10.5061/DRYAD.79T4B
Drews, Anna
Lund University
Strandh, Maria
Lund University
RÃ¥berg, Lars
Lund University
Westerdahl, Helena
Lund University
Data from: Expression and phylogenetic analyses reveal paralogous lineages
of putatively classical and non-classical MHC-I genes in three sparrow
species (Passer)
Dryad
dataset
2017
Classical genes
MHC class I
Sparrow
Passer montanus
Passer domesticus
Passer
Non-classical genes
Passer hispaniolensis
2017-06-21T13:47:30Z
2017-06-21T13:47:30Z
en
https://doi.org/10.1186/s12862-017-0970-7
4833989 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Background: The Major Histocompatibility Complex (MHC) plays a central
role in immunity and has been given considerable attention by evolutionary
ecologists due to its associations with fitness-related traits. Songbirds
have unusually high numbers of MHC class I (MHC-I) genes, but it is not
known whether all are expressed and equally important for immune function.
Classical MHC-I genes are highly expressed, polymorphic and present
peptides to T-cells whereas non-classical MHC-I genes have lower
expression, are more monomorphic and do not present peptides to T-cells.
To get a better understanding of the highly duplicated MHC genes in
songbirds, we studied gene expression in a phylogenetic framework in three
species of sparrows (house sparrow, tree sparrow and Spanish sparrow),
using high-throughput sequencing. We hypothesize that sparrows could have
classical and non-classical genes, as previously indicated though never
tested using gene expression. Results: The phylogenetic analyses reveal
two distinct types of MHC-I alleles among the three sparrow species, one
with high and one with low level of polymorphism, thus resembling
classical and non-classical genes, respectively. All individuals had both
types of alleles, but there was copy number variation both within and
among the sparrow species. However, the number of highly polymorphic
alleles that were expressed did not vary between species, suggesting that
the structural genomic variation is counterbalanced by conserved gene
expression. Overall, 50% of the MHC-I alleles were expressed in sparrows.
Expression of the highly polymorphic alleles was very variable, whereas
the alleles with low polymorphism had uniformly low expression.
Interestingly, within an individual only one or two alleles from the
polymorphic genes were highly expressed, indicating that only a single
copy of these is highly expressed. Conclusions: Taken together, the
phylogenetic reconstruction and the analyses of expression suggest that
sparrows have both classical and non-classical MHC-I genes, and that the
evolutionary origin of these genes predate the split of the three
investigated sparrow species seven million years ago. Because only the
classical MHC-I genes are involved in antigen presentation, the function
of different MHC-I genes should be considered in future ecological and
evolutionary studies of MHC-I in sparrows and other songbirds.
Pado_Primercomb1_rawdataRaw (unfiltered) 454 amplicon sequence data for
house sparrows using primer combination 1. Demultiplexed using the
software jMHC (2011).Pahi_Primercomb1_rawdataRaw (unfiltered) 454 amplicon
sequence data for Spanish sparrow using primer combination 1.
Demultiplexed using the software jMHC (2011).Pamo_Primercomb1_rawdataRaw
(unfiltered) 454 amplicon sequence data for tree sparrow using primer
combination 1. Demultiplexed using the software jMHC
(2011).Pado_Primercomb2_rawdataRaw (unfiltered) 454 amplicon sequence data
for house sparrow using primer combination 2. Demultiplexed using the
software jMHC (2011).Pahi_Primercomb2_rawdataRaw (unfiltered) 454 amplicon
sequence data for Spanish sparrow using primer combination 2.
Demultiplexed using the software jMHC (2011).Pamo_Primercomb2_rawdataRaw
(unfiltered) 454 amplicon sequence data for tree sparrow using primer
combination 2. Demultiplexed using the software jMHC
(2011).Pado_primercomb_3_rawdataRaw (unfiltered) 454 amplicon sequence
data for house sparrow using primer combination 3. Demultiplexed using the
software jMHC (2011).Pahi_primer_comb_3_rawdataRaw (unfiltered) 454
amplicon sequence data for Spanish sparrow using primer combination 3.
Demultiplexed using the software jMHC (2011).Pamo_primercomb_3_rawdataRaw
(unfiltered) 454 amplicon sequence data for house sparrow using primer
combination 3. Demultiplexed using the software jMHC
(2011).Pado_Primercomb4_rawdataRaw (unfiltered) 454 amplicon sequence data
for house sparrow using primer combination 4. Demultiplexed using the
software jMHC (2011).Pahi_Primercomb4_rawdataRaw (unfiltered) 454 amplicon
sequence data for Spanish sparrow using primer combination 4.
Demultiplexed using the software jMHC (2011).Pamo_Primercomb4_rawdataRaw
(unfiltered) 454 amplicon sequence data for tree sparrow using primer
combination 4. Demultiplexed using the software jMHC
(2011).Name_codeDetails of the samples included in the study. The column
"Name in publication" indicates the name a samples has been
given in the published article. The column "Name in 454 files"
indicates the corresponding sample in the raw data
files.Passer_concate_all_seqAlignment of the 129 concatenated exon 3
alleles identified. Alignment performed manually using BioEdit V.7.2.5
Sequence Alignment Editor (Hall 1999). In FASTA
format.Tree_alignmentAlignment of all alleles identified with primer
combination 1 and used for building the phylogenetic tree.