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Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements

Plastomes of heterotrophs went through varying degrees of degradation along with the transition from autotrophic to heterotrophic lifestyle. Here, we identified the plastome of mycoheterotrophic species Burmannia itoana and compared it with those of its reported relatives including three autotrophs...

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Autores principales: Li, Xiaojuan, Qian, Xin, Yao, Gang, Zhao, Zhongtao, Zhang, Dianxiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788436/
https://www.ncbi.nlm.nih.gov/pubmed/31608171
http://dx.doi.org/10.7717/peerj.7787
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author Li, Xiaojuan
Qian, Xin
Yao, Gang
Zhao, Zhongtao
Zhang, Dianxiang
author_facet Li, Xiaojuan
Qian, Xin
Yao, Gang
Zhao, Zhongtao
Zhang, Dianxiang
author_sort Li, Xiaojuan
collection PubMed
description Plastomes of heterotrophs went through varying degrees of degradation along with the transition from autotrophic to heterotrophic lifestyle. Here, we identified the plastome of mycoheterotrophic species Burmannia itoana and compared it with those of its reported relatives including three autotrophs and one heterotroph (Thismia tentaculata) in Dioscoreales. B. itoana yields a rampantly degraded plastome reduced in size and gene numbers at the advanced stages of degradation. Its length is 44,463 bp with a quadripartite structure. B. itoana plastome contains 33 tentatively functional genes and six tentative pseudogenes, including several unusually retained genes. These unusual retention suggest that the inverted repeats (IRs) regions and possibility of being compensated may prolong retention of genes in plastome at the advanced stage of degradation. Otherwise, six rearrangements including four inversions (Inv1/Inv2/Inv3/Inv4) and two translocations (Trans1/Trans2) were detected in B. itoana plastome vs. its autotrophic relative B. disticha. We speculate that Inv1 may be mediated by recombination of distinct tRNA genes, while Inv2 is likely consequence of extreme gene losses due to the shift to heterotrophic lifestyle. The other four rearrangements involved in IRs and small single copy region may attribute to multiple waves of IRs and overlapping inversions. Our study fills the gap of knowledge about plastomes of heterotroph in Burmannia and provides a new evidence for the convergent degradation patterns of plastomes en route to heterotrophic lifestyle.
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spelling pubmed-67884362019-10-11 Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements Li, Xiaojuan Qian, Xin Yao, Gang Zhao, Zhongtao Zhang, Dianxiang PeerJ Genomics Plastomes of heterotrophs went through varying degrees of degradation along with the transition from autotrophic to heterotrophic lifestyle. Here, we identified the plastome of mycoheterotrophic species Burmannia itoana and compared it with those of its reported relatives including three autotrophs and one heterotroph (Thismia tentaculata) in Dioscoreales. B. itoana yields a rampantly degraded plastome reduced in size and gene numbers at the advanced stages of degradation. Its length is 44,463 bp with a quadripartite structure. B. itoana plastome contains 33 tentatively functional genes and six tentative pseudogenes, including several unusually retained genes. These unusual retention suggest that the inverted repeats (IRs) regions and possibility of being compensated may prolong retention of genes in plastome at the advanced stage of degradation. Otherwise, six rearrangements including four inversions (Inv1/Inv2/Inv3/Inv4) and two translocations (Trans1/Trans2) were detected in B. itoana plastome vs. its autotrophic relative B. disticha. We speculate that Inv1 may be mediated by recombination of distinct tRNA genes, while Inv2 is likely consequence of extreme gene losses due to the shift to heterotrophic lifestyle. The other four rearrangements involved in IRs and small single copy region may attribute to multiple waves of IRs and overlapping inversions. Our study fills the gap of knowledge about plastomes of heterotroph in Burmannia and provides a new evidence for the convergent degradation patterns of plastomes en route to heterotrophic lifestyle. PeerJ Inc. 2019-10-08 /pmc/articles/PMC6788436/ /pubmed/31608171 http://dx.doi.org/10.7717/peerj.7787 Text en © 2019 Li et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Genomics
Li, Xiaojuan
Qian, Xin
Yao, Gang
Zhao, Zhongtao
Zhang, Dianxiang
Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements
title Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements
title_full Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements
title_fullStr Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements
title_full_unstemmed Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements
title_short Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements
title_sort plastome of mycoheterotrophic burmannia itoana mak. (burmanniaceae) exhibits extensive degradation and distinct rearrangements
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788436/
https://www.ncbi.nlm.nih.gov/pubmed/31608171
http://dx.doi.org/10.7717/peerj.7787
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