Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family

Title:
Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family
Authors:
Sun, Yanxia; Moore, Michael J.; Lin, Nan; Adelalu, Kole F.; Meng, Aiping; Jian, Shuguang; Yang, Linsen; Li, Jianqiang; Wang, Hengchang
Abstract:
BACKGROUND: Among the 13 familiesofearly-diverging eudicots, only Circaeasteraceae (Ranunculales),which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements amongearly-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution inearly-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae. RESULTS: Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora. Plastome structure and gene content were compared between these two plastomes, and with those of otherearly-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large similar to 49 kb inversion and a small similar to 3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (psi ndhA, psi ndhB, psi ndhD, psi ndhH and psi ndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses. CONCLUSION: The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales.
Citation:
Sun, Yanxia, Michael J. Moore, Nan Lin, et al. 2017. "Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family." BMC Genomics 18: 592.
Publisher:
Biomed Central Ltd.
DATE ISSUED:
2017-08-09
Department:
Biology
Type:
Article
PUBLISHED VERSION:
10.1186/s12864-017-3956-3
Additional Links:
http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3956-3
PERMANENT LINK:
http://hdl.handle.net/11282/620493

Full metadata record

DC FieldValue Language
dc.contributor.authorSun, Yanxiaen
dc.contributor.authorMoore, Michael J.en
dc.contributor.authorLin, Nanen
dc.contributor.authorAdelalu, Kole F.en
dc.contributor.authorMeng, Aipingen
dc.contributor.authorJian, Shuguangen
dc.contributor.authorYang, Linsenen
dc.contributor.authorLi, Jianqiangen
dc.contributor.authorWang, Hengchangen
dc.date.accessioned2017-09-13T12:14:25Z-
dc.date.available2017-09-13T12:14:25Z-
dc.date.issued2017-08-09-
dc.identifier.citationSun, Yanxia, Michael J. Moore, Nan Lin, et al. 2017. "Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family." BMC Genomics 18: 592.en
dc.identifier.issn1471-2164-
dc.identifier.urihttp://hdl.handle.net/11282/620493-
dc.description.abstractBACKGROUND: Among the 13 familiesofearly-diverging eudicots, only Circaeasteraceae (Ranunculales),which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements amongearly-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution inearly-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae. RESULTS: Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora. Plastome structure and gene content were compared between these two plastomes, and with those of otherearly-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large similar to 49 kb inversion and a small similar to 3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (psi ndhA, psi ndhB, psi ndhD, psi ndhH and psi ndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses. CONCLUSION: The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales.en
dc.language.isoen_USen
dc.publisherBiomed Central Ltd.en
dc.identifier.doi10.1186/s12864-017-3956-3-
dc.relation.urlhttp://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3956-3en
dc.subject.departmentBiologyen_US
dc.titleComplete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene familyen_US
dc.typeArticleen
dc.identifier.journalBMC Genomicsen
dc.subject.keywordEarly-diverging eudicotsen_US
dc.subject.keywordCircaeasteraceaeen_US
dc.subject.keywordPlastomeen_US
dc.subject.keywordRearrangementsen_US
dc.subject.keywordGene lossen_US
dc.subject.keywordPhylogenetic analysesen_US
dc.identifier.volume18en_US
dc.rightsArchived with thanks to BMC Genomicsen
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