The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history DOI Creative Commons
Jie Wang, Junhu Kan, Jie Wang

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: June 3, 2024

Backgrounds Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used a traditional ornamental flowering plant fruit tree China. Although some population genetic analyses have been conducted for this species, no extensive comparisons of variation from plastomes yet investigated. Methods We de novo assembled total 322 complete P. study did series comparative better resolve pan-plastomic patterns . To determine phylogeny domestication history we reconstructed phylogenetic genus, resolved structure also examined nucleotide find potential DNA barcodes. Results The exhibited typical quadripartite ranged 157,871 bp 158,213 size with GC content ranging 36.73 36.75%. A 112 unique genes were identified. Single variants (SNVs) most common found among plastomes, followed by insertions/deletions (InDels), block substitutions intergenic spacer (IGS) regions containing greatest number variants. From pan-plastome data six well-supported clusters using multiple different analyses. cultivars unevenly distributed clades. species understand genus level diversity which complex introgressive relationship between other apricots/plums was resolved. Conclusion This constructed , indicated involved origins possible matrilineal introgression species. analysis provide an important maternal groundwork future studies on intergenomic sequence transfers, cytonuclear incompatibility, conservation genetics.

Language: Английский

Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective DOI Open Access
Beatriz E. García-Gómez, Juan Alfonso Salazar, María Nicolás-Almansa

et al.

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

Citations

73
Population genomics of apricots unravels domestication history and adaptive events DOI Creative Commons
Alexis Groppi, Shuo Liu, Amandine Cornille

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: June 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.

Language: Английский

Citations

73
GreeNC 2.0: a comprehensive database of plant long non-coding RNAs DOI Creative Commons

Marco Di Marsico,

Andreu Paytuví-Gallart, Walter Sanseverino

et al.

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D1442 - D1447

Published: Oct. 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.

Language: Английский

Citations

57
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways DOI
Marcela K. Tello‐Ruiz, Pankaj Jaiswal, Doreen Ware

et al.

Methods in molecular biology, Journal Year: 2022, Volume and Issue: unknown, P. 101 - 131

Published: Jan. 1, 2022

Language: Английский

Citations

46
Transposable element evolution in plant genome ecosystems DOI Creative Commons
M. Pulido, Josep Casacuberta

Current Opinion in Plant Biology, Journal Year: 2023, Volume and Issue: 75, P. 102418 - 102418

Published: July 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.

Language: Английский

Citations

24
Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness DOI Creative Commons
Songtao Jiu,

Zhengxin Lv,

Moyang Liu

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(7)

Published: June 21, 2024

Chinese cherry (

Language: Английский

Citations

10
Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae DOI
Zhongchi Liu, Hong Mā, Sook Jung

et al.

Annual Review of Plant Biology, Journal Year: 2020, Volume and Issue: 71(1), P. 547 - 573

Published: April 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.

Language: Английский

Citations

64
Chromosome-level draft genome of a diploid plum (Prunus salicina) DOI Creative Commons
Chaoyang Liu, Chao Feng,

Weizhuo Peng

et al.

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

Citations

56
Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees DOI Creative Commons
Xia Wang, Shengjun Liu, Hao Zuo

et al.

Current Biology, Journal Year: 2021, Volume and Issue: 31(17), P. 3848 - 3860.e8

Published: July 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.

Language: Английский

Citations

56
Variability of Chemical Profile in Almonds (Prunus dulcis) of Different Cultivars and Origins DOI Creative Commons
Ana Beltrán Sanahuja, Salvador E. Maestre Pérez,

Núria Grané Teruel

et al.

Foods, Journal Year: 2021, Volume and Issue: 10(1), P. 153 - 153

Published: Jan. 13, 2021

Almonds show a great variability in their chemical composition. This is result of the existence diverse range almond cultivars, self-incompatibility most and heterogeneous harvesting conditions found around different locations where almons are grown. In last years, discrimination among cultivars has been focal point some research studies to avoid fraud protected geographical indications products also for selecting best specific food application or interesting ones from nutritional view. this work, revision recent works related characterization classification origins carried out. The content macronutrients, tocopherols, phytosterols, polyphenols, minerals, amino acids, volatile compounds together with DNA fingerprint have reported as possible cultivar origin markers. analysis results showed that no individual compound could be considered universal biomarker find differences cultivars. Hence, an adequate selection variables employment metabolomics multivariate statistical techniques necessary when out obtain valuable results. Meanwhile, fingerprinting perfect tool compared based on genetic origin.

Language: Английский

Citations

41