Annals of Botany, Journal Year: 2023, Volume and Issue: 132(1), P. 15 - 28
Published: Jan. 31, 2023
Species of the genus Buddleja in Asia are mainly distributed Sino-Himalayan region and form a challenging taxonomic group, with extensive hybridization polyploidization. A phylogenetic approach to unravelling history reticulation this lineage will deepen our understanding speciation biodiversity hotspots.
Language: Английский
Horticulture Research, Journal Year: 2023, Volume and Issue: 10(1)
Published: Jan. 1, 2023
Abstract Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is complex octoploid with high heterozygosity at most loci. However, there no research on haplotype of genome. Here we aimed obtain high-quality genome cultivated cultivar, “Yanli”, using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The “Yanli” was 823 Mb in size, long terminal repeat assembly index 14.99. phased into two haplotypes, Hap1 (825 contig N50 26.70 Mb) Hap2 (808 27.51 Mb). Using combination Hap2, obtained for first time haplotype-resolved 56 chromosomes strawberry. We identified ~ 10 inversion translocation 2-1. 104 957 102 356 protein-coding genes were annotated respectively. Analysis related anthocyanin biosynthesis pathway revealed structural diversity complexity expression alleles F. ananassa In summary, ananassa, which will provide foundation investigating gene function evolution
Language: Английский
Citations
39
Nature Plants, Journal Year: 2023, Volume and Issue: 9(8), P. 1252 - 1266
Published: Aug. 3, 2023
Language: Английский
Citations
24
Science Advances, Journal Year: 2024, Volume and Issue: 10(6)
Published: Feb. 7, 2024
Butylphthalide is one of the first-line drugs for ischemic stroke therapy, while no biosynthetic enzyme butylphthalide has been reported. Here, we present a haplotype-resolved genome
Language: Английский
Citations
13
Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 64(8), P. 1487 - 1501
Published: June 24, 2022
Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide de novo chromosome-level genome sequence the cultivar "Qiu Jinxing." We assembled 823.41 Mb encoding 40 571 genes further anchored 779.24 into 17 pseudo-chromosomes, which account 94.64% genome. Phylogenomic analyses revealed that cultivated diverged from other species within Maleae (apple tribe) at approximately 35.4 Mya. Notably, involved flavonoid triterpenoid biosynthetic pathways have been significantly amplified In addition, our results indicated share unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected hawthorn. The amplification non-specific terminal repeat retrotransposons contributed most to expansion Furthermore, identified two paleo-sub-genomes extant found these sub-genomes showed different rearrangement mechanisms. also reconstructed ancestral chromosomes Rosaceae discussed possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) Maleae. Overall, study provides improved context understanding evolution species, this new high-quality reference useful resource horticultural improvement
Language: Английский
Citations
31
Horticulture Research, Journal Year: 2023, Volume and Issue: 10(7)
Published: May 10, 2023
Sour cherry (
Language: Английский
Citations
23
Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)
Published: April 19, 2023
Language: Английский
Citations
19
Horticulture Research, Journal Year: 2024, Volume and Issue: 11(6)
Published: April 9, 2024
Ginseng (Panax ginseng) is a representative of Chinese traditional medicine, also used worldwide, while the triterpene saponin ginsenoside most important effective compound within it. an allotetraploid, with complex genetic background, making study its metabolic evolution challenging. In this study, we assembled telomere-to-telomere ginseng reference genome, constructed 3.45 Gb 24 chromosomes and 77 266 protein-coding genes. Additionally, genome was divided into two subgenomes, designated as subgenome A B. Subgenome contains larger number genes, whereas B has general expression advantage, suggesting that subgenomes experienced asymmetric gene loss biased expression. The separated approximately 6.07 million years ago, shows closest relation to Panax vietnamensis var. fuscidiscus. Comparative genomics revealed expansion families associated biosynthesis in both subgenomes. Furthermore, tandem duplications proximal play crucial roles biosynthesis. We screened functional genes identified previous research found some these located colinear regions between have divergence functions, revealing unbalanced pathway ginseng. Our work provides resources for future studies breeding programs ginseng, well ginsenosides.
Language: Английский
Citations
9
BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)
Published: April 23, 2024
Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, comprehensive genetic pool encompassing all variations within species, serves as an invaluable tool, unaffected by confounding factors intraspecific diversity. This allows for more nuanced exploration TE evolution.
Language: Английский
Citations
9
Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)
Published: Aug. 17, 2024
Biological invasions pose a significant threat to ecosystems, disrupting local biodiversity and ecosystem functions. The genomic underpinnings of invasiveness, however, are still largely unknown, making it difficult predict manage invasive species effectively. common reed (Phragmites australis) is dominant grass in wetland ecosystems has become particularly when transferred from Europe North America. Here, we present high-quality gap-free, telomere-to-telomere genome assembly Phragmites australis consisting 24 pseudochromosomes B chromosome. Fully phased subgenomes demonstrated considerable subgenome dominance revealed the divergence diploid progenitors approximately 30.9 million years ago. Comparative genomics using chromosome-level scaffolds for three other lineages previously published draft an lineage that gene family expansions form tandem duplications may have contributed invasiveness lineage. This study sheds light on evolution Arundinoideae grasses suggests genetic drivers, such as duplications, underly processes biological invasion plants. These findings provide crucial step toward understanding managing basis plant species.
Language: Английский
Citations
8
Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)
Published: June 22, 2024
Synthetic hexaploid wheats (SHWs) are effective genetic resources for transferring agronomically important genes from wild relatives to common wheat (Triticum aestivum L.). Dozens of reference-quality pseudomolecule assemblies have been generated, but none is reported SHW-derived cultivars. Here, we generated a chromosome-scale assembly the cultivar 'Chuanmai 104' based on PacBio HiFi reads and chromosome conformation capture sequencing. The total size was 14.81 Gb with contig N50 length 58.25 Mb. A BUSCO analysis yielded completeness score 99.30%. In total, repetitive elements comprised 81.36% genome 122,554 high-confidence protein-coding gene models were predicted. summary, first chromosome-level presents promising outlook study utilization SHWs in improvement, which essential meet global food demand.
Language: Английский
Citations
7