The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative

Tao, Wu; Ma, Ting; Xu, Tian; Li, Pan; Li, Yongjie; Ning, Delu

doi:10.3389/fgene.2022.868540

Cited by 2 publications

(2 citation statements)

References 72 publications

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“…‘Picual’ is the most cultivated variety in the world, responsible for approximately 25% of the production of olive oil worldwide, and ‘Arbequina’ is of special interest because of its lower vigor, which allows mechanized harvesting and dense planting for intensive agriculture. Moreover, in 2022, the genomes of two olive trees of the subspecies cuspidata were sequenced because of their usability as rootstock with better disease resistance, and adaptation to East Asian climate [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

OliveAtlas: A Gene Expression Atlas Tool for Olea europaea

Bullones

Castro

Lima-Cabello

et al. 2023

Plants

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The olive (Olea europaea L.) is an ancient crop of great importance in the Mediterranean basin due to the production of olive oil and table olives, which are important sources of fat and have benefits for human health. This crop is expanding and increasing its production worldwide and five olive genomes have recently been sequenced, representing a wild olive and important cultivars in terms of olive oil production, intensive agriculture, and adaptation to the East Asian climate. However, few bioinformatic and genomic resources are available to assist olive research and breeding, and there are no platforms to query olive gene expression data. Here, we present OliveAtlas, an interactive gene expression atlas for olive with multiple bioinformatics tools and visualization methods, enabling multiple gene comparison, replicate inspection, gene set enrichment, and data downloading. It contains 70 RNA-seq experiments, organized in 10 data sets representing the main olive plant organs, the pollen germination and pollen tube elongation process, and the response to a collection of biotic and abiotic stresses, among other experimental conditions. OliveAtlas is a web tool based on easyGDB with expression data based on the ‘Picual’ genome reference and gene annotation.

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Section: Introductionmentioning

confidence: 99%

OliveAtlas: A Gene Expression Atlas Tool for Olea europaea

Bullones

Castro

Lima-Cabello

et al. 2023

Plants

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“…Three years later, also using the PacBio long-read and NGS data, the reference of the Indian rhesus macaque (Mmul_10) was improved significantly (~120-fold) in sequence contiguity (46Mb of contig N50) relative to rheMac8 [19]. In recent years, another big step forward for de novo genome assembly comes from the development of the Nanopore long-read sequencing with its cost-effective advantage [36,37], which improved the genome references for multiple species, such as humans [38][39][40][41], mammals [42][43][44], birds [45,46], plants [47][48][49], fishes [50,51], fruit flies [52], etc. However, there is still no nanopore derived reference assembly and related analyses (such as methylation, recombination rate, etc.)…”

Section: Introductionmentioning

confidence: 99%

The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations

Chen

Zhong

et al. 2022

Preprint

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Rhesus macaques (Macaca mulatta) are the most extensively studied nonhuman primate species for human biomedical modeling. However, little is known about the biological pattern of genome-wide structural variations (SVs) and the evolutionary forces underlying SVs. Here, we conducted genomic sequencing and analyses based on Nanopore long reads and Illumina short reads technology. We called SVs between the two subspecies (China vs. India), using three methods of assembly-based and long-reads-based algorithms. Interestingly, we found significantly more SVs in X-chromosome than in autosomes, consistent with the expectation of the faster-X divergence at the subspecies level. With the fine-scale methylation frequencies and recombination rates, we found duplications with significantly lower methylation frequencies while higher recombination rates than other types of SVs, suggesting a higher level of transcriptional and evolutionary potential for duplications than for other SVs types. A genome-wide scan of selective sweep revealed that over 3% of SVs are under positive selection. Moreover, X chromosome showed significantly higher number of positively selected SVs than do autosomes, suggesting the “faster-X effect” of SVs. Our study revealed a different evolutionary importance for duplications compared with other SVs forms. We also revealed the “faster-X effect” of SVs, which could provide raw material upon which positive selection can further play.

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The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative

Cited by 2 publications

References 72 publications

OliveAtlas: A Gene Expression Atlas Tool for Olea europaea

OliveAtlas: A Gene Expression Atlas Tool for Olea europaea

The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations

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