Comprehensive genomic resources and analysis for avocado research
The species overview provides detailed information about the avocado species, including the common name, vernacular name, botanical name, species description, external morphology image, cross-references with NCBI, and its taxonomical classification. The species description extensively covers:
We analyzed 299 transcriptome datasets from 13 projects using our self-encapsulated transcriptome analysis workflow.
Projects with controlled experiments (7): Expression level results with corresponding heatmaps and volcano plots. View differential analysis →
Projects without controlled experiments (6): Expression level results. View non-differential analysis →
Terpenoids are specialized metabolites encompassing over 65,000 structures, making them the largest known class of plant natural products. Plants rely on terpenoids for pathogen and herbivore defense, signaling, and pollinator attraction.
Terpene synthases (TPSs) catalyze the formation of terpene backbones and are classified into eight subfamilies (a-h) based on phylogenetic relationships.
We identified 93 TPS genes in avocado, determined their chromosomal locations, and conducted preliminary analyses.
We conducted GO and KEGG enrichment analysis on the identified TPS family genes, annotated them using eggNOG-mapper, and visualized the results using TBtools.
In addition to the TPS gene family, we expanded our analysis to include KO enrichment analyses for all genes in the dataset.
Using RIdeogram (Hao et al., 2020), we created visual models of chromosome distributions for:
The visualization shows gene density distribution on each chromosome, with direct links to JBrowse for detailed exploration.
Key findings: Our T2T assembly revealed differences in chromosome density compared to NCBI reference genomes, particularly on chromosomes 1, 3, 8 and 12, with nearly 500 additional genes identified.
Explore chromosome visualizations →
Reference:
Nath, O., Fletcher, S. J., Hayward, A., Shaw, L. M., Masouleh, A. K.,
Furtado, A., Henry, R. J., & Mitter, N. (2022).
A haplotype resolved chromosomal level avocado genome allows analysis
of novel avocado genes. Horticulture Research.
Reference:
Hao, Z., Lv, D., Ge, Y., Shi, J., Weijers, D., Yu, G., & Chen, J. (2020). RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ. Computer science, 6, e251.
We conducted comprehensive GO and KEGG enrichment analysis on the TPS gene family:
Additionally, we performed KO enrichment analysis across all genes in the dataset.
