Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

Title:
Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species
Authors:
Sun, Yanxia; Moore, Michael J.; Meng, Aiping; Soltis, Pamela S.; Soltis, Douglas E.; Li, Jianqiang; Wang, Hengchang
Abstract:
The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots), but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ~4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8) that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.
Citation:
Sun Y-x, Moore MJ, Meng A-p, Soltis PS, Soltis DE, Li, J-q, and Wang, H-c. (2013) Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species. PLoS ONE 8(4): e60429. doi:10.1371/journal.pone.0060429
Publisher:
Public Library of Science
DATE ISSUED:
2013-04-05
Department:
Biology
Type:
article
PUBLISHED VERSION:
10.1371/journal.pone.0060429
PERMANENT LINK:
http://hdl.handle.net/11282/309695

Full metadata record

DC FieldValue Language
dc.contributor.authorSun, Yanxiaen_US
dc.contributor.authorMoore, Michael J.en_US
dc.contributor.authorMeng, Aipingen_US
dc.contributor.authorSoltis, Pamela S.en_US
dc.contributor.authorSoltis, Douglas E.en_US
dc.contributor.authorLi, Jianqiangen_US
dc.contributor.authorWang, Hengchangen_US
dc.date.accessioned2013-12-23T16:15:28Zen
dc.date.available2013-12-23T16:15:28Zen
dc.date.issued2013-04-05en
dc.identifier.citationSun Y-x, Moore MJ, Meng A-p, Soltis PS, Soltis DE, Li, J-q, and Wang, H-c. (2013) Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species. PLoS ONE 8(4): e60429. doi:10.1371/journal.pone.0060429en_US
dc.identifier.issn1932-6203en_US
dc.identifier.urihttp://hdl.handle.net/11282/309695en
dc.description.abstractThe early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots), but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ~4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8) that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.en_US
dc.language.isoen_USen_US
dc.publisherPublic Library of Scienceen_US
dc.identifier.doi10.1371/journal.pone.0060429en
dc.subject.departmentBiologyen_US
dc.titleComplete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Speciesen_US
dc.typearticleen_US
dc.identifier.journalPLoS ONEen_US
dc.subject.keywordComplete chloroplast genomeen_US
dc.subject.keywordWestern North Americaen_US
dc.subject.keywordAngiosperm phylogenyen_US
dc.subject.keywordBasal eudicotsen_US
dc.subject.keywordPotomac Groupen_US
dc.subject.keywordNordenskioldia trochodendraceaeen_US
dc.subject.keywordTetracentron trochodendraceaeen_US
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