Shared transcriptional control and disparate gain and loss of aphid parasitism genes and loci acquired via horizontal gene transfer

AbstractBackgroundAphids are a diverse group of taxa that contain hundreds of agronomically important species, which vary in their host range and pathogenicity. However, the genome evolution underlying agriculturally important aphid traits is not well understood.ResultsWe generated highly-contiguous draft genome assemblies for two aphid species: the narrow host range Myzus cerasi, and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these genome assemblies, and those of three related species (Acyrthosiphon pisum, D. noxia and M. persicae), we show that aphid genomes consistently encode similar gene numbers, and in the case of A. pisum, fewer and larger genes than previously reported. We compare gene content, gene duplication, synteny, horizontal gene transfer events, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites.Aphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth, and are characterized by disparate gain and loss of genes acquired by horizontal gene transfer (HGT). Such HGT events account for approximately 1% of loci, and contribute to the protein-coding content of aphid species analysed. Putative effector repertoires, originating from duplicated loci, putative HGT events and other loci, have an unusual genomic organisation and evolutionary history. We identify a highly conserved effector-pair that is tightly genetically-linked in all aphid species. In R. padi, this effector pair is tightly transcriptionally-linked, and shares a transcriptional control mechanism with a subset of approximately 50 other putative effectors distributed across the genome.ConclusionsThis study extends our current knowledge on the evolution of aphid genomes and reveals evidence for a shared control mechanism, which underlies effector expression, and ultimately plant parasitism.

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Archaeal integrases and mechanisms of gene capture

Biochemical Society Transactions ◽

10.1042/bst0320222 ◽

2004 ◽

Vol 32 (2) ◽

pp. 222-226 ◽

Cited By ~ 46

Author(s):

Q. She ◽

B. Shen ◽

L. Chen

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Evolution ◽

Trna Genes ◽

Gene Fragment ◽

Integrase Gene ◽

Site Specific ◽

Conjugative Plasmids ◽

Site Specific Integration ◽

Target Sites

Archaeal integrases facilitate the formation of two distinctive types of integrated element within archaeal chromosomes: the SSV type and pNOB8 type. The former carries a smaller N-terminal and a larger C-terminal integrase gene fragment, and the latter an intact integrase gene. All integrated elements overlap tRNA genes that were target sites for integration. It has been demonstrated that SSV (Sulfolobus spindle virus) viruses, carrying an SSV-type integrase gene, and conjugative plasmids, carrying a pNOB8-type integrase, are integrative elements. Two mechanisms have been proposed for stably maintaining an integrated element within archaeal chromosomes. There is also evidence for changes having occurred in the captured integrated elements present in archaeal genomes. Thus we infer that site-specific integration constitutes an important mechanism for horizontal gene transfer and genome evolution.

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Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”

Frontiers in Microbiology ◽

10.3389/fmicb.2016.00797 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 19

Author(s):

Sophie R. Ullrich ◽

Carolina González ◽

Anja Poehlein ◽

Judith S. Tischler ◽

Rolf Daniel ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Evolution ◽

Gene Loss

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Horizontal gene transfer and genome evolution in Methanosarcina

BMC Evolutionary Biology ◽

10.1186/s12862-015-0393-2 ◽

2015 ◽

Vol 15 (1) ◽

Cited By ~ 9

Author(s):

Sofya K. Garushyants ◽

Marat D. Kazanov ◽

Mikhail S. Gelfand

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Evolution

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Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage

10.1101/487215 ◽

2018 ◽

Cited By ~ 2

Author(s):

Chelsea L. Murphy ◽

Noha H. Youssef ◽

Radwa A. Hanafy ◽

MB Couger ◽

Jason E. Stajich ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Gene Duplication ◽

Substrate Utilization ◽

High Rank ◽

Eukaryotic Lineage ◽

Fungal Lineage ◽

Fermentative Bacteria ◽

Survival And Growth

AbstractSurvival and growth of the anaerobic gut fungi (AGF, Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. Patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 283 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. The majority of HGT events were AGF specific (91.5%) and wide (70.7%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This work strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.ImportanceThe anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryotes dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. This manuscript assesses the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota post sequestration in the herbivorous gut. Analysis of twenty-seven transcriptomes that represent the broad Neocallimastigomycota diversity identified 283 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This work represents a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.

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Horizontal Gene Transfer in Microbial Genome Evolution

Theoretical Population Biology ◽

10.1006/tpbi.2002.1596 ◽

2002 ◽

Vol 61 (4) ◽

pp. 489-495 ◽

Cited By ~ 117

Author(s):

Ravi Jain ◽

Maria C. Rivera ◽

Jonathan E. Moore ◽

James A. Lake

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Evolution ◽

Microbial Genome

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Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage

Applied and Environmental Microbiology ◽

10.1128/aem.00988-19 ◽

2019 ◽

Vol 85 (15) ◽

Cited By ~ 21

Author(s):

Chelsea L. Murphy ◽

Noha H. Youssef ◽

Radwa A. Hanafy ◽

M. B. Couger ◽

Jason E. Stajich ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Gene Duplication ◽

Substrate Utilization ◽

High Rank ◽

Eukaryotic Lineage ◽

Fungal Lineage ◽

Fermentative Bacteria ◽

Survival And Growth

ABSTRACTSurvival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCEThe anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.

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Mobilizable narrow host range plasmids as natural suicide vectors enabling horizontal gene transfer among distantly related bacterial species

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.2011.02432.x ◽

2011 ◽

Vol 326 (1) ◽

pp. 76-82 ◽

Cited By ~ 20

Author(s):

Maria Smorawinska ◽

Magdalena Szuplewska ◽

Piotr Zaleski ◽

Paweł Wawrzyniak ◽

Anna Maj ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Host Range ◽

Bacterial Species ◽

Narrow Host Range

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Genetic Diversity and Host Range of Rhizobia Nodulating Lotus tenuis in Typical Soils of the Salado River Basin (Argentina)

Applied and Environmental Microbiology ◽

10.1128/aem.02405-08 ◽

2008 ◽

Vol 75 (4) ◽

pp. 1088-1098 ◽

Cited By ~ 56

Author(s):

Marï¿½a Julia Estrella ◽

Socorro Muï¿½oz ◽

Marï¿½a Josï¿½ Soto ◽

Oscar Ruiz ◽

Juan Sanjuï¿½n

Keyword(s):

Genetic Diversity ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

16S Rrna ◽

16S Rrna Gene ◽

Host Range ◽

River Basin ◽

Rrna Gene ◽

Narrow Host Range ◽

Salado River

ABSTRACT A total of 103 root nodule isolates were used to estimate the diversity of bacteria nodulating Lotus tenuis in typical soils of the Salado River Basin. A high level of genetic diversity was revealed by repetitive extragenic palindromic PCR, and 77 isolates with unique genomic fingerprints were further differentiated into two clusters, clusters A and B, after 16S rRNA restriction fragment length polymorphism analysis. Cluster A strains appeared to be related to the genus Mesorhizobium, whereas cluster B was related to the genus Rhizobium. 16S rRNA sequence and phylogenetic analysis further supported the distribution of most of the symbiotic isolates in either Rhizobium or Mesorhizobium: the only exception was isolate BA135, whose 16S rRNA gene was closely related to the 16S rRNA gene of the genus Aminobacter. Most Mesorhizobium-like isolates were closely related to Mesorhizobium amorphae, Mesorhizobium mediterraneum, Mesorhizobium tianshanense, or the broad-host-range strain NZP2037, but surprisingly few isolates grouped with Mesorhizobium loti type strain NZP2213. Rhizobium-like strains were related to Rhizobium gallicum, Rhizobium etli, or Rhizobium tropici, for which Phaseolus vulgaris is a common host. However, no nodC or nifH genes could be amplified from the L. tenuis isolates, suggesting that they have rather divergent symbiosis genes. In contrast, nodC genes from the Mesorhizobium and Aminobacter strains were closely related to nodC genes from narrow-host-range M. loti strains. Likewise, nifH gene sequences were very highly conserved among the Argentinian isolates and reference Lotus rhizobia. The high levels of conservation of the nodC and nifH genes suggest that there was a common origin of the symbiosis genes in narrow-host-range Lotus symbionts, supporting the hypothesis that both intrageneric horizontal gene transfer and intergeneric horizontal gene transfer are important mechanisms for the spread of symbiotic capacity in the Salado River Basin.

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Plant nodulation inducers enhance horizontal gene transfer ofAzorhizobium caulinodanssymbiosis island

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1615121113 ◽

2016 ◽

Vol 113 (48) ◽

pp. 13875-13880 ◽

Cited By ~ 40

Author(s):

Jun Ling ◽

Hui Wang ◽

Ping Wu ◽

Tao Li ◽

Yu Tang ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Host Range ◽

Regulatory Protein ◽

Genomic Islands ◽

Mutualistic Symbiosis ◽

Transcriptional Regulatory ◽

Lysr Family ◽

Integrative And Conjugative Element

Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of theSesbania rostratasymbiont,Azorhizobium caulinodans, is an 87.6-kb integrative and conjugative element (ICEAc) that is able to excise, form a circular DNA, and conjugatively transfer to a specific site of gly-tRNA gene of other rhizobial genera, expanding their host range. The HGT frequency was significantly increased in the rhizosphere. An ICEAc-located LysR-family transcriptional regulatory protein AhaR triggered the HGT process in response to plant flavonoids that induce the expression of nodulation genes through another LysR-type protein, NodD. Our study suggests that rhizobia may sense rhizosphere environments and transfer their symbiosis gene contents to other genera of rhizobia, thereby broadening rhizobial host-range specificity.

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