A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis

Horticulture Research, Journal Year: 2021, Volume and Issue: 8(1)

Published: July 6, 2021

Abstract Pitaya ( Hylocereus ) is the most economically important fleshy-fruited tree of Cactaceae family that grown worldwide, and it has attracted significant attention because its betalain-abundant fruits. Nonetheless, lack a pitaya reference genome significantly hinders studies focused on evolution, as well potential for genetic improvement this crop. Herein, we employed various sequencing approaches, namely, PacBio-SMRT, Illumina HiSeq paired-end, 10× Genomics, Hi-C (high-throughput chromosome conformation capture) to provide chromosome-level genomic assembly ‘GHB’ H. undatus , 2n = 2x 22 chromosomes). The size assembled was 1.41 Gb, with scaffold N50 ~127.15 Mb. In total, 27,753 protein-coding genes 896.31 Mb repetitive sequences in were annotated. undergone WGT (whole-genome triplication), recent WGD duplication) occurred after gamma event, which common other species Cactaceae. A total 29,328 intact LTR-RTs (~696.45 Mb) obtained two expanded lineages, Ty1/copia Ty3/gypsy, main drivers genome. high-density map F1 hybrid populations × ‘Dahong’ pitayas monacanthus their parents constructed, 20,872 bin markers identified (56,380 SNPs) 11 linkage groups. More importantly, through transcriptomic WGCNA (weighted gene coexpression network analysis), global view regulatory network, including structural transcription factors involved fruit betalain biosynthesis, presented. Our data present valuable resource facilitating molecular breeding programs shed novel light modulation biosynthesis edible

Language: Английский

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Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution

Horticulture Research, Journal Year: 2021, Volume and Issue: 8(1)

Published: Sept. 1, 2021

As one of the largest families angiosperms, Orchidaceae family is diverse. Dendrobium represents second genus Orchidaceae. However, an assembled high-quality genome species in this lacking. Here, we report a chromosome-scale reference chrysotoxum, important ornamental and medicinal orchid species. The size D. chrysotoxum was 1.37 Gb, with contig N50 value 1.54 Mb. Of sequences, 95.75% were anchored to 19 pseudochromosomes. There 30,044 genes predicted genome. Two whole-genome polyploidization events occurred chrysotoxum. In terms event, duplication (WGD) also found have other members, which diverged mainly via gene loss immediately after WGD event occurred; first most monocots (tau event). We identified sugar transporter (SWEET) expansion, might be related abundant compounds fleshy stems MADS-box as well members TPS Hsp90 families, are associated resistance, may contribute adaptive evolution orchids. investigated interplay among carotenoid, ABA, ethylene biosynthesis elucidate regulatory mechanisms short flowering period orchids yellow flowers. will provide insights for further research on active ingredients breeding enhances understanding evolution.

Language: Английский

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A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics

Horticulture Research, Journal Year: 2021, Volume and Issue: 8(1)

Published: June 18, 2021

Abstract Rosa rugosa , commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with mild fragrance and colorful seed pods. Unlike many other cultivated roses, R. adapts to wide range of habitat types harsh environmental conditions such salinity, alkaline, shade, drought, high humidity, frigid temperatures. Here, we produced analyzed high-quality genome sequence for understand its ecology, floral characteristics evolution. PacBio HiFi reads were initially used construct the draft then Hi-C sequencing was applied assemble contigs into 7 chromosomes. We obtained 382.6 Mb encoding 39,704 protein-coding genes. The appears be conserved no additional whole-genome duplication after gamma triplication (WGT), which occurred ~100 million years ago in ancestor core eudicots. Based on comparative analysis assembly Rosaceae genomes, found unique large inverted segment Chinese rose chinensis retroposition strawberry caused by post-WGT events. also that development- stress response signaling-related gene modules retained WGT. Two MADS-box genes involved development stress-related transcription factors DREB2A-INTERACTING PROTEIN 2 ( DRIP2 ) PEPTIDE TRANSPORTER 3 PTR3 positively selected evolution, may have contributed ability this plant adapt environments. In summary, provides map genetic studies molecular breeding enables genomic near future.

Language: Английский

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Roles of Auxin in the Growth, Development, and Stress Tolerance of Horticultural Plants

Cells, Journal Year: 2022, Volume and Issue: 11(17), P. 2761 - 2761

Published: Sept. 5, 2022

Auxin, a plant hormone, regulates virtually every aspect of growth and development. Many current studies on auxin focus the model Arabidopsis thaliana, or field crops, such as rice wheat. There are relatively few what role plays in various physiological processes range horticultural plants. In this paper, recent growth, development, stress response reviewed to provide novel insights for researchers cultivators improve quality application crops.

Language: Английский

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Melatonin: Biosynthesis, content, and function in horticultural plants and potential application

Scientia Horticulturae, Journal Year: 2021, Volume and Issue: 288, P. 110392 - 110392

Published: July 10, 2021

Language: Английский

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The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Abstract Background Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava a highly heterozygous with repetitive difficult-to-assemble genome. Findings Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, combination the assembler hifiasm, produced genome assemblies at near complete haplotype resolution higher continuity accuracy compared to conventional long reads. We present 2 chromosome-scale haploid genomes phased Hi-C technology for diploid African variety TME204. With consensus >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, 35k gene loci, it most accurate, continuous, complete, haplotype-resolved assembly so far. Ab initio prediction RNA-seq data Iso-Seq transcripts identified abundant novel enriched functionality related chromatin organization, meristem development, cell responses. During tissue differentially expressed different origins were functionality. In each tissue, 20–30% showed allele-specific expression (ASE) differences. ASE bias was often specific inconsistent across tissues. Direction-shifting observed <2% transcripts. Despite high synteny, HiFi revealed extensive chromosome rearrangements intra-genomic inter-genomic divergent sequences, large structural variations mostly LTR retrotransposons. use reference-quality build pan-genome its importance representing genetic diversity downstream reference-guided omics analysis breeding. Conclusions The annotated pairs allow systematic view organization improved accuracy, completeness, resolution. They will be valuable resource research. Our study may also provide insights into developing cost-effective efficient strategies resolving complex resolution, continuity.

Language: Английский

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Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance surging drug prices etc., harnessing healing power plants gifted from mother nature is more urgent than ever helping us survive future sustainable way. PNP research efforts pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- inter-disciplinary approaches integrating interrogating all accessible data genomics, metabolomics, structural biology, chemical informatics necessary to accelerate full characterization biosynthetic regulatory circuitry producing PNPs plants. In this review, attempt provide brief update current focusing how different state-of-the-art biotechnologies facilitate their discovery, molecular basis biosynthesis, as well synthetic biology. Finally, humbly foresight trend understanding biology coming decades.

Language: Английский

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TheChrysanthemum lavandulifoliumgenome and the molecular mechanism underlying diverse capitulum types

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Abstract Cultivated chrysanthemum (Chrysanthemum × morifolium Ramat.) is a beloved ornamental crop due to the diverse capitula types among varieties, but molecular mechanism of capitulum development remains unclear. Here, we report 2.60 Gb chromosome-scale reference genome C. lavandulifolium, wild Chrysanthemum species found in China, Korea and Japan. The evolutionary analysis revealed that only recent tandem duplications occurred lavandulifolium after shared whole triplication (WGT) Asteraceae. Based on transcriptomic profiling six important developmental stages radiate genes MADS-box, TCP, NAC LOB gene families were involved disc ray floret primordia differentiation. Notably, NAM LOB30 homologs specifically expressed capitulum, suggesting their pivotal roles genetic network differentiation chrysanthemum. present study not provides high-quality also insight into underlying

Language: Английский

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Bioinformatics and Functional Genomics

Springer eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 243 - 271

Published: Jan. 1, 2024

Language: Английский

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The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

Genome Biology and Evolution, Journal Year: 2020, Volume and Issue: 13(2)

Published: Oct. 13, 2020

Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome vary remarkably among eukaryotes at all levels taxonomic resolution. Changes in regularly serve as indication major events, notably polyploidy and dysploidy. Here, we review recent advancements our ability make inferences regarding historical events that led alterations number chromosomes We first mechanistic processes underlying changes numbers, focusing on structural chromosomal rearrangements. Then, focus experimental procedures, encompassing comparative cytogenomics genomics approaches, computational methodologies are based explicit models chromosome-number evolution. Together, these tools offer valuable predictions changed genome structures, well their temporal placements.

Language: Английский

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