What is a reference genome?

A reference genome is the assembled DNA sequence of one individual, used as the standard for its species. It supports research in conservation, ecology, evolution, taxonomy, behaviour, agriculture and forestry.

Researchers can compare it with other species to see how genes and chromosomes have changed. They can also align lower-cost short-read data from many individuals to the reference, then study relationships, population size and connectivity, natural selection and gene exchange.

Three tiers of genomic data

Each tier answers different questions, at a different cost.

  1. How a DNA barcode identifies a speciesA butterfly of unknown species gives a short, standard stretch of DNA. Each of its bases, A, C, G or T, becomes a coloured bar, forming a barcode. The barcode is compared with the barcodes of four Heliconius species in a reference library. Three differ at a few positions, marked with crosses; one is identical, so the specimen is identified, first as Heliconius cydno. A button swaps in another unknown butterfly and the same comparison names it. Sixteen bases are drawn; a real animal barcode is about 650 bases of the COI gene.TATTAGGAGCTTCAATH. cydno16 of about 650 bases shown (COI gene)H. hecaleH. ismeniusH. clysonimusH. cydno

    Which species is this butterfly?

    All 16 bases match H. cydno. A cross marks each base where another species differs.

    Tier 1

    DNA barcodes

    A short, standard stretch of DNA, matched against a reference library, identifies the species. It is the cheapest of the three tiers.

  2. How population resequencing compares populationsThree butterflies from one population and three from another are sequenced as short reads. The reads line up along a reference genome, one row per butterfly: the first population above it and the second below. Five sites are read one after another and each gets a mark. At two, all six butterflies carry the same letter. At two, both letters occur in both populations, so that site cannot tell them apart. At one, every butterfly above carries a T and every butterfly below a C: a site where the two populations differ.=≈=≠≈CAGTCCGGTTCAGTCCGGCCCAGCCCAGCT

    Where do the two populations differ?

    • =same in all
    • ≈mixed in both
    • ≠differs

    1 of 5 sites tells the populations apart: T above, C below. The others are shared or mixed.

    Tier 2

    Population resequencing

    Short reads from many individuals, aligned to a reference genome, show where populations differ and help tell species apart.

  3. How a reference genome is assembledThe DNA of one butterfly is sequenced as long reads, which arrive in no particular order. Reads that end and begin with the same letters overlap, so they can be lined up and joined into one continuous sequence. Hi-C data then orders the joined pieces, giving a chromosome-scale reference with the 21 chromosomes of a typical Heliconius. This is costly but done once per species: later butterflies need only cheaper short reads, aligned to the reference.21 chromosomes

    Tier 3

    Reference genomes

    Chromosome-scale assemblies: one continuous sequence per chromosome instead of many fragments. Resequenced reads are aligned to them.

Learn by analysing together

Caligo will analyse these genomes together, so each dataset is also a chance to train. Courses and learning materials come with hands-on work that pairs experienced genomicists with researchers learning new skills.

This starts with the first pilot projects. To take part, contact the project leads.

Explore the proposed pilot projects
  1. 3 months ago

    Bogotá sequencing workshop

    Bogotá, Colombia

    The network’s first activity in Latin America, with the Red Colombiana de Genómica. Eight Heliconius species were sequenced during the workshop.

    The Heliconius pilot project
  2. In 5 months

    Campinas hackathon

    Campinas, Brazil

    Hackathon at the Biology of Butterflies and ELEN (Neotropical Lepidoptera meeting) congress: participants assemble reference genomes and analyse the data together.

    Congress website

What Neotropical genomes already reveal

These studies show how reference genomes and population data can uncover chromosome change, rapid radiations and hybrid origins.

From published evidence to new questions

Four published findings lead into Caligo’s proposed pilot projects and show what new samples or genomic data could reveal next.

How can butterfly chromosomes split and fuse, yet still work?

Most Heliconius have 21 chromosomes; five sapho-group species have up to 60.

Chromosome number remains stable for millions of years in many animal lineages. Some butterflies and moths are different. Most Heliconius species carry 21 chromosomes in the haploid set, but five species in the sapho group have up to 60 after repeated fissions.

Lepidopteran chromosomes are holocentric. During cell division, the machinery that moves them can attach along the whole chromosome instead of at one centromere. A broken fragment can therefore retain the machinery needed to move into a daughter cell. This may help chromosome fissions persist, but it does not explain why they spread through a population.

Chromosome fissions with and without a single centromereTwenty-one chromosomes, as in most Heliconius. Fissions are added one by one, each splitting one chromosome in two, up to 39 fissions and 60 chromosomes, the highest count in the sapho group. When the division machinery can attach along the whole chromosome, as in butterflies and moths, every piece can still be passed on to the daughter cells. With a single centromere, as in most animals, each piece left without the centromere is lost. This is a simplified picture.60 chromosomes

In the Heliconius sapho group, genomic studies identified three W-autosome fusion events. The W fused with chromosome 4 in their common ancestor, followed by separate fusions with chromosomes 9 and 14 in two descendant lineages.

See the proposed Heliconius study
A Heliconius sapho butterfly resting with its blue-black wings open, revealing broad white bands.

Heliconius sapho, dorsal view, Colombia. This species belongs to the chromosome-variable sapho group.

Photo: desertnaturalist / iNaturalist, via GBIF. · Source · CC BY 4.0

Are threatened butterfly populations still connected a decade later?

In 2016, most surviving populations still exchanged migrants.

Parides ascanius is restricted to coastal restinga and wetlands in south-eastern Brazil. The IUCN assessed it as Vulnerable globally in 2018. Brazil’s national assessment listed it as Endangered in 2021.

Seraphim and colleagues used mitochondrial COI sequences and eight microsatellite markers to compare the surviving populations. Their 2016 study found little genetic structure, no evidence of inbreeding and high migration among most sampled sites, although one population was more isolated by the metropolitan landscape.

The 2016 result provides a baseline but does not show whether the populations remain connected today. A chromosome-scale reference and new population sampling could measure how much diversity remains and whether habitat loss, drainage or fragmentation has interrupted gene flow.

See how Caligo would revisit connectivity
A living Parides ascanius resting with its wings open on green foliage, showing broad white and pink-red bands.

Parides ascanius, dorsal view, Brazil.

Photo: Pablo Cauã da Silva Toledo / iNaturalist, via GBIF. · Source · CC BY 4.0

How do crop pests move and evolve resistance across soybean landscapes?

Similar-looking moth species can differ in how they move and resist control.

Several closely related moth species occur in Brazilian soybean fields and can be difficult to distinguish during monitoring. Reliable identification matters because movement and resistance can differ among species.

Brazilian studies have found that susceptibility to insecticidal proteins is changing, so each species needs repeated testing. Genomic data can distinguish the species, compare movement among populations and identify variants associated with resistance.

Genomes do not measure crop damage or prove that a variant causes resistance by themselves. Field trials, bioassays, agronomy and growers’ observations are still needed to choose a management response.

See the proposed soybean landscape study
Rows of green soybean plants fill a field bordered by trees in Novo Barreiro, southern Brazil.

Soybean field in Novo Barreiro, Rio Grande do Sul, Brazil.

Photo: Lucas Friederich / Wikimedia Commons. · Source · CC BY-SA 4.0

Thousands of Panacea prola fly north-east. Where do they come from?

Of 2,509 Panacea prola counted in Peru, all but 19 flew north-east.

In 2020, Gallice and colleagues recorded 2,509 Panacea prola in 50 one-hour observations in south-eastern Peru. Only 19 flew in another direction. They presented the observation as the first evidence of an Amazonian insect migration.

The closest available genomic reference is from another member of the same subfamily, Batesia hypochlora. It cannot reveal where these butterflies came from, whether they belonged to one population or several, or whether the movement repeats each year.

Comparing samples from different places, seasons and years could estimate ancestry and connectivity. Genomes would still need to be combined with field observations, environmental data or other movement evidence.

See how Caligo would trace the migration wave
A living Panacea prola with its wings fully open, showing iridescent blue dorsal wings with broad pale bands.

Panacea prola, dorsal view, Peru.

Photo: desertnaturalist / iNaturalist, via GBIF. · Source · CC BY 4.0

Planning responsible sampling

Sampling plans need permits, specimen records, agreements on how research results, training and other benefits will be shared, and a plan for managing data.

Requirements differ among countries, and sequencing or exporting samples may require additional permits. Sampling on Indigenous Peoples’ lands requires their consent. Caligo will only support sampling with strong involvement from local researchers.