Menu

Javascript is not activated in your browser. This website needs javascript activated to work properly.
You are here

The success of sequence capture in relation to phylogenetic distance from a reference genome : a case study of avian haemosporidian parasites

Author:
  • Xi Huang
  • Roland Hansson
  • Vaidas Palinauskas
  • Gediminas Valkiūnas
  • Olof Hellgren
  • Staffan Bensch
Publishing year: 2018-08-11
Language: English
Pages: 947-954
Publication/Series: International Journal for Parasitology
Volume: 48
Issue: 12
Document type: Journal article
Publisher: Elsevier

Abstract english

Genomic sequencing of avian haemosporidian parasites (Haemosporida) has been challenging due to excessive contamination from host DNA. In this study, we developed a cost-effective protocol to obtain parasite sequences from naturally infected birds, based on targeted sequence capture and next generation sequencing. With the genomic data of Haemoproteus tartakovskyi as a reference, we successfully sequenced up to 1000 genes from each of the 15 selected samples belonging to nine different cytochrome b lineages, eight of which belong to Haemoproteus and one to Plasmodium. The targeted sequences were enriched to ∼104-fold, and mixed infections were identified as well as the proportions of each mixed lineage. We found that the total number of reads and the proportions of exons sequenced decreased when the parasite lineage became more divergent from the reference genome. For each of the samples, the recovery of sequences from different exons varied with the function and GC content of the exon. From the obtained sequences, we detected within-lineage variation in both mitochondrial and nuclear genes, which may be a result of local adaptation to different host species and environmental conditions. This targeted sequence capture protocol can be applied to a broader range of species and will open a new door for further studies on disease diagnostics and comparative analysis of haemosporidians evolution.

Keywords

  • Immunology
  • Microbiology
  • Avian haemosporidians
  • Exon coverage
  • GC content
  • Phylogenetic distance
  • Reference genome
  • Sequence capture

Other

Published
  • Molecular Ecology and Evolution Lab
  • ISSN: 0020-7519
Staffan Bensch
E-mail: staffan [dot] bensch [at] biol [dot] lu [dot] se

Professor

MEMEG

+46 46 222 42 92

E-C213

Sölvegatan 37, Lund

50

Head of unit

MEMEG

+46 46 222 42 92

E-C213

Sölvegatan 37, Lund

50

Research group

Molecular Ecology and Evolution Lab

Projects

Doctoral students and postdocs

PhD students, main supervisor

Downloads & links