• Question: Does the approximate time taken to sequence an animal differ depending on which group they belong to? Are there more complex families?

    Asked by Amber on 16 Jun 2021.
    • Photo: Kerstin Howe

      Kerstin Howe answered on 16 Jun 2021: last edited 16 Jun 2021 12:12 pm

      The time it takes to put an assembly of an animal together depends on the size of their genome and its complexity and these traits do run in clades.

      For instance, most mammals have genome sizes around 3 Giga base pairs (Gb), birds and fishes are often a bit smaller at around 1 Gb, amphibians can be very big (even > 30 Gb), insects come at varying sizes. The bigger a genome is, the more sequencing data needs to be generated which can take some time and also the longer all the informatics and quality checking processes can take.

      The content of a genome also influences how long it takes to assemble the data and make sure that it’s in good shape. If a genome for instance contains very many repetitive regions, it might be very fiddly to put them together correctly and sometimes makes lengthy manual intervention necessary. It gets really tricky if a species is polyploid, as the presence of additional near identical chromosomes requires complicated informatics tricks to distinguish between simply repetitive sequence regions and those that are derived from a different chromosome.

    • Photo: anon

      anon answered on 16 Jun 2021:

      From the wet-lab perspective, factors such as how easy it is to extract high-quality DNA that is free of contaminants, the size of the genome and whether a sample is a symbiont (made up of multiple organisms each with their own unique genome) will affect how quickly a sample progresses from collection to sequence assembly.

      I realise your question specifically mentions animals, but if I use the mistletoe plant as an example:
      – has a huuuuuuuge genome (some 40x larger than the human genome) which means we need to collect more tissue and extract more DNA for sequencing
      – plants are tricky to extract because they have cell walls which need breaking open to get at the DNA inside (+ processing time)
      – plants are extra tricky as they contain molecules such as polysaccharides which are tricky to remove during DNA extraction and clean-up. These and may interfere with the sequencing process itself (+ research into how to remove)