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 the tree morphology, leaves and flowers, fruit and other organ morphology, native habitat, current suitable cultivation areas, as well as its partial nutritional and economic value.
RNA-seq analysis results
We used the self-encapsulated transcriptome analysis workflow to analyze the 299 transcriptome data collected for a total of 13 projects. Among them, 7 projects (Click here to go to the corresponding page) with controlled experiments were provided with expression level results and corresponding heat maps and volcano maps, and 6 projects (Click here to go to the corresponding page) without controlled experiments were provided with expression level results.
TPS(Terpene synthase) gene family
Terpenoids are a class of specialized metabolites. Plant terpenoids are incredibly diverse and encompass over 65,000 structures40, making them the largest known class of plant natural products. Plants rely on terpenoids for many interactions, including pathogen and herbivore defense,signaling, and pollinator attraction. Terpene synthases (TPSs) catalyze the formation of terpene backbones from diphosphate isoprenoid precursors and are classified into eight subfamilies (a-h) based on their phylogenetic relationships . Here we identified the TPS gene family of avocado, and identified 93 genes belonging to the TPS family. We determined the chromosomal location and briefly analyzed them, and provided the preview and download of the results.
Due to the importance of TPS gene family in plants, we conducted GO and KEGG enrichment analysis on the above identified TPS family genes, annotated them using egggnog-mapper, and further processed, analyzed and visualized the annotation results using TBtools. Results are also available for preview and download. In addition to our focus on the TPS gene family, we have expanded our analysis to include KO enrichment analyses for all other genes in the dataset, and these results are also available for download.
We used a RIdeogram (a convenient R package) to create a visual model of the avocado chromosome distribution. While visualizing the twelve chromosomes of avocado, it shows the distribution of genes on each chromosome (gene density), which is convenient for users to more intuitively view the distribution area and density of genes on chromosomes. In addition, each chromosome is also linked with the 12 chromosome visualization of JBrowse browser, supporting users to jump to the corresponding chromosome JBrowse browser visualization needs by clicking on each chromosome. By the way, the chromosome diagrams of two model species, P. trichocarpa and A. thaliana, were simultaneously drawn, which had the same jump function as that of avocado. It is worth noting that there are some differences in chromosome density between the chromosome map we drew based on T2T assembly and that drawn by NCBI reference genome (Onkar Nath et al.), which are specifically reflected in the extremely high density regions on chromosomes 1, 3, 8 and 12. Compared with the results obtained by Onkar Nath et al. By increasing the number of genes by nearly 500, several more brightly colored spots are visible on the gene density map.
KEGG/GO Enrich Analysis results
Due to the importance of TPS gene family in plants, we conducted GO and KEGG enrichment analysis on the above identified TPS family genes, eggNOG-mapper was used for annotation, TBtools was used for further processing, analysis and visualization of annotation results, and results preview and download were provided. In addition to our focused effort on the TPS gene family, we expanded our analysis to include KO enrichment analysis across all other genes in the dataset, and these results are likewise accessible for download.
