Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species

BACKGROUND AND AIMS

Hybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles of sympatry and isolation, creating conditions for extensive hybridization and introgression. Polyploidization is another genome-wide process with a major influence on plant evolution. Both hybridization and polyploidization can have complex effects on plant evolution. However, these effects are often difficult to understand in recently evolved species complexes.

METHODS

We combined flow cytometry, analyses of transcriptomic sequences and pollen tube growth assays to investigate the consequences of polyploidization, hybridization and introgression on the recent evolution of several Erysimum (Brassicaceae) species from the South of the Iberian Peninsula, a well-known glacial refugium. This species complex differentiated in the last 2 million years, and its evolution has been hypothesized to be determined mainly by polyploidization, interspecific hybridization and introgression.

KEY RESULTS

Our results support a scenario of widespread hybridization involving both extant and 'ghost' taxa. Several taxa studied here, most notably those with purple corollas, are polyploids, probably of allopolyploid origin. Moreover, hybridization in this group might be an ongoing phenomenon, as pre-zygotic barriers appeared weak in many cases.

CONCLUSIONS

The evolution of Erysimum spp. has been determined by hybridization to a large extent. Species with purple (polyploids) and yellow flowers (mostly diploid) exhibit a strong signature of introgression in their genomes, indicating that hybridization occurred regardless of colour and across ploidy levels. Although the adaptive value of such genomic exchanges remains unclear, our results demonstrate the significance of hybridization for plant diversification, which should be taken into account when studying plant evolution.

Comparative phylogenetic analysis of oolong tea (Phoenix Dancong tea) using complete chloroplast genome sequences

Phoenix Dancong tea, a variety of oolong tea, is produced in Chaozhou, Guangdong Province, China, and is characterized by numerous hybridizations and polyploidization. To assess the genetic diversity and phylogenetic relationships among Phoenix Dancong tea and other oolong teas, an integrated circular chloroplast genome was constructed for thirty species of Phoenix Dancong tea from Chaozhou. The genome of Phoenix dancong tea is a circular molecule of 157,041-157,137 bp, with a pair of inverted repeats (26,072-26,610 bp each) separated by a large single copy (86,615-86,658 bp) and small single copy (18,264-18,284 bp). A total of 135 unique genes were encoded, including 90 protein coding genes, 37 tRNAs and 8 rRNAs. A comparative analysis with the other seven species in the oolong tea family that have been sequenced to date revealed similarities in structural organization, gene content and arrangement. Repeated sequence analysis identified 17-23 tandem repeats, 20-24 forward repeats and 25-27 palindromic repeats. Additionally, a total of 65-70 simple sequence repeats were detected, with mononucleotide repeats being the most common. Phylogenetic analyses showed that Phoenix Dancong tea and Fujian oolong tea were clustered with other cultivated Camellia sinensis in the genus Camellia of the family Theaceae, while the two oolong tea species were relatively independently cross-embedded in the genus, Camellia. Close genetic relationships were observed between Phoenix Dancong tea and other oolong teas, and the overall chloroplast genomes of oolong tea showed patterns with low variations and conserved evolution. The availability of Phoenix Dancong tea chloroplast genomes not only elucidated the relationship among oolong teas from different origins in Guangdong and Fujian but also provided valuable genetic resources to assist further molecular studies on the taxonomic and phylogenomic resolution of the genus Camellia.