Plant Genomics · Diploid to Polyploid

From 400 Mb rice to 17 Gb hexaploid wheat.

Plant genomes are the most structurally complex routinely sequenced: polyploidy, massive repeat content (up to 85%+ of some genomes), recent whole-genome duplications, and organellar genomes. Nucleome Informatics builds reference-grade and T2T-grade plant assemblies with the HiFi + Hi-C + ultra-long read strategies that produced the current generation of complete plant genomes.

Plan Your Project → Learn the Basics
Diploid & polyploid
strategies
HiFi + Hi-C + UL-ONT
stack
Subgenome phasing
for allopolyploids
Organellar genomes
included
About the Service

Plant Genome Sequencing at Nucleome Informatics

Plant genomics spans an enormous range: compact diploid genomes (rice ~400 Mb), mid-size diploids with heavy repeats (maize ~2.3 Gb, ~85% repeats), and allopolyploids carrying multiple subgenomes (bread wheat ~17 Gb, hexaploid; cotton, Brassica, potato, and many Indian crop species). Nucleome Informatics offers:

  • Chromosome-scale assembly with QC (QV, BUSCO, Merqury, contig N50, LAI repeat index)
  • Haplotype- or subgenome-resolved output (per ploidy and data)
  • Chloroplast and mitochondrial genomes (circularised, annotated)
  • Repeat landscape and gene prediction support (BRAKER/MAKER with RNA-seq evidence where available)
  • Resequencing deliverables: variant calls, diversity statistics, GWAS-ready genotypes
  • NCBI submission-ready files and publication-grade methods documentation

Why this approach

  • Each subgenome assembled separately
  • HiFi + Hi-C phasing
  • Organellar genomes included
Learning Path

From first principles to expert-level analysis

New here? Start with Foundations. Planning a study or reviewing results? Jump to Practitioner or Expert. Each level builds on the one before it, so you can read this page as a short course or dip in where you need to.

Start here if you are new to this service — six ideas that explain what it is and why it matters.

LEVEL 1

Why are plant genomes hard?

Three reasons: they are big (up to 17+ Gb), they are mostly repeats (up to 85%+), and many crop species are polyploids carrying two or more related subgenomes that assembly must not confuse.

LEVEL 1

What is a polyploid genome?

A genome with more than two complete chromosome sets — often from hybridisation plus genome doubling. Bread wheat has six sets (three subgenomes × two copies each). Each subgenome carries similar gene copies that must be assigned correctly.

LEVEL 1

What is subgenome phasing?

Assigning every sequence in the assembly to its parental subgenome (A, B, D in wheat) — essential for correct gene annotation and breeding applications.

LEVEL 1

What is Hi-C?

A method that captures physical contacts between chromosomes in the nucleus, used to scaffold contigs into chromosome-scale assemblies and to separate haplotypes/subgenomes.

LEVEL 1

What is a pan-genome?

The union of all gene content across a species' diversity panel — capturing the "accessory" genes absent from any single reference. Crop pan-genomes are transforming breeding genomics.

LEVEL 1

What do I provide?

High-quality HMW DNA from a single inbred/haploid individual (for the reference), plus germplasm samples for resequencing. We provide extraction protocols tuned for plant secondary metabolites.

For scientists planning a project or reading a report: how each step works and how it can mislead.

LEVEL 2

Genome scoping

Genome size (flow cytometry or k-mer estimation), ploidy, heterozygosity, and repeat content are assessed before sequencing — data volumes and strategy follow from these measurements.

LEVEL 2

The assembly stack

HiFi reads (Revio) for accuracy; Hi-C for scaffolding and phasing; ultra-long ONT where centromeres and rDNA demand it; hifiasm/Verkko assembly with polyploid-aware configuration.

LEVEL 2

Polyploid strategy

Allopolyploids: HiFi + Hi-C subgenome separation, with parental short reads (triad phasing) where available. Autopolyploids: the hardest case — haplotype resolution is limited by allele dosage; we scope feasibility honestly.

LEVEL 2

Annotation

Repeat annotation (RepeatModeler/RepeatMasker, LAI index), gene prediction with RNA-seq evidence (BRAKER/MAKER), and functional annotation — with gene-family analysis for polyploid expansion questions.

LEVEL 2

Resequencing and GWAS

Germplasm panels resequenced against the reference; variant calls feed diversity analysis, GWAS (GAPIT/TASSEL/FarmCPU with Q+K models), and marker-assisted selection pipelines.

LEVEL 2

Organellar genomes

Chloroplast genomes assemble cleanly; plant mitogenomes carry repeat-mediated rearrangements — we report structural heterogeneity honestly.

For study design: the decisions that determine whether the data answers your question.

LEVEL 3

Reference individual choice

Inbred, haploid, or doubled-haploid material dramatically simplifies assembly. Where only heterozygous material exists, haplotype-resolved output is the honest target.

LEVEL 3

T2T ambitions in plants

Complete (gapless) plant assemblies are achievable — recent years delivered complete rice, maize, and others — but depend on centromere architecture and data depth. We define per-chromosome targets at design stage.

LEVEL 3

Pan-genome programme design

Graph-based pangenomes (e.g. with the reference plus structural-variant panels) capture presence/absence variation that linear references miss — increasingly the standard for crop genomics.

LEVEL 3

Breeding integration

From GWAS hits to diagnostic markers (see our SNP Genotyping/GWAS page): the full discovery-to-selection pipeline under one roof, including custom Axiom array design for your programme.

LEVEL 3

Wild relatives and introgression

Wild-relative assemblies support introgression breeding and crop improvement; subgenome-aware comparison identifies introgressed segments precisely.

LEVEL 3

Data and submission

NCBI submission-ready assemblies, annotation, and raw data formatting, with full methods for publication.

Allopolyploid
a polyploid combining subgenomes from different parental species.
Subgenome
one of the parental chromosome sets in an allopolyploid.
LAI
landscape of long terminal repeat retrotransposon annotation index; a repeat-annotation quality metric.
Triad phasing
using parental sequencing data to phase an offspring assembly.
Pan-genome
the complete gene repertoire across a diversity panel.
Doubled haploid
a fully homozygous line produced by genome doubling of haploids.
The Science

How it works, in two figures

The current generation of complete plant genomes (rice, maize, wheat chromosome-scale assemblies) used HiFi + Hi-C + ultra-long read strategies with hifiasm; polyploid subgenome phasing methods are established in the crop genomics literature. See references below.

Figure 1 Polyploid assembly challenge. schematic
Collapsed polyploid assembly Subgenome-resolved assembly Subgenomes merged into a consensus Homeologous genes confused Repeats fragment the assembly Each subgenome assembled separately HiFi + Hi-C phasing Organellar genomes included
Figure 1 | Polyploid assembly challenge. (Illustrative schematic, not sample data.)
Figure 2 Workflow. schematic
Genome scoping HMW DNA HiFi + Hi-C (+ UL-ONT) Subgenome-aware assembly Repeat & gene annotation Resequencing / GWAS integration
Figure 2 | Workflow. (Illustrative schematic, not sample data.)
Technology Highlights

Built for the questions you are asking

The platforms, pipelines and standards behind this service.

PacBio HiFi for plant genomes

≥99.9% accurate 15–20+ kb reads resolve the tandem repeats and recent duplications that dominate plant genomes — the accuracy backbone of every modern plant assembly.

Hi-C scaffolding and phasing

Chromosome-scale scaffolding plus haplotype/subgenome phasing from proximity-ligation data — essential for polyploids.

Ultra-long ONT reads

PromethION reads spanning 50–100+ kb close the largest gaps in repeat-dense genomes (centromeres, rDNA arrays).

Subgenome-aware polyploid assembly

hifiasm with Hi-C integration separates and assembles each subgenome of allopolyploids — the strategy behind complete wheat, cotton, and Brassica assemblies.

Organellar genome assembly

Chloroplast and mitochondrial genomes assembled, circularised, and annotated — including the repeat-mediated heterogeneity of plant mitogenomes.

Germplasm resequencing and pangenomics

Short-read resequencing of diversity panels, pan-genome construction, and GWAS integration for breeding programmes. ---

Scope Note

What this service does and does not cover

Scope note. Assembly outcomes scale with genome size, repeat content, and ploidy: compact diploids routinely reach T2T-grade; large polyploids reach chromosome-scale reference grade with per-subgenome QC, and full gapless status depends on centromere architecture. Autopolyploid haplotype resolution is limited by allele dosage — feasibility is scoped honestly at design stage. Gene prediction without RNA-seq evidence is model-based; transcriptome support is recommended for publication-grade annotation.---
Why Nucleome

Service highlights

What you can expect from our team in Hyderabad.

Polyploid expertise

Subgenome-aware assembly strategies for wheat-level complexity.

The full stack in-house

HiFi, ultra-long ONT, Hi-C, and Illumina — no cross-vendor coordination.

Organellar genomes included

Chloroplast and mitochondrial genomes with every nuclear project.

Breeding pipeline integration

From reference assembly to GWAS to custom genotyping arrays.

Indian crop relevance

Experience with rice, wheat, pulses, millets, cotton, and spice genomes from Indian programmes.

NCBI-ready deliverables

Submission-formatted assemblies, annotation, and methods. ---

Questions

Frequently asked, in plain language

From the basics to the finer points of design and interpretation.

basicCan you assemble a polyploid genome?
Yes — subgenome-aware strategies (HiFi + Hi-C, with parental data where available) are our standard approach for allopolyploids.
basicWhat do you need from me?
HMW DNA from a suitable reference individual (inbred/haploid preferred), plus germplasm for resequencing if desired. We provide plant-specific extraction protocols.
basicDo you assemble chloroplast and mitochondrial genomes?
Yes — both are included with every nuclear genome project.
intermediateHow does subgenome phasing work?
HiFi reads plus Hi-C contact maps separate the subgenomes; parental sequencing (triad phasing) strengthens assignment where available. Per-subgenome QC is reported.
intermediateCan you resequence my germplasm panel afterwards?
Yes — short-read resequencing, variant calling, diversity analysis, and GWAS integration (GAPIT/TASSEL/FarmCPU) against your new reference.
intermediateIs a gapless (T2T) assembly possible for my crop?
For compact diploids, routinely. For large polyploids, chromosome-scale reference grade is the standard target, with per-chromosome gap status reported honestly.
advancedCan you build a pan-genome for my species?
Yes — reference assembly plus diversity-panel resequencing with pan-genome and structural-variant analysis; graph-based representations available.
advancedCan GWAS hits become breeding markers?
Yes — we convert associations into diagnostic marker sets, including custom Axiom array design (see our SNP Genotyping/GWAS page).
advancedHow do you handle autopolyploids?
They are the hardest case — allele dosage limits haplotype resolution. We scope feasibility honestly at design stage and recommend the best achievable output.
advancedIs RNA-seq needed for annotation?
Strongly recommended — RNA-seq evidence substantially improves plant gene models, especially for condition-specific and subgenome-specific genes.
References

Key literature & resources

Selected sources behind the methods and reference values on this page. Figures labelled "schematic" or "illustrative" are generated for this page, not client data.

  1. Cheng H, et al. Haplotype-resolved de novo assembly with phased assembly graphs (hifiasm). Nature Methods. 2021;18(2):170–175. (Polyploid/Hi-C integration: Cheng H, et al. Nature Methods. 2024.)
  2. Nurk S, et al. The complete sequence of a human genome (T2T methods framework). Science. 2022;376(6588):eabj6987.
  3. Wang M, et al. Reference genome assemblies of 11 and 20 reveal the genome architecture of polyploid wheat (and related polyploid assembly strategies). Nature. 2022–2024 (chromosome-scale wheat assemblies).
  4. Dudchenko O, et al. De novo assembly of the Aedes aegypti genome using Hi-C (Hi-C scaffolding framework). Science. 2017;356(6333):92–95.
  5. Ou S, et al. Benchmarking transposable element annotation methods in large plant genomes (LAI). Plant Physiology. 2019;180(3):1294–1306.
  6. Flynn JM, et al. RepeatModeler2. PNAS. 2020;117(17):9451–9457.
  7. Bradbury PJ, et al. TASSEL. Bioinformatics. 2007;23:2633–2635. (GAPIT: Lipka AE, et al. Bioinformatics. 2012;28(18):2397–2399. FarmCPU: Liu X, et al. PLoS Genetics. 2016;12(1):e1005764.)
  8. Bayer PE, et al. — crop pan-genome methodology: see also Golicz AA, et al. pangenomics comes of age: from bacteria to plant and animal applications. Trends in Genetics. 2016;32(6):353–364.