Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

Although Pentapetalae (comprising all core eudicots except Gunnerales) include ≈70% of all angiosperms, the origin of and relationships among the major lineages of this clade have remained largely unresolved. Phylogenetic analyses of 83 protein-coding and rRNA genes from the plastid genome for 86 species of seed plants, including new sequences from 25 eudicots, indicate that soon after its origin, Pentapetalae diverged into three clades: (i) a "superrosid" clade consisting of Rosidae, Vitaceae, and Saxifragales; (ii) a "superasterid" clade consisting of Berberidopsidales, Santalales, Caryophyllales, and Asteridae; and (iii) Dilleniaceae. Maximum-likelihood analyses support the position of Dilleniaceae as sister to superrosids, but topology tests did not reject alternative positions of Dilleniaceae as sister to Asteridae or all remaining Pentapetalae. Molecular dating analyses suggest that the major lineages within both superrosids and superasterids arose in as little as 5 million years. This phylogenetic hypothesis provides a crucial historical framework for future studies aimed at elucidating the underlying causes of the morphological and species diversity in Pentapetalae.Angiosperm Tree of Life | Pentapetalae | plastid genome T he Eudicotyledoneae (sensu) (1), or eudicots, comprise ≈75% of all angiosperm species (2) and encompass enormous morphological, biochemical, and ecological diversity. More than 90% of eudicot species diversity is found within the clade Pentapetalae (1), which includes major clades such as Rosidae, Caryophyllales, Saxifragales, Asteridae, and Santalales, as well as smaller lineages such as Berberidopsidales and Dilleniaceae (3-8). Previous analyses of multigene data sets have failed to resolve relationships among the major clades of Pentapetalae (6, 9). The inability to resolve these relationships suggests that the major lineages of Pentapetalae diverged rapidly, a hypothesis supported by the fossil record (10, 11). However, our understanding of the origins and evolution of Pentapetalae diversity, and consequently much of angiosperm diversity, is hindered by the lack of a well-supported phylogenetic hypothesis.Phylogenetic analyses based on complete plastid genome sequences have resolved several enigmatic relationships within angiosperms (12, 13). However, these analyses have not included data for many crucial eudicot clades. To resolve relationships among the major clades of Eudicotyledoneae (with a focus on Pentapetalae), we performed phylogenetic analyses using a data set composed of 83 genes derived from 86 complete plastid genome sequences, 25 of which were eudicot sequences generated for this study. To date, this is the largest plastid genome data set used for phylogenetic inference and includes representatives of nearly all (37 of 42) orders of eudicots sensu Angiosperm Phylogeny Group (APG) III (14). The resulting phylogenetic hypothesis helps to clarify the diversification of Pentapetalae and provides an improved framework for investigating evolutionary processes that accompanie...

Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (Ϸ42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae ؉ magnoliids as sister to a well supported clade of monocots ؉ (Ceratophyllum ؉ eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 ؎ 4.8 and 140.3 ؎ 4.8 Mya.

Background Plastome (plastid genome) sequences provide valuable information for understanding the phylogenetic relationships and evolutionary history of plants. Although the rapid development of high-throughput sequencing technology has led to an explosion of plastome sequences, annotation remains a significant bottleneck for plastomes. User-friendly batch annotation of multiple plastomes is an urgent need. Results We introduce Plastid Genome Annotator (PGA), a standalone command line tool that can perform rapid, accurate, and flexible batch annotation of newly generated target plastomes based on well-annotated reference plastomes. In contrast to current existing tools, PGA uses reference plastomes as the query and unannotated target plastomes as the subject to locate genes, which we refer to as the reverse query-subject BLAST search approach. PGA accurately identifies gene and intron boundaries as well as intron loss. The program outputs GenBank-formatted files as well as a log file to assist users in verifying annotations. Comparisons against other available plastome annotation tools demonstrated the high annotation accuracy of PGA, with little or no post-annotation verification necessary. Likewise, we demonstrated the flexibility of reference plastomes within PGA by annotating the plastome of Rosa roxburghii using that of Amborella trichopoda as a reference. The program, user manual and example data sets are freely available at https://github.com/quxiaojian/PGA . Conclusions PGA facilitates rapid, accurate, and flexible batch annotation of plastomes across plants. For projects in which multiple plastomes are generated, the time savings for high-quality plastome annotation are especially significant.