Chromosome‐scale genome assembly of areca palm (<i>Areca catechu</i>)

Yang, Yaodong; Huang, Liyun; Xu, Chunyan; Lei, Qi; Wu, Zhangyan; Li, Jia; Chen, Haixin; Wu, Yi; Fu, Tao; Zhu, Haishan; Saand, Mumtaz Ali; Li, Jing; Liu, Liyun; Fan, Haikou; Zhou, Huanqi; Qin, Weiquan

doi:10.1111/1755-0998.13446

Cited by 25 publications

(28 citation statements)

References 108 publications

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“…However, we questioned whether there are other DOF genes of A. catechu that also participate in the regulation of abscission. Therefore, based on the A. catechu genome data [ 30 ], a total of 36 AcDOF genes were identified. For the AcDOF proteins, the amino acid length ranges from 189 to 518, the predicted molecular weight ranges from 20.61 kDa to 56.23 kDa, and the isoelectric point ranges from 5.16 to 9.41 ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

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Genome-Wide Identification of the DOF Gene Family Involved in Fruitlet Abscission in Areca catechu L.

Jia

Yang

et al. 2022

IJMS

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Fruitlet abscission frequently occurs in Areca catechu L. and causes considerable production loss. However, the inducement mechanism of fruitlet abscission remains mysterious. In this study, we observed that the cell architecture in the abscission zone (AZ) was distinct with surrounding tissues, and varied obviously before and after abscission. Transcriptome analysis of the “about-to-abscise” and “non-abscised” AZs were performed in A. catechu, and the genes encoding the plant-specific DOF (DNA-binding with one finger) transcription factors showed a uniform up-regulation in AZ, suggesting a role of the DOF transcription in A. catechu fruitlet abscission. In total, 36 members of the DOF gene family distributed in 13 chromosomes were identified from the A. catechu genome. The 36 AcDOF genes were classified into nine subgroups based on phylogenic analysis. Six of them showed an AZ-specific expression pattern, and their expression levels varied according to the abscission process. In total, nine types of phytohormone response cis-elements and five types of abiotic stress related cis-elements were identified in the promoter regions of the AcDOF genes. In addition, histochemical staining showed that lignin accumulation of vascular bundles in AZ was significantly lower than that in pedicel and mesocarp, indicating the specific characteristics of the cell architecture in AZ. Our data suggests that the DOF transcription factors might play a role in fruitlet abscission regulation in A. catechu.

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Section: Resultsmentioning

confidence: 99%

“…Based on the recently released A. catechu genome database [ 30 ], a total of 36 AcDOF genes were identified ( Table 1 ). The numbers of the DOF gene family in diverse plant species are close to each other.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of the DOF Gene Family Involved in Fruitlet Abscission in Areca catechu L.

Jia

Yang

et al. 2022

IJMS

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“…Although the impact of new sequencing technologies is certainly evident, it has not been possible to assemble a gap-free genome from telomere to telomere only by shortread sequencing. In more recent genome sequencing projects with high-quality published genomes [36][37][38][39][40][41], the scaffolding of long-read assemblies was complemented with high-throughput long-range data, such as optical maps (BioNano Genomics, San Diego, CA, USA [42,43]), chromosomal conformation sequencing (Hi-C with in vivo fixation of chromosomes [44,45]), or linked-reads sequencing (10× Genomics, 10× Genomics, Inc., Pleasanton, US [46]). Long-range mapping data and long-read sequencing allow haplotype/subgenome-phasing of several tree genomes [47][48][49], solving, to a certain extent, challenges in the complete assembly of highly heterozygous and complex genomes.…”

Section: Approaches For Sequencing Of the Large And Heterozygous Tree...mentioning

confidence: 99%

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

Cao

Gailing

2022

IJMS

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Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.

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“…This study reveals the molecular basis of the accumulated indole alkaloids of S. cusia . Yang et al (2021a) presented a reference chromosome level genome of Areca catechu by Illumina and PacBio data. The assembled genome was 2.51 Gb with a N50 scaffold size of 1.7 Mb and predicted 31,571 protein-coding genes.…”

Section: Application Of High Throughput Sequencing In Bioactive Compo...mentioning

confidence: 99%

Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds

Liu

Gong²,

Liu³

et al. 2022

Front. Plant Sci.

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The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.

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Chromosome‐scale genome assembly of areca palm (Areca catechu)

Cited by 25 publications

References 108 publications

Genome-Wide Identification of the DOF Gene Family Involved in Fruitlet Abscission in Areca catechu L.

Genome-Wide Identification of the DOF Gene Family Involved in Fruitlet Abscission in Areca catechu L.

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds

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