10.5061/DRYAD.KG87554
Wang, Xu
Auburn University
Wang, Xiaozhu
Auburn University
Xiong, Xiao
Auburn University
Cao, Wenqi
Auburn University
Zhang, Chao
Tongji University
Werren, John
University of Rochester
Data from: Phylogenomic analysis of Wolbachia strains reveals patterns of
genome evolution and recombination
Dryad
dataset
2019
phylogenomic
Wolbachia
recombination
multilocus sequence typing (MLST)
intracellular Alphaproteobacteria
Auburn University Intramural Grant Program Award
AUIGP 180271
National Institute of Food and Agriculture
https://ror.org/05qx3fv49
Hatch project 1018100
2020-02-18T00:00:00Z
2020-02-18T00:00:00Z
en
https://doi.org/10.1101/508408
7058775 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Wolbachia are widespread intracellular bacteria that mediate many
important biological processes in arthropod species. In this study, we
identified 210 conserved single-copy genes in 33 genome-sequenced
Wolbachia strains in the A, B, C, D, E and F supergroups. Phylogenomic
analysis with these core genes indicate that all 33 Wolbachia strains
maintain the supergroup relationship classified previously based on the
multilocus sequence typing (MLST) genes. Using an interclade recombination
screening method, 14 inter-supergroup recombination events were discovered
in six genes (2.9%) among 210 single copy orthologs. This finding suggests
a relatively low frequency of intergroup recombination. Interestingly,
they have occurred not only between A and B supergroups (9 events), but
also between A and E supergroups (5 events). Maintenance of such transfers
suggests possible roles in Wolbachia infection related functions.
Comparisons of strain divergence using the five genes of the MLST system
show a high correlation (Pearson correlation coefficient r = 0.98) between
MLST and whole genome divergences, indicating that MLST is a reliable
method for identifying related strains when whole genome data are not
available. The phylogenomic analysis and the identified core gene set in
our study will serve as a valuable foundation for strain identification
and the investigation of recombination and genome evolution in Wolbachia.
Data S1. List of 210 orthogroups identified in 34 Wolbachia strains. Data
S2. Nucleotide sequence alignments for 210 core ortholog genes among 33
Wolbachia strains. Data S3. RAxML phylogenetic trees constructed with
concatenated nucleotide sequence alignment and six individual gene
alignments with inter-supergroup recombination events. Data S4. Protein
sequence alignments for 210 core ortholog genes among 33 Wolbachia
strains. Data S5. RAxML phylogenetic trees constructed with concatenated
protein sequence alignment and six individual protein alignments with
inter-supergroup recombination events. Data S6. Estimates of Evolutionary
Divergence between multiple Wolbachia strains with 210 core gene set and
five MLST genes.