A haplotype-resolved genome of an AAB allotriploid cultivated mulberry

About TWCG

Morus laevigataLong-fruited mulberry Morus albaWhite mulberry TWCGAAB triploid

Origin: an AAB triploid

TWCG is a seedless triploid arising from an interspecific cross between long-fruited mulberry (Morus laevigata) and white mulberry (M. alba). Of its three haplotypes, HapA1 and HapA2 derive from M. laevigata, while HapB derives from M. alba.

Superpower: complete immunity

TWCG is fully immune to the necrotrophic fungus Ciboria shiraiana, the causal agent of hypertrophic sorosis sclerote disease (HSS). Dissecting this immunity offers new strategies for molecular breeding of crops resistant to necrotrophic fungi.

Value: food and medicine

Mulberry fruit is rich in anthocyanins, rutin, resveratrol and polysaccharides, and is regarded as one of the outstanding functional fruits of the 21st century. Fruit-use mulberry still covers only 5–9% of mulberry acreage in China, with disease being the main barrier to expansion.

Taiwan Changguosang (TWCG) long mulberry bearing healthy elongated fruits on the tree
"Taiwan Changguosang" (TWCG, AAB allotriploid) — healthy elongated fruits on the tree. This variety is fully immune to Ciboria shiraiana.
White mulberry (Morus alba) fruits showing hypertrophic sorosis sclerote disease after Ciboria shiraiana infection
White mulberry (Morus alba) — fruits showing typical hypertrophic sorosis sclerote (HSS) symptoms after Ciboria shiraiana infection.

Genome Overview

A highly contiguous, highly complete, gap-free haplotype-resolved assembly.

Tool Center

Browse, align, search and profile the TWCG haplotype-resolved genome, and predict effectors from fungal secretomes. Each tool opens with a link back to this page.

Gene Search
TWCG Annotation API
Look up genes by ID or functional keyword (product / GO / KEGG) and inspect their annotation.
Open tool
BLAST
SequenceServer
Run sequence similarity searches against TWCG genomes, CDS and protein sets, plus Botrytis cinerea B05.10 and Sclerotinia sclerotiorum 1980 proteomes.
Open tool
HMMER
HMMER 3.4 · Pfam-A
Search homologs (phmmer), annotate protein domains (hmmscan) or mine gene families (hmmsearch) across TWCG, C. shiraiana, B. cinerea, S. sclerotiorum and related proteomes.
Open tool
MSA Viewer
In-browser progressive alignment · BLOSUM62
Align 2–30 protein sequences and visualize conserved columns, conservation bars and pairwise identity. Runs entirely in your browser.
Open tool
Phylogenetic Tree
MAFFT · trimAl · IQ-TREE2
Build a maximum-likelihood tree from FASTA sequences or a list of TWCG gene IDs. ModelFinder picks the substitution model and ultrafast bootstrap reports branch support.
Open tool
Structural Alignment
AlphaFold DB · Kabsch superposition
Superpose two protein structures — paste PDB coordinates or give a UniProt accession — and read RMSD, TM-score, sequence identity and per-residue deviations.
Open tool
PPI Prediction
Evidence fusion · AF3 / ColabFold · TWCG × Cs
Rank TWCG interaction candidates from four lines of local evidence, or model a cross-species pair (TWCG × Cs) directly — package either for AlphaFold3 Server or ColabFold and read the returned ipTM / pTM / PAE.
Open tool
Effector Pipeline
SignalP 6.0 → TMHMM → TargetP → GPI → EffectorP 3.0
Run the published five-stage funnel on raw protein sequences, or skip straight to EffectorP 3.0 (fungal or oomycete model) when you already have a secretome — every protein reported with the stage that removed it, or its apoplastic / cytoplasmic call.
Open tool
DeepEffector
Protein language model · ProtT5 / esm1b
Score fungal or oomycete proteins with a protein-language-model classifier (accuracy 0.987 on the fungal test set), computed on the authors' server.
Open tool
Genome Browser
JBrowse 2
Interactively browse the three TWCG haplotypes, gene models and variant sites.
Open tool
Expression Atlas
RNA-seq TPM matrix
Profile TPM across 10 samples: stem, leaf, bud and seven fruit stages F1–F7.
Open tool
Functional Enrichment
clusterProfiler · GO & KEGG
Test a gene list for over-represented GO terms (BP / MF / CC) and KEGG pathways, with fold-enrichment, corrected p-values and the intersecting genes.
Open tool
Debugging
KEGG Pathway
KEGG Orthology · maps drawn locally
Browse KEGG pathways across the three TWCG haplotypes, and draw any map locally from KEGG coordinates — coloured by KO presence or by expression.
Open tool
Hormone Network
Literature-anchored · KEGG KO & Pfam
Explore crosstalk among the nine plant hormone pathways, the KEGG branch reactions, the transport proteins and the direct protein–protein interactions — every node anchored to real TWCG annotation, every gap declared.
Open tool
Defense Pathways
Literature-anchored · PTI / ETI / SA–JA
Explore six plant immune pathways — PTI, MAPK cascades, ETI & NLR, SA, SA–JA crosstalk and the Sclerotinia/Ciboria spotlight — with TWCG haplotype homologs and female-flower infection expression on every node.
Open tool

Plant Immunity AI Q&A

Ask in Chinese or English and get answers grounded in 4,397 full-text papers on plant immunity and plant–pathogen interactions. Every claim carries a numbered citation with a DOI link to the original article.

Research Team & Data Availability

The genome was produced by the State Key Laboratory of Resource Insects, Southwest University and collaborating groups.

Authors (#equal contribution)

Wei Fan#, Yuane Chen#, Mengxia Xu#, Zhongqiang Xia, Chengli Zhou, Caiquan Tao, Zhennan Li, Duanyang Liu, Xiaohui Gu, Xiling Wang, Zhiguang Song, Zhengang Li, Aichun Zhao*

* Corresponding author: zhaoaichun@hotmail.com · zhaoaichun@swu.edu.cn

Affiliations

  • State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
  • Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
  • Institute of Sericulture and Apiculture, Yunnan Academy of Agricultural Sciences, Mengzi, China
  • Chongqing Sericulture Science and Technology Research Institute, Chongqing, China

Fan W, Chen Y, Xu M, et al. AAB allotriploid cultivated mulberry genome, Disease resistance.