Animal and Plant Genomics with Long-Read Sequencing — PacBio & ONT Services

A wheat breeder staring at a fragmented draft genome knows the frustration: the disease resistance gene cluster sits in a centromeric gap that short reads cannot span. A livestock geneticist calculating breeding values from unphased SNP data knows the limitation: two beneficial alleles on opposite haplotypes look like one mediocre signal. An evolutionary biologist comparing gene families across species knows the risk: collapsed paralogs in a short-read assembly produce spurious gene loss calls. These are not edge cases — they are the norm in animal and plant genomics, where large genomes, polyploidy, and repetitive architecture push short-read sequencing past its physical limits.

CD Genomics provides comprehensive long-read sequencing services for animal and plant genomics, powered by both PacBio HiFi and Oxford Nanopore Technologies (ONT) platforms. We offer nine specialized services — from de novo genome assembly and T2T gap-free genomes to pan-genome analysis and full-length transcriptomics — covering the complete research pipeline from sample to publication-ready data. We have sequenced hundreds of eukaryotic species, and if your species is not on our list, we will design a custom workflow for it. This page is your directory to all animal and plant genomics services within our LongSeq division.

Why Animal and Plant Genomes Demand Long-Read Sequencing

Animal and plant genomes are structurally different from the compact, diploid genomes that made short-read sequencing famous. Wheat (Triticum aestivum) carries a 14.5 Gb hexaploid genome — three subgenomes, each with its own complement of transposable elements, nested within a single nucleus. Sugarcane (Saccharum officinarum) is octoploid. Cultivated strawberry (Fragaria × ananassa) is octoploid. Cotton (Gossypium hirsutum) is allotetraploid. Even diploid crop genomes like maize (Zea mays, ~2.3 Gb) are 85% repetitive, dominated by long terminal repeat retrotransposons that scatter across centromeres and intergenic space.

When a short-read sequencer fragments these genomes into 150 bp pieces and attempts computational reassembly, three things break. First, repeats longer than the read length collapse — transposable elements, segmental duplications, and centromeric satellites disappear into single collapsed contigs. Second, haplotypes blend — in a polyploid, it becomes impossible to assign a given read to its subgenome of origin, turning three distinct subgenomes into one consensus blur. Third, structural variants vanish — insertions, deletions, inversions, and copy-number variations larger than the insert size are invisible to the alignment algorithm. A 2025 study that assembled the first T2T hexaploid wheat genome found that short-read assemblies missed entire gene clusters embedded in centromeric and pericentromeric regions — precisely the regions that harbor agronomically important disease resistance loci.

Long-read sequencing — with reads routinely exceeding 20 kb for PacBio HiFi and 100 kb for Oxford Nanopore — spans these repetitive regions natively. A single PacBio HiFi read covers a full-length LTR retrotransposon and its flanking unique sequence. An ONT ultra-long read traverses an entire centromeric satellite array. The result is a contiguous, phased assembly that preserves subgenome identity, captures structural variation, and reveals the complete gene repertoire — not just the fraction that happens to sit in unique sequence.

Animal and Plant Genomics Services at CD Genomics

Below is our complete animal and plant genomics service catalog. Each linked service page includes detailed workflows, sample requirements, bioinformatics deliverables, and project consultation information.

Genome Assembly and Resequencing Services

Whether you are building a reference genome from scratch or characterizing population-level variation against an existing assembly, long-read sequencing delivers the contiguity and completeness that short reads cannot match.

• Animal/Plant Whole Genome De Novo Sequencing — Chromosome-scale genome assembly for any eukaryotic species, including polyploid crops, livestock, and non-model organisms. Our pipeline combines PacBio HiFi reads for base accuracy with ONT ultra-long reads for gap closure, supported by Hi-C data for chromosome-level scaffolding. We routinely deliver assemblies with contig N50 exceeding 10 Mb for complex plant genomes and BUSCO completeness above 95%.
• Animal/Plant Whole Genome Sequencing — Resequencing of individuals or populations against an existing reference genome for comprehensive variant discovery. Long reads capture the full spectrum of genetic variation — SNPs, indels, structural variants (>50 bp), and copy-number variations — in a single experiment. For livestock breeding programs, this means phased genotypes that improve genomic estimated breeding values (GEBVs). For crop improvement, this means capturing presence/absence variation (PAV) in gene clusters that SNP arrays miss entirely.
• T2T Genome Assembly — Complete, gap-free genome assembly from telomere to telomere, including centromeres, telomeres, ribosomal DNA arrays, and segmental duplications. Enabled by ultra-long ONT reads combined with PacBio HiFi for polishing, T2T assemblies reveal the full genomic landscape — including the repetitive regions where functional elements often reside. This is the gold standard for reference genome construction and is increasingly expected by reviewers for high-impact genome publications.
• Haplotype-resolved T2T Genome Assembly — Phased, diploid T2T assembly that independently resolves both parental haplotypes, rather than collapsing them into a single consensus. This is essential for species with high heterozygosity — many aquaculture species, outcrossing plants, and hybrid crops. Haplotype-resolved assemblies reveal allele-specific expression, heterosis mechanisms, and the true extent of structural heterozygosity.

Targeted Sequencing and Transcriptome Services

• Animal/Plant Long Amplicon Sequencing — Targeted sequencing of genomic regions up to 20 kb — gene clusters, biosynthetic pathways, QTL intervals, and resistance gene analogs. Long amplicons preserve linkage phase across entire gene families, enabling accurate haplotype reconstruction in polyploid genomes where short amplicons produce ambiguous phasing.
• Animal/Plant RNA Sequencing — Full-length transcript isoform identification and quantification using PacBio Iso-Seq or ONT cDNA/direct RNA sequencing. Unlike short-read RNA-seq, which assembles transcripts computationally from fragmented reads — often producing incomplete or chimeric isoforms — long-read transcriptomics captures complete transcript structures from 5' cap to poly(A) tail. For non-model species without well-annotated genomes, this enables reference-free isoform discovery and annotation.
• Mitochondrial/Chloroplast Genome Sequencing — Complete organellar genome assembly from total genomic DNA — no organelle enrichment required. Long reads routinely assemble mitochondrial and chloroplast genomes as single circular contigs, revealing heteroplasmy, structural rearrangements, and organellar-nuclear DNA transfers that short reads fragment. For plant researchers, complete chloroplast genomes support phylogenomic analysis, species identification, and conservation genetics.

Advanced Genomic Analysis Services

• Pan-Genome Analysis — Multi-individual genome comparison to capture the full gene repertoire of a species, including presence/absence variation and structural diversity. For crop breeding, pan-genomes reveal dispensable genes — those present in some accessions but absent in others — that often encode agronomic traits such as disease resistance, stress tolerance, and quality characteristics. For livestock, pan-genomes identify breed-specific gene content underlying production traits.
• Comparative Genomic Analysis — Multi-species genome comparison for evolutionary biology, phylogenomics, and gene family analysis. Services include orthology inference (OrthoFinder), phylogenomic tree construction, synteny analysis, positive selection detection, and gene family expansion/contraction analysis. Complete, long-read-based assemblies are essential — fragmented assemblies produce spurious gene duplication and loss calls that undermine evolutionary conclusions.

For services not listed here, our sibling category hubs cover Human Genomics with Long-Read Sequencing, Microbial Genomics with Long-Read Sequencing, and Transcriptomics with Long-Read Sequencing.

Beyond the List — We Sequence Any Eukaryotic Species

The species catalog above represents our most frequent projects — but it is not a menu. CD Genomics' long-read sequencing platforms and bioinformatics pipelines are species-agnostic. Our assembly algorithms do not require a reference genome. Our annotation pipelines can be configured for any eukaryotic lineage using BUSCO lineage datasets, repeat libraries, and ab initio gene predictors appropriate to your species' taxonomic group.

We have successfully delivered genome assemblies, transcriptomes, and comparative analyses for insects (Lepidoptera, Coleoptera, Hymenoptera), reptiles (snakes, lizards, turtles), amphibians (frogs, salamanders), fungi (Ascomycota, Basidiomycota), algae (Chlorophyta, Rhodophyta), forest trees (poplar, eucalyptus, oak, pine, spruce), and marine invertebrates (corals, sea urchins, mollusks). Each project begins with a consultation: you tell us your species, your genome size estimate (if known), and your research question, and our team designs a customized workflow with platform recommendation, sequencing depth calculation, and bioinformatics plan.

How to start: Contact our project consultation team through the inquiry form with your species name, estimated genome size, ploidy level (if known), sample type and quantity, and your primary research question. We will respond with a customized project proposal within 1-2 business days.

Sample Preparation and Requirements for Animal and Plant Genomics

Animal and plant genomics projects present unique sample logistics. A crop geneticist collecting leaf tissue from a field trial faces different challenges than a marine biologist sampling fin clips on a research vessel. CD Genomics has processed samples from every continent and most major ecosystem types.

For high-molecular-weight (HMW) DNA extraction — critical for long-read sequencing — we follow protocols optimized for plant and animal tissues. Plant HMW extraction uses nuclei isolation to separate DNA from organellar and polysaccharide contaminants. Animal HMW extraction uses gentle lysis with wide-bore pipette tips to preserve fragment length. Both protocols are validated on our sequencing platforms and include QC checkpoints: NanoDrop for purity, Qubit for concentration, and FEMTO Pulse for fragment size distribution.

Comprehensive sample preparation guidelines are available at our Sample Submission Guideline page.

Frequently Asked Questions

For research use only. Not for use in diagnostic procedures.