Scholarlink

Background <p>Avocado (<i>Persea americana</i>) is an economically important fruit with growing global production. While multiple genome assemblies and transcriptomic datasets are publicly available—including the dedicated platform AvoBase—these resources remain fragmented and lack integration with pre‑computed multi‑omics analyses and reproducible workflows.</p> Results <p>We present the <i>Persea americana</i> Genome Database (PAGD; <a href="http://bioinfor.kib.ac.cn/">http://bioinfor.kib.ac.cn/</a>), an integrated platform consolidating two high‑quality genome assemblies (Hass chromosome‑level and West Indian telomere‑to‑telomere). It also hosts RNA‑seq datasets from 13 NCBI BioProjects, each linked to detailed biosample metadata, all uniformly re‑processed. Pre‑computed results include gene family classification (68 TPS genes), collinearity, gene density, and expression profiles. PAGD offers BLAST, JBrowse, interactive heatmaps, and data download. Additionally, we developed three Docker‑encapsulated Snakemake workflows for reference‑based and reference‑free transcriptome analysis, eliminating manual software configuration.</p> Conclusion <p>PAGD advances existing avocado genomic resources by integrating multi‑omics data with pre‑computed analyses and a reproducible transcriptome workflow. The encapsulated workflows lower the technical barrier for RNA‑seq analysis, are adaptable to other plant species, and support functional genomics, breeding, and comparative studies.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

PAGD: the Persea americana Genome Database and a Docker-based transcriptome analysis workflow

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年6月1日

查看全文
  • Siyi Ma,
  • Huadong Feng,
  • Danni Yang,
  • Zhenzhen Wu,
  • Ruiyuan Li,
  • Xin Geng,
  • Chenyi Shi,
  • Shimeng Liu,
  • Yunqiang Yang,
  • Chengjun Zhang

摘要

Background

Avocado (Persea americana) is an economically important fruit with growing global production. While multiple genome assemblies and transcriptomic datasets are publicly available—including the dedicated platform AvoBase—these resources remain fragmented and lack integration with pre‑computed multi‑omics analyses and reproducible workflows.

Results

We present the Persea americana Genome Database (PAGD; http://bioinfor.kib.ac.cn/), an integrated platform consolidating two high‑quality genome assemblies (Hass chromosome‑level and West Indian telomere‑to‑telomere). It also hosts RNA‑seq datasets from 13 NCBI BioProjects, each linked to detailed biosample metadata, all uniformly re‑processed. Pre‑computed results include gene family classification (68 TPS genes), collinearity, gene density, and expression profiles. PAGD offers BLAST, JBrowse, interactive heatmaps, and data download. Additionally, we developed three Docker‑encapsulated Snakemake workflows for reference‑based and reference‑free transcriptome analysis, eliminating manual software configuration.

Conclusion

PAGD advances existing avocado genomic resources by integrating multi‑omics data with pre‑computed analyses and a reproducible transcriptome workflow. The encapsulated workflows lower the technical barrier for RNA‑seq analysis, are adaptable to other plant species, and support functional genomics, breeding, and comparative studies.