Ontology highlight
ABSTRACT:
PROVIDER: PRJNA763547 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR14191093_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:Bidens hawaiensis genome assembly with High-Fidelity Sequences
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Project description:<p><strong>BACKGROUND:</strong> Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value.</p><p><strong>FINDINGS:</strong> Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2 and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified.</p><p><strong>CONCLUSIONS:</strong> Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.</p>
2022-05-18 | MTBLS3657 | MetaboLights
Project description:<p> The casuarina moth (Lymantria xylina) is a notorious forestry pest, posing severe ecological and economic threats due to its destructive defoliation outbreaks and high invasive potential. Despite its significance, a high-quality reference genome has been lacking, limiting molecular-level investigations into its biology and hindering the development of effective pest management strategies. In this study, we report the first chromosome-level genome assembly of L. xylina generated through a combination of illumina short-reads, Oxford Nanopore long-reads, and Hi-C scaffolding. The final assembly spans 977.74 Mb, with 95.17% anchored to 31 pseudo-chromosomes, achieving a scaffold N50 of 34.15 Mb. Importantly, telomeric sequences were identified at both ends of all 31 pseudo-chromosomes, underscoring the exceptional quality and completeness of this reference genome. Quality assessment further revealed a BUSCO completeness of 94.5% and a consensus QV of 31.72. We also annotated 18,484 protein-coding genes, 95.21% of which were functionally assigned, and characterized genome-wide repetitive elements (77.18%).</p><p> Beyond the genome assembly, we generated comprehensive RNA-seq and metabolomic datasets across multiple diapause stages, enabling insights into gene expression dynamics and metabolic regulation during egg development. Together, these resources provide a valuable foundation for studying the genetic basis of host adaptation, invasiveness, and interactions with natural enemies such as nucleopolyhedrovirus and Beauveria bassiana.</p>
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Project description:Identifying non-coding regulatory elements in the genome poses a challenge in most organisms. Classical methods rely on trial and error to test the regulatory activities of DNA fragments using reporter constructs. In large eukaryotic genomes, where cis-regulatory elements can spread over long distances, separated by large stretches of non-functional DNA, this trial and error approach is particularly challenging. Here, we generate two types of resources that can be used to narrow the search for such cis-regulatory elements in the 3.6 Gbp genome of Parhyale hawaiensis (comparable in size to the human genome). First, we use bulk ATACseq to uncover genome-wide patterns of chromatin accessibility in embryonic and adult tissues of Parhyale (whole embryos and legs), and single-nucleus ATACseq to identify regions of open chromatin in diverse cell types recovered from adult legs, including epidermal, neuronal, muscle and blood cells. Second, by sequencing the genomes of three congeneric species of Parhyale hawaiensis – P. darvishi, P. aquilina and P. plumicornis – we identify islands of sequence conservation across the genome, corresponding to DNA elements that are functionally constrained during evolution. We present an approach by which low-coverage (10-15x) short-read genome sequencing, without genome assembly, is sufficient to provide reliable maps of sequence conservation. This approach cuts the cost and labour required to generate these maps, making the identification of cis-regulatory elements more widely accessible. We demonstrate the utility of these resources by identifying cis-regulatory elements that drive robust expression of fluorescent reporters ubiquitously and in specific cell types.
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