Chromosome-Level Genome Assembly of the Hemiparasitic <i>Taxillus chinensis</i> (DC.) Danser

Fu, Jine; Wan, Lingyun; Song, Lina; He, Lili; Jiang, Ni; Long, Hairong; Huo, Juan; Ji, Xiaowen; Hu, Fengyun; Wei, Shugen; Pan, Limei

doi:10.1093/gbe/evac060

Cited by 4 publications

(1 citation statement)

References 46 publications

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“…Genomic DNA was extracted from the fresh leaf tissue (200 mg) that had been ground in liquid nitrogen using cetyltrimethylammonium bromide buffer (60-minute incubation at 65°C), followed by phenol/chloroform/isoamyl purification (25:24:1) and isopropanol and ethanol precipitation. The resulting purified DNA was resuspended in Tris-EDTA buffer for subsequent sequencing [ 40 ]. Total RNA was extracted from the fresh samples of roots, stems, leaves, flowers, and fruits according the instructions of RNAprep Pure Plant Plus Kit (DP441, Tiangen, China).…”

Section: Methodsmentioning

confidence: 99%

The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family

et al. 2022

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Background The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. Findings We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28%, and transposable element sequences accounted for 43.98%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. Conclusions This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.

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Section: Methodsmentioning

confidence: 99%

The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family

et al. 2022

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Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta’s unconventional solution for its replacement

Fischer,

Jordbræk,

Olsen

et al. 2025

Molecular Phylogenetics and Evolution

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Recent developments in parasitic plant biology

Stanga

2022

CABI Reviews

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Parasitic plants are taxonomically diverse, globally distributed, and capable of parasitizing a wide array of host plants, often with preferences for specific hosts. Some parasitic plants are damaging pests of numerous crops; their effects can be especially detrimental in low-input agriculture. Effective breeding and management strategies rely on comprehensive information about the life history, evolution, genetics, biochemistry, physiology, communication, and ecology of parasitic plants and their hosts. High-throughput sequencing approaches are used to advance research in genome evolution, to identify genetic loci for breeding, to characterize microbial communities associated with parasitic plants, and to discover molecular mechanisms of parasitism and host responses. Molecular and biochemical investigations are elucidating the mechanisms by which parasitic seeds germinate in response to host phytohormones in the rhizosphere. Structural information guides synthesis- and screening-based methods to identify chemicals that could be used to promote or inhibit parasitic seed germination. Microbial communities in the rhizosphere influence parasitic plants and hosts as a system; fungal and bacterial species themselves, and products derived from them, have the potential for agronomic application. Proteins and nucleic acids exchanged through the haustorium reveal the complex interplay between parasitic plant pathogenesis and host defense responses. This review focuses on the latest developments published within the last two years.

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Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser

Cited by 4 publications

References 46 publications

The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family

The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family

Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta’s unconventional solution for its replacement

Recent developments in parasitic plant biology

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