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Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae

We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum jap...

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Autores principales: Kado, Tomoyuki, Innan, Hideki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294234/
https://www.ncbi.nlm.nih.gov/pubmed/30407540
http://dx.doi.org/10.1093/gbe/evy219
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author Kado, Tomoyuki
Innan, Hideki
author_facet Kado, Tomoyuki
Innan, Hideki
author_sort Kado, Tomoyuki
collection PubMed
description We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampyrum roseum) are facultative parasites. By using reference genome sequences and/or transcriptomes of 14 species from Fabaceae and Poaceae, their major host families, we detected 106 horizontally transferred genes (HGT genes), only in the genomes of the two obligate parasites (22 and 84 for Oro. minor and Ae. indica, respectively), whereas none in the three facultative parasites. The HGT genes, respectively, account for roughly 0.1% and 0.2% of the coding genes in the two species. We found that almost all HGT genes retained introns at the same locations as their homologs in potential host species, indicating a crucial role of DNA-mediated gene transfer, rather than mRNA mediated retro transfer. Furthermore, some of the HGT genes might have transferred simultaneously because they located very closely in the host reference genome, indicating that the length of transferred DNA could exceed 100 kb. We confirmed that almost all introns are spliced in the current genome of the parasite species, and that about half HGT genes do not have any missense mutations or frameshift-causing indels, suggesting that some HGT genes may be still functional. Evolutionary analyses revealed that the nonsynonymous–synonymous substitution ratio is on average elevated on the lineage leading to HGT genes, due to either relaxation of selection or positive selection.
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spelling pubmed-62942342018-12-19 Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae Kado, Tomoyuki Innan, Hideki Genome Biol Evol Research Article We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampyrum roseum) are facultative parasites. By using reference genome sequences and/or transcriptomes of 14 species from Fabaceae and Poaceae, their major host families, we detected 106 horizontally transferred genes (HGT genes), only in the genomes of the two obligate parasites (22 and 84 for Oro. minor and Ae. indica, respectively), whereas none in the three facultative parasites. The HGT genes, respectively, account for roughly 0.1% and 0.2% of the coding genes in the two species. We found that almost all HGT genes retained introns at the same locations as their homologs in potential host species, indicating a crucial role of DNA-mediated gene transfer, rather than mRNA mediated retro transfer. Furthermore, some of the HGT genes might have transferred simultaneously because they located very closely in the host reference genome, indicating that the length of transferred DNA could exceed 100 kb. We confirmed that almost all introns are spliced in the current genome of the parasite species, and that about half HGT genes do not have any missense mutations or frameshift-causing indels, suggesting that some HGT genes may be still functional. Evolutionary analyses revealed that the nonsynonymous–synonymous substitution ratio is on average elevated on the lineage leading to HGT genes, due to either relaxation of selection or positive selection. Oxford University Press 2018-11-08 /pmc/articles/PMC6294234/ /pubmed/30407540 http://dx.doi.org/10.1093/gbe/evy219 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Kado, Tomoyuki
Innan, Hideki
Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae
title Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae
title_full Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae
title_fullStr Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae
title_full_unstemmed Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae
title_short Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae
title_sort horizontal gene transfer in five parasite plant species in orobanchaceae
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294234/
https://www.ncbi.nlm.nih.gov/pubmed/30407540
http://dx.doi.org/10.1093/gbe/evy219
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AT innanhideki horizontalgenetransferinfiveparasiteplantspeciesinorobanchaceae