[Paper Review] An end-to-end assembly of the Aedes aegypti genome

Daisy E. Pagete|arXiv (Cornell University)|May 16, 2016

Insect symbiosis and bacterial influences561 citations

TL;DR

The paper reports an end-to-end assembly of the female Aedes aegypti genome with high contiguity and extensive chromosomal anchoring, plus comparative synteny analyses across dipterans; the work was later withdrawn by arXiv admin.

ABSTRACT

We present an end-to-end genome assembly of a female Aedes aegypti mosquito, which spreads viral diseases such as yellow fever, dengue, chikungunya, and Zika to humans. The assembly is based on an earlier genome published in 2007 and improved in 2013. The new assembly has a scaffold N50 of 419Mb, with 96.9% of the ungapped sequence anchored to chromosomes. We used the new assembly to examine the conservation of A. aegypti chromosomes. Our results suggest that synteny is strongly conserved between Ae. aegypti and An. gambiae. Comparison to D. melanogaster highlights the extent to which the identity of entire chromosome arms is preserved across dipterans.

Motivation & Objective

• Motivate improved genome assemblies for Aedes aegypti to study vector biology and disease transmission.
• Provide a highly contiguous reference genome enabling chromosomal anchoring and comparative genomics.
• Assess chromosomal conservation (synteny) between Aedes aegypti and related species (Anopheles gambiae and Drosophila melanogaster).

Proposed method

• Assemble an end-to-end genome for a female Aedes aegypti using an updated assembly built on prior work (2007; improved in 2013).
• Evaluate scaffold contiguity with a scaffold N50 of 419 Mb.
• Anchor 96.9% of ungapped sequence to chromosomes.
• Perform comparative genomic analyses to assess chromosomal synteny with Anopheles gambiae and Drosophila melanogaster.

Experimental results

Research questions

• RQ1 What is the contiguity and chromosomal anchoring quality of the end-to-end Aedes aegypti genome assembly?
• RQ2 How conserved are Aedes aegypti chromosomes in synteny with Anopheles gambiae and Drosophila melanogaster?
• RQ3 What do chromosome-level comparisons reveal about chromosome-arm conservation across dipterans?

Key findings

• Scaffold N50 of 419 Mb indicates very high assembly contiguity.
• 96.9% of ungapped sequence is anchored to chromosomes.
• Synteny is strongly conserved between Aedes aegypti and Anopheles gambiae.
• Comparison to Drosophila melanogaster suggests preservation of entire chromosome-arm identities across dipterans.