors during handling, along with further characterization phytochemicals synthesis cultivars, could help increase leading future improvement not only enhance organoleptic characteristics but also for benefit

Language: Английский

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

GigaScience, Journal Year: 2020, Volume and Issue: 9(12)

Published: Dec. 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.

Language: Английский

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Improved nutritional quality in fruit tree species through traditional and biotechnological approaches

Trends in Food Science & Technology, Journal Year: 2021, Volume and Issue: 117, P. 125 - 138

Published: Feb. 5, 2021

Language: Английский

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Genome of tetraploid sour cherry (Prunus cerasus L.) ‘Montmorency’ identifies three distinct ancestral Prunus genomes

Horticulture Research, Journal Year: 2023, Volume and Issue: 10(7)

Published: May 10, 2023

Sour cherry (

Language: Английский

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