understanding complex communities Flashcards
what can we find using other meta- techniques besides metabarcoding
evolutionary relationships, functional interactions
metabarcoding uses =
PCR amplicons
metagenomics uses =
whole genomes
what is metagenomics
direct genetic analysis of entire genomes contained within an environmental sample
what are the steps of metagenomics
- DNA extraction
- sequencing
- genome assembly and annotation
- community diversity and structure
- functional and evolutionary analysis
what community is metagenomics most useful for and why
microbial
can identify mixed communities with bacteria, archaea, fungi and viruses
what information is revealed by metagenomics
evolutionary processes, community function and interaction
what are the disadvantages of metagenomics
expensive,
computationally challenging
what is a metatranscriptome
the complete collection of transcribed sequences in a community (mRNA and ncRNA)
what does metatranscriptomics use
transcriptomes
what are the steps of metatranscriptomics
- RNA extraction and cDNA conversion
- sequencing
- transcript assembly and annotation
- transmit quantification
- functional analysis
what does metatranscriptomics tell us
function of mixed communities,
response to different environments,
potential impact on the system / host
what is the disadvantage of metatranscriptomics
needs high quality, fresh samples as RNA degrades quickly
what does metaproteomics use
protein expression
what are the steps of metaproteomics
- extract and digest proteins
- HPLC separation
- mass spectrometry
- database comparisons
- functional predictions
