Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

Title:
Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries
Authors:
Kim, Hyoung Tae; Kim, Jung Sung; Moore, Michael J.; Neubig, Kurt M.; Williams, Norris H.; Whitten, W. Mark; Kim, Joo-Hwan
Abstract:
Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.
Citation:
Kim, H.T., J.S. Kim, M.J. Moore, et al. 2015. "Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries." PLoS ONE 10(11): e0142215.
Publisher:
Public Library of Science
DATE ISSUED:
2015-11-11
Department:
Biology
Type:
Article
PUBLISHED VERSION:
10.1371/journal.pone.0142215
PERMANENT LINK:
http://hdl.handle.net/11282/593487

Full metadata record

DC FieldValue Language
dc.contributor.authorKim, Hyoung Taeen
dc.contributor.authorKim, Jung Sungen
dc.contributor.authorMoore, Michael J.en
dc.contributor.authorNeubig, Kurt M.en
dc.contributor.authorWilliams, Norris H.en
dc.contributor.authorWhitten, W. Marken
dc.contributor.authorKim, Joo-Hwanen
dc.date.accessioned2016-01-14T16:18:38Zen
dc.date.available2016-01-14T16:18:38Zen
dc.date.issued2015-11-11en
dc.identifier.citationKim, H.T., J.S. Kim, M.J. Moore, et al. 2015. "Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries." PLoS ONE 10(11): e0142215.en
dc.identifier.issn1932-6203en
dc.identifier.urihttp://hdl.handle.net/11282/593487en
dc.description.abstractEarlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.en
dc.language.isoen_USen
dc.publisherPublic Library of Scienceen
dc.identifier.doi10.1371/journal.pone.0142215en
dc.subject.departmentBiologyen_US
dc.titleSeven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundariesen_US
dc.typeArticleen
dc.identifier.journalPLoS ONEen
dc.identifier.volume10en_US
dc.identifier.issue11en_US
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