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Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens.
PLoS One. 2016; 11(5):e0156250.Plos

Abstract

The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated.

Authors+Show Affiliations

INRA, MycSA, Villenave d'Ornon, France. Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand. School of Science, Mae Fah Luang University, Chiang Rai, Thailand.INRA, MycSA, Villenave d'Ornon, France.Department of Biology, McMaster University, Hamilton, Ontario, Canada.Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China. Beijing Engineering Research Center for Edible Mushroom, Beijing, China.INRA, MycSA, Villenave d'Ornon, France.State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand. School of Science, Mae Fah Luang University, Chiang Rai, Thailand.INRA, MycSA, Villenave d'Ornon, France.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27228131

Citation

Chen, Jie, et al. "Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus Subrufescens." PloS One, vol. 11, no. 5, 2016, pp. e0156250.
Chen J, Moinard M, Xu J, et al. Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens. PLoS ONE. 2016;11(5):e0156250.
Chen, J., Moinard, M., Xu, J., Wang, S., Foulongne-Oriol, M., Zhao, R., Hyde, K. D., & Callac, P. (2016). Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens. PloS One, 11(5), e0156250. https://doi.org/10.1371/journal.pone.0156250
Chen J, et al. Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus Subrufescens. PLoS ONE. 2016;11(5):e0156250. PubMed PMID: 27228131.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens. AU - Chen,Jie, AU - Moinard,Magalie, AU - Xu,Jianping, AU - Wang,Shouxian, AU - Foulongne-Oriol,Marie, AU - Zhao,Ruilin, AU - Hyde,Kevin D, AU - Callac,Philippe, Y1 - 2016/05/26/ PY - 2016/02/03/received PY - 2016/05/11/accepted PY - 2016/5/27/entrez PY - 2016/5/27/pubmed PY - 2017/8/2/medline SP - e0156250 EP - e0156250 JF - PloS one JO - PLoS ONE VL - 11 IS - 5 N2 - The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/27228131/Genetic_Analyses_of_the_Internal_Transcribed_Spacer_Sequences_Suggest_Introgression_and_Duplication_in_the_Medicinal_Mushroom_Agaricus_subrufescens_ L2 - http://dx.plos.org/10.1371/journal.pone.0156250 DB - PRIME DP - Unbound Medicine ER -