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

Huang, Xi LU ; Hansson, Roland; Palinauskas, Vaidas; Valkiūnas, Gediminas; Hellgren, Olof LU and Bensch, Staffan LU (2018) In International Journal for Parasitology 48(12). p.947-954
Abstract

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... (More)

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.

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author
organization
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type
Contribution to journal
publication status
published
subject
keywords
Avian haemosporidians, Exon coverage, GC content, Phylogenetic distance, Reference genome, Sequence capture
in
International Journal for Parasitology
volume
48
issue
12
pages
947 - 954
publisher
Elsevier
external identifiers
  • scopus:85051653114
ISSN
0020-7519
DOI
10.1016/j.ijpara.2018.05.009
language
English
LU publication?
yes
id
5676582f-aae2-49a1-9cc1-6d90a2e526c5
date added to LUP
2018-08-30 13:34:26
date last changed
2019-03-19 03:58:37
@article{5676582f-aae2-49a1-9cc1-6d90a2e526c5,
  abstract     = {<p>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 ∼10<sup>4</sup>-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.</p>},
  author       = {Huang, Xi and Hansson, Roland and Palinauskas, Vaidas and Valkiūnas, Gediminas and Hellgren, Olof and Bensch, Staffan},
  issn         = {0020-7519},
  keyword      = {Avian haemosporidians,Exon coverage,GC content,Phylogenetic distance,Reference genome,Sequence capture},
  language     = {eng},
  month        = {08},
  number       = {12},
  pages        = {947--954},
  publisher    = {Elsevier},
  series       = {International Journal for Parasitology},
  title        = {The success of sequence capture in relation to phylogenetic distance from a reference genome : a case study of avian haemosporidian parasites},
  url          = {http://dx.doi.org/10.1016/j.ijpara.2018.05.009},
  volume       = {48},
  year         = {2018},
}