Biodiversity initiative:

Integrating Taxonomy, Genomics and Biodiversity

+ +

= ?????Speaker: Benjamin Linard

Alfried Vogler Team

Arthropods metagenomics 1 / 8

DNA extraction

PCR barcodes

Mixed sample

All 480 beetles Est. 288

species

1x Illumina MiSeq run

(8.5Gb)

Mitochondrial contigs

De novo assembly into

contigs

Pool DNA by

volume

1 SAMPLE: 480 beetle specimens captured in Borneo

Mitochondrial DNA 2 / 8

Harpalinae

Chrysomelidae

Coccinelidae

Curculionidae

Tenebrionidae

Buprestidae

Log(Biomass) = -2.37 + 0.85(log(No. Reads))P<0.001; F1,84=73.32; R2=0.47

~5% beetle mitochondrial DNA

Shotgun output

No. reads 33,796,432

Est. proportion mitochondrial reads

4.94%

Complete mitogenomes 35

Partial mitogenomes >10kb

85

Partial mitogenomes2-10kb

420

Results of Alex Crampton Plat

Genomic information ? 3 / 8

~95% genomic information ,

~45 % is Coleoptera DNA

~5% beetle mitochondria TaxomomyAbundance

Genomic analysesFunctional information ?

Tribolium castaneum, chromosome 3

# ho

mol

ogou

s co

ntig

s

position

Homologous contig % GCChromosome region with known sequence

NNNN region (unresolved sequence)

Homologous DNAbetween 4

beetle metagenomic samples

Arthropods metagenomics

Computational requirements to analyse 1 arthropod soup :

Server: ~128Gb RAM, 24 cores Xeon 2.4 GHz

Assemblies Type RAM (Gb) Time (6 cores) Disk (Go)

Mitochondrial < 10 < 12 hours < 30

Total DNA ~ 100 ~ 5 days ~ 300-500

( in the best case... when data complexity is manageable by current algorithms )

Our last DNA assembly

One assembly at a time, unpredictible risk of memory overload

Several assemblies (~1.5 per week)

Successful

Aborted

4 / 8

Arthropods metagenomics

Computational requirements to analyse 1 arthropod soup :

Server: ~128Gb RAM, 24 cores Xeon 2.4 GHz

Assemblies Type RAM (Gb) Time (6 cores) Disk (Go)

Mitochondrial < 10 < 12 hours < 30

Total DNA ~ 100 ~ 5 days ~ 300-500

( in the best case... when data complexity is manageable by current algorithms )

5 / 8

Genomicanalyses :

Type RAM (Gb) Time (6 cores) Disk (Go)

Homology/ alignments < 2 ~ 5 days < 10

Statistics / graphs < 2 ~ 1 day < 2

Need support of SQLdatabase.

Currenlty ~ 300 Gb

5 / 8

Future ?for the analysisof 1 arthropod soup

~1 000 arthropods trancriptomes/genomes~50 beetle species transcriptomes~50 beetle draft/complete genomes

Long term perspective: Disk space consuming... # more reference genomes # larger/more complex databases

Growth of analysis pipeline !More CPU to perform a complete metagenomic analyses

• standard MIGS (D Field & al, 2008)

• standards MINIMESS (J Raes & al, 2007)

Biodiversity & functional analysis

Arthropods biodiversity

n traps per site:(soil, canopy,Ground…)

N plots

Mitochondrial analysis, not a problem

Full DNA analysis... Which computational power could we access ? More computations to answer more interesting questions

Pooling DNA? We will loose metagenomic resolution... More complex assemblies

Many soup analyses...

6 / 7

A source of DNA collection 7 / 8

Metadata (1 arthropod soup) General: Sampling localisation, date, methods...

Mitochondrial information: Identified species/taxonsAbundanceOther identified species (plants, fungi...)

Genomic information: Identified genesIdentified functions (sugar degradation)

Soup metadata125 species,

French Guyana

Soup metadata24 unidentified tenebrionidae

from Madagascar

Soup metadata53 species +

abundance data

Soup metadata24 species,

Congo,

Scientificcommunity

in NHM

accessNHM data

portal

Kemu

Integration, links, queries ...

“I want all NHM collection data concerning the species X”

Data storage ? NHM databases integration ?

8 specimens, 4 images, 2 metagenomic samples ...

Thank youfor your attention. BEETLE SOUP,

Your daily source of DNA!

BEETLE

SOUP