Aarhus University Seal / Aarhus Universitets segl

Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Standard

Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex. / Cavassim, Maria Izabel A; Moeskjær, Sara; Moslemi, Camous; Fields, Bryden; Bachmann, Asger; Vilhjálmsson, Bjarni J; Schierup, Mikkel Heide; W Young, J Peter; Andersen, Stig U.

I: Microbial Genomics, Bind 6, Nr. 4, 04.2020.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Harvard

APA

CBE

MLA

Vancouver

Author

Bibtex

@article{9e7beb12c2b2431d89b2629cd0ab420d,
title = "Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex",
abstract = "Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.",
keywords = "CONJUGAL TRANSFER, EVOLUTION, IV SECRETION SYSTEM, LATERALLY TRANSFERRED GENES, MANTEL TEST, NODULATING STRAINS, PHASEOLUS-VULGARIS, POPULATION GENOMICS, SEQUENCE, SINORHIZOBIUM, conjugation, genome assembly, introgression, rhizobia, symbiosis, white clover",
author = "Cavassim, {Maria Izabel A} and Sara Moeskj{\ae}r and Camous Moslemi and Bryden Fields and Asger Bachmann and Vilhj{\'a}lmsson, {Bjarni J} and Schierup, {Mikkel Heide} and {W Young}, {J Peter} and Andersen, {Stig U}",
year = "2020",
month = apr,
doi = "10.1099/mgen.0.000351",
language = "English",
volume = "6",
journal = "Microbial Genomics",
issn = "2057-5858",
publisher = "Microbiology Society",
number = "4",

}

RIS

TY - JOUR

T1 - Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex

AU - Cavassim, Maria Izabel A

AU - Moeskjær, Sara

AU - Moslemi, Camous

AU - Fields, Bryden

AU - Bachmann, Asger

AU - Vilhjálmsson, Bjarni J

AU - Schierup, Mikkel Heide

AU - W Young, J Peter

AU - Andersen, Stig U

PY - 2020/4

Y1 - 2020/4

N2 - Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.

AB - Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.

KW - CONJUGAL TRANSFER

KW - EVOLUTION

KW - IV SECRETION SYSTEM

KW - LATERALLY TRANSFERRED GENES

KW - MANTEL TEST

KW - NODULATING STRAINS

KW - PHASEOLUS-VULGARIS

KW - POPULATION GENOMICS

KW - SEQUENCE

KW - SINORHIZOBIUM

KW - conjugation

KW - genome assembly

KW - introgression

KW - rhizobia

KW - symbiosis

KW - white clover

U2 - 10.1099/mgen.0.000351

DO - 10.1099/mgen.0.000351

M3 - Journal article

C2 - 32176601

VL - 6

JO - Microbial Genomics

JF - Microbial Genomics

SN - 2057-5858

IS - 4

ER -