Genome Observatory Live

Assemblies—

Species—

First-time species—

In annotation—

Recent annotations—

30-day calendar-day pace—

Past week

Chromosome-scale genome deposits

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— species represented · — first-time species

Annual depositscurrent year is year-to-date

Newest arrival

Latest qualifying assembly with an available image

Composition

Broad taxonomic composition: recent versus all-time deposits

Past week

All time

Deposit weather

A year of chromosome-scale genome deposits

Each square is one calendar day. Darker days contain more deposited assemblies; hover for assemblies, represented species and first-time species. Recent dates are displayed immediately, but counts may rise as NCBI indexes more assemblies. A zero is provisional, not proof that nothing was deposited.

Cumulative coverage

Assemblies and first-time species through time

AssembliesFirst-time species

RefSeq

Annotation activity

In progress

Recently completed

Past week

Broad groups

Milestones

When did we cross each total?

Recent deposits

Rolling assembly metadata

Recent per-assembly metadata only; lifetime history is stored as compact aggregates.

Collection metrics

What do deposited genome assemblies contain?

Metadata-derived properties of the chromosome-scale and complete GenBank eukaryote collection. These metrics describe what is explicitly associated or labelled in NCBI records; they do not infer missing biological features.

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Organelle association

Mitochondrial genome associated

Share of all tracked genome deposits with an associated mitochondrial genome in the NCBI assembly record.

Plant organelles

Plastid genome associated

Share of tracked Viridiplantae genome deposits with an associated chloroplast/plastid genome in the NCBI assembly record.

Chromosome labelling

Sex-chromosome labels

Explicit X/Y/Z/W-style labels or explicitly identified other sex-chromosome names in NCBI sequence reports, across all tracked genome deposits.

Karyotype audit

Chromosome count vs expected

For species with Tree of Sex chromosome counts, compare the number of chromosomes represented by the NCBI assembly with the reported biological karyotype.

Assembly architecture

Genome size & contiguity

NCBI assembly statistics across all qualifying deposits. The summaries include median assembly length, contig N50 and reported chromosome count; the histograms show assembly-length and chromosome-count bins.

Assembly length (binned)

Chromosome number

Genome architecture

Genome size × chromosome number

One representative assembly per species with both measurements. The horizontal axis is reported chromosome count and the vertical axis is assembly length; both are logarithmic.

Genome-size landscape · Animals

Animal genome-size distributions · classes

Up to ten groups ranked by species coverage, with one assembly per species. Each ribbon shows the relative distribution within its row (height normalized separately). The horizontal Mb/Gb axis is linear and shared within this panel; genomes beyond the displayed range are flagged.

Genome-size landscape · Plants

Plant genome-size distributions · orders

Genome-size landscape · Fungi

Fungal genome-size distributions · orders

Repeat sequencing

Species ranked by published chromosome-scale assemblies

Top 15 organism names ranked by the number of qualifying chromosome-level or complete GenBank assemblies; repeated deposits for the same organism count separately.

Technology history

Sequencing technologies through time

Primary read technologies behind chromosome-scale and complete eukaryotic assemblies across NCBI release years. PacBio is shown as a single platform family regardless of HiFi/CLR reporting, alongside Oxford Nanopore, Illumina and other platforms; Hi-C and other proximity-ligation data are shown separately.

Long-range scaffolding

Hi-C / proximity scaffolding through time

Share of assemblies whose NCBI sequencing-technology metadata reports Hi-C or a related proximity-ligation method such as Arima, Omni-C, Dovetail/Chicago, Phase Genomics or PacBio CiFi. This is supplementary long-range information, not a primary read technology.

Assembly history

Assemblers through time

The changing assembly software reported for chromosome-scale and complete eukaryotic genome deposits. Versions and spelling variants are collapsed into assembler families, and the most represented named families are shown.

Observed vs expected

Expected sex-chromosome annotation

For species with a Tree of Sex sex-chromosome-system record, compare expected sex-chromosome labels with labels explicitly found in NCBI sequence reports.

Expected system: Tree of Sex · observed labels: NCBI sequence reports.

Interpretation

What these metrics mean

Mitochondrial / plastid: an organelle is counted only when NCBI's assembly metadata explicitly associates that organelle genome with the nuclear assembly.

Sex chromosomes: expectations use species records first, then conservative concordant clade evidence. The source level is retained in the generated data.

Karyotype: NCBI's reported assembly chromosome count is compared with Tree of Sex female/male 2N. Because many assemblies represent a haploid complement, both 2N and N are considered and the closer expectation is used.

No observed label means no explicit sex-chromosome-style chromosome name was found in the NCBI sequence report. It is missing annotation, not evidence that the organism lacks the expected sex chromosomes.

Technology / assembler trends: free-text NCBI sequencingTech and assemblyMethod values are normalized into broad named families. Primary read technologies are separated from Hi-C/proximity-ligation methods, which are tracked independently. Percentages use the relevant metadata-bearing assemblies for each release year; hybrid primary sequencing workflows can appear in multiple technology series.

IUCN Red List

Genome deposition for threatened and extinct species

Chromosome-scale and complete GenBank assemblies, restricted to taxa carrying current IUCN Red List categories.

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Vectors · parasites · fungi

Pathogens & vectors

Chromosome-scale and complete GenBank genomes for vector surveillance taxa, disease-causing protists, parasitic worms and selected pathogenic fungi. Explore disease-causing organisms and vector surveillance taxa separately. CDC and WHO sources define the initial pathogen catalogue; this is not an exhaustive list.

Pathogen group

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Assemblies—

Species—

First-time species—

In annotation—

Recent annotations—

30-day calendar-day pace—

Pathogens & vectors · all time

Pathogen and vector genome deposits

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— species represented · — first-time species

Newest arrival

Most recent matching deposited genome

Composition

Genome deposits by organism group and species coverage

Group genome deposits by

Source species coverage

All-time comparison

Genome coverage by organism group

Click a group to explore its species below. Coverage is the fraction of species in the selected catalogue with at least one matched chromosome-scale or complete genome.

Vector coverage follows the supplied MapVEu export. Parasites and fungi follow the curated species list linked below. Groups with no matched qualifying genomes remain visible; vector-list membership does not establish transmission.

Assemblies over time

Deposits per year

Cumulative coverage

Assemblies and first-time species through time

AssembliesFirst-time species

Geographic origin

Pathogen genome sample origins

Broad group

All-time qualifying assemblies by reported BioSample collection country. This shows the origins of sequenced samples, not disease prevalence or the full distribution of a species. Ocean markers represent named water bodies, not precise collection coordinates.

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RefSeq

Matching annotation activity

In progress

Recently completed

All time

Organism groups

Recent deposits

Rolling matching assembly metadata

MapVEu · CDC · WHO · curated species matching

Source coverage

Species inventory

Organism groupFind a species

Zero means no qualifying assembly was matched, rather than no genome exists. Only explicit aliases in the curated list are matched. Strain and subspecies names of pathogens roll up to species; uncertain source labels are excluded.

Download curated pathogen & parasite list · Review the list on GitHub · Download original vector taxon labels

Food · farming · crop protection

Agricultural genomes

Chromosome-scale and complete GenBank genomes for cultivated crops, livestock and aquaculture, agricultural pests, and eukaryotic pathogens of plants and livestock. Explore a selected FAO, EPPO and WOAH catalogue; this is not an exhaustive list.

Broad group

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Comparative taxonomic history

Compare chromosome-scale sequencing by phylum or order

Select two phyla or orders. Their cumulative assembly counts and assembly-length distributions use paired scales; geographic-origin maps use the same colour scale. Only phyla and orders are indexed to keep the site compact.

Left taxon

Right taxon

Paired scales update when either taxon changes. Assembly-length curves use a shared linear Mb/Gb range with high-end outliers flagged. Maps use BioSample origin, including ocean/sea localities—not the natural ranges of the taxa.

Choose a taxon for the left side.

Choose a taxon for the right side.

Chromosome-scale genome deposits

Latest qualifying assembly with an available image

Broad taxonomic composition: recent versus all-time deposits

Past week

All time

A year of chromosome-scale genome deposits

Assemblies and first-time species through time

Annotation activity

In progress

Recently completed

Broad groups

When did we cross each total?

Rolling assembly metadata

What do deposited genome assemblies contain?

Mitochondrial genome associated

Plastid genome associated

Sex-chromosome labels

Chromosome count vs expected

Genome size & contiguity

Assembly length (binned)

Chromosome number

Genome size × chromosome number

Animal genome-size distributions · classes

Plant genome-size distributions · orders

Fungal genome-size distributions · orders

Species ranked by published chromosome-scale assemblies

Sequencing technologies through time

Hi-C / proximity scaffolding through time

Assemblers through time

Expected sex-chromosome annotation

What these metrics mean

Genome deposition for threatened and extinct species

Threatened species genome deposits

Most recent matching deposited genome

Red List category and broad taxonomic composition

IUCN category

Broad groups

Deposits per year

Matching annotation activity

In progress

Recently completed

Assemblies and first-time species through time

Broad groups

When did we cross each total?

Rolling matching assembly metadata

Pathogens & vectors

Pathogen and vector genome deposits

Most recent matching deposited genome

Genome deposits by organism group and species coverage

Source species coverage

Genome coverage by organism group

Deposits per year

Assemblies and first-time species through time

Pathogen genome sample origins

Matching annotation activity

In progress

Recently completed

Organism groups

When did we cross each total?

Rolling matching assembly metadata

Species inventory

Agricultural genomes

Genome deposits

Most recent matching genome

Organism groups and catalogue coverage

Broad groups

Source taxa coverage

Deposits per year

Assemblies and first-time taxa through time

Genome sample origins

Latest matching assemblies

Species inventory

Genome deposition by geography

Sample-origin activity

Top orders by species represented

Explore all-time genome deposition by country

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Cumulative assemblies and first-time species

Compare chromosome-scale sequencing by phylum or order

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