Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution

Title:
Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution
Authors:
Sun, Yanxia; Moore, Michael J.; Zhang, Shoujun; Soltis, Pamela S.; Soltis, Douglas E.; Zhao, Tingting; Meng, Aiping; Li, Xiaodong; Li, Jianqiang; Wang, Hengchang
Abstract:
The grade of early-diverging eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging eudicots; IRs ranged from 24.3 to 36.4 kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was resolved as sister to Sabiaceae with the highest support (bootstrap >90%) yet observed in plastome-scale phylogenetic analyses.
Citation:
Sun, Yanxia, Michael J. Moore, Shoujun Zhang, et al. 2016. "Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution." Molecular Phylogenetics and Evolution 96: 93-101.
Publisher:
Elsevier for Academic Press
DATE ISSUED:
2016-03
Department:
Biology
Type:
Article
PUBLISHED VERSION:
10.1016/j.ympev.2015.12.006
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S1055790315003851
PERMANENT LINK:
http://hdl.handle.net/11282/617294

Full metadata record

DC FieldValue Language
dc.contributor.authorSun, Yanxiaen
dc.contributor.authorMoore, Michael J.en
dc.contributor.authorZhang, Shoujunen
dc.contributor.authorSoltis, Pamela S.en
dc.contributor.authorSoltis, Douglas E.en
dc.contributor.authorZhao, Tingtingen
dc.contributor.authorMeng, Aipingen
dc.contributor.authorLi, Xiaodongen
dc.contributor.authorLi, Jianqiangen
dc.contributor.authorWang, Hengchangen
dc.date.accessioned2016-07-20T19:43:51Z-
dc.date.available2016-07-20T19:43:51Z-
dc.date.issued2016-03-
dc.identifier.citationSun, Yanxia, Michael J. Moore, Shoujun Zhang, et al. 2016. "Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution." Molecular Phylogenetics and Evolution 96: 93-101.en
dc.identifier.issn1055-7903-
dc.identifier.urihttp://hdl.handle.net/11282/617294-
dc.description.abstractThe grade of early-diverging eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging eudicots; IRs ranged from 24.3 to 36.4 kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was resolved as sister to Sabiaceae with the highest support (bootstrap >90%) yet observed in plastome-scale phylogenetic analyses.en
dc.language.isoen_USen
dc.publisherElsevier for Academic Pressen
dc.identifier.doi10.1016/j.ympev.2015.12.006-
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S1055790315003851en
dc.subject.departmentBiologyen_US
dc.titlePhylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolutionen_US
dc.typeArticleen
dc.identifier.journalMolecular Phylogenetics and Evolutionen
dc.identifier.volume96en_US
dc.identifier.startpage93en_US
dc.rightsArchived with thanks to Molecular Phylogenetics and Evolutionen
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