Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)

A revision of Lycianthes (Solanaceae) in tropical Asia

The genus Lycianthes (Dunal) Hassl. (Solanaceae) has in the past been treated as a section of the large genus Solanum L. but is more closely related to Capsicum L. Outside of the Americas, where the highest species diversity occurs, the genus is found in tropical and subtropical habitats from India to Japan and the Philippines, including the islands of Indonesia, New Guinea and the Solomons. The 19 species from Australia, New Guinea and the Pacific were treated in 'PhytoKeys 209'. Here I treat the remaining 10 species occurring across Asia; including two native species, L.biflora (Lour.) Bitter and L.oliveriana (Lauterb. & K.Schum) Bitter, and one cultivated species, L.rantonnetii (Carrière) Bitter that were also included in the earlier work. The Asian species treated here occupy a wide range of forested and disturbed habitats and are diverse in habit, ranging from epiphytic vines to small or medium sized trees, shrubs or creeping herbs. Many of the species are weedy plants of highly disturbed habitats and are best characterised as "ochlospecies", with complex polymorphic variation. Lycianthesrantonnetii, a species native to southern South America, is recorded as cultivated in India and Pakistan, but may be more widespread than collections indicate. The history of taxonomic treatments of Lycianthes in Asia is discussed, along with details of morphology found in all species. All species are treated in full, with complete morphological descriptions, including synonymy, lecto- or neotypifications, discussions of ecology and vernacular names, distribution maps and preliminary conservation assessments (for all except the cultivated L.rantonnetii). Searchable lists of all specimens examined are presented as Suppl. materials 1, 2.

Fossil berries reveal global radiation of the nightshade family by the early Cenozoic

Fossil discoveries can transform our understanding of plant diversification over time and space. Recently described fossils in many plant families have pushed their known records farther back in time, pointing to alternative scenarios for their origin and spread. Here, we describe two new Eocene fossil berries of the nightshade family (Solanaceae) from the Esmeraldas Formation in Colombia and the Green River Formation in Colorado (USA). The placement of the fossils was assessed using clustering and parsimony analyses based on 10 discrete and five continuous characters, which were also scored in 291 extant taxa. The Colombian fossil grouped with members of the tomatillo subtribe, and the Coloradan fossil aligned with the chili pepper tribe. Along with two previously reported early Eocene fossils from the tomatillo genus, these findings indicate that Solanaceae were distributed at least from southern South America to northwestern North America by the early Eocene. Together with two other recently discovered Eocene berries, these fossils demonstrate that the diverse berry clade and, in turn, the entire nightshade family, is much older and was much more widespread in the past than previously thought.

Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.

Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.

A revision of Lycianthes (Solanaceae) in Australia, New Guinea, and the Pacific

The genus Lycianthes (Dunal) Hassl. (Solanaceae) has in the past been treated as a section of the large genus Solanum L., but is more closely related to Capsicum L. The eighteen species of Lycianthes occurring in Australia, New Guinea (defined as the island of New Guinea, comprising Papua New Guinea [incl. Bougainville] and the Indonesian provinces of Papua Barat and Papua, plus the surrounding islands connected during the last glacial maximum) and the Pacific Islands are here treated in full, with complete descriptions, including synonymy, typifications and synonyms, distribution maps and illustrations. The history of taxonomic treatment of the genus in the region is also discussed. These taxa occupy a diverse range of forested habitats, and are in diverse in habit, from small shrubs to large canopy lianas to epiphytic shrubs. They are for the most part rarely collected, and many are endemic (14 of the 18 species treated here). Australia has a single endemic Lycianthes species (L.shanesii (F.Muell.) A.R.Bean). Nine species are found in both Indonesia and Papua New Guinea, one in Indonesia only, four in Papua New Guinea only, and L.vitiensis (Seem). A.R.Bean is known from Bougainville (Papua New Guinea) and the south Pacific as far east as Samoa. Lyciantheslucens S.Knapp sp. nov. is described from the islands of Lihir, New Ireland and the Louisiade Archipelago of Papua New Guinea. The cultivated L.rantonnetii (Carrière) Bitter is also treated in full, in this region known currently only from Australia; it is native to southern South America. Preliminary conservation assessments are presented for all species except the cultivated L.rantonnetii.

Monograph of wild and cultivated chili peppers (Capsicum L., Solanaceae)

Capsicum L. (tribe Capsiceae, Solanaceae) is an American genus distributed ranging from the southern United States of America to central Argentina and Brazil. The genus includes chili peppers, bell peppers, ajíes, habaneros, jalapeños, ulupicas and pimientos, well known for their economic importance around the globe. Within the Solanaceae, the genus can be recognised by its shrubby habit, actinomorphic flowers, distinctive truncate calyx with or without appendages, anthers opening by longitudinal slits, nectaries at the base of the ovary and the variously coloured and usually pungent fruits. The highest diversity of this genus is located along the northern and central Andes. Although Capsicum has been extensively studied and great advances have been made in the understanding of its taxonomy and the relationships amongst species, there is no monographic treatment of the genus as a whole. Based on morphological and molecular evidence studied from field and herbarium specimens, we present here a comprehensive taxonomic treatment for the genus, including updated information about morphology, anatomy, karyology, phylogeny and distribution. We recognise 43 species and five varieties, including C.mirum Barboza, sp. nov. from São Paulo State, Brazil and a new combination C.muticum (Sendtn.) Barboza, comb. nov.; five of these taxa are cultivated worldwide (C.annuumL.var.annuum, C.baccatumL.var.pendulum (Willd.) Eshbaugh, C.baccatumL.var.umbilicatum (Vell.) Hunz. & Barboza, C.chinense Jacq. and C.frutescens L.). Nomenclatural revision of the 265 names attributed to chili peppers resulted in 89 new lectotypifications and five new neotypifications. Identification keys and detailed descriptions, maps and illustrations for all taxa are provided.

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

PREMISE

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.

METHODS

A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set).

RESULTS

While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy.

CONCLUSIONS

We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.

The genus Lycianthes (Solanaceae, Capsiceae) in Mexico and Guatemala

Lycianthes, the third most species-rich genus in the Solanaceae, is distributed in both the New and Old Worlds and is especially diverse in Mexico. Here we provide an identification key, taxonomic descriptions, distribution maps, and illustrations of specimens, trichomes, flowers, and fruits for the 53 known Lycianthes taxa of Mexico and Guatemala. The new combination Lycianthes scandens (Mill.) M.Nee is made and replaces the name Lycianthes lenta (Cav.) Bitter, which is placed in synonymy. Within L. scandens, two varieties are recognized (Lycianthes scandens var. scandens and Lycianthes scandens var. flavicans (Bitter) J.Poore & E.Dean, comb. nov.). In addition, one new species (Lycianthes rafatorresii E.Dean, sp. nov.) is described from eastern Mexico, and 10 names (either recognized taxa or synonyms of recognized taxa) are lectotypified, including the names Solanum heteroclitum Sendtn., S. rantonnetii Carrière, and S. synantherum Sendtn. The species L. multiflora Bitter and L. synanthera (Sendtn.) Bitter are excluded from the treatment, as research indicates that they do not occur in Mexico and Guatemala, however full synonymy for both names is given.

Tandem gene duplication and recombination at the AT3 locus in the Solanaceae, a gene essential for capsaicinoid biosynthesis in Capsicum

Capsaicinoids are compounds synthesized exclusively in the genus Capsicum and are responsible for the burning sensation experienced when consuming hot pepper fruits. To date, only one gene, AT3, a member of the BAHD family of acyltransferases, is currently known to have a measurable quantitative effect on capsaicinoid biosynthesis. Multiple AT3 paralogs exist in the Capsicum genome, but their evolutionary relationships have not been characterized well. Recessive alleles at this locus result in absence of capsaicinoids in pepper fruit. To explore the evolution of AT3 in Capsicum and the Solanaceae, we sequenced this gene from diverse Capsicum genotypes and species, along with a number of representative solanaceous taxa. Our results revealed that the coding region of AT3 is highly conserved throughout the family. Further, we uncovered a tandem duplication that predates the diversification of the Solanaceae taxa sampled in this study. This pair of tandem duplications were designated AT3-1 and AT3-2. Sequence alignments showed that the AT3-2 locus, a pseudogene, retains regions of amino acid conservation relative to AT3-1. Gene tree estimation demonstrated that AT3-1 and AT3-2 form well supported, distinct clades. In C. rhomboideum, a non-pungent basal Capsicum species, we describe a recombination event between AT3-1 and AT3-2 that modified the putative active site of AT3-1, also resulting in a frame-shift mutation in the second exon. Our data suggest that duplication of the original AT3 representative, in combination with divergence and pseudogene degeneration, may account for the patterns of sequence divergence and punctuated amino acid conservation observed in this study. Further, an early rearrangement in C. rhomboidium could account for the absence of pungency in this Capsicum species.

Four new species of Capsicum (Solanaceae) from the tropical Andes and an update on the phylogeny of the genus

Four new species of Capsicum (Capsiceae, Solanaceae) from Andean tropical forests in South America are described. Capsicum benoistii Hunz. ex Barboza sp. nov. (incertae sedis) is endemic to a restricted area in south-central Ecuador and is most similar to the more widespread C. geminifolium (Dammer) Hunz. (Colombia, Ecuador, and Peru). Capsicum piuranum Barboza & S. Leiva sp. nov. (Andean clade) is found in northern Peru (Department Piura) and is morphologically most similar to C. caballeroi M. Nee of the Bolivian yungas (Departments Santa Cruz and Cochabamba) but closely related to C. geminifolium and C. lycianthoides Bitter. Capsicum longifolium Barboza & S. Leiva sp. nov. (Andean clade) occurs from northern Peru (Departments Amazonas, Cajamarca, and Piura) to southern Ecuador (Province Zamora-Chinchipe), and is morphologically most similar to C. dimorphum (Miers) Kuntze (Colombia, Ecuador, and Peru). Capsicum neei Barboza & X. Reyes sp. nov. (Bolivian clade) is endemic to southeastern Bolivia (Departments Chuquisaca and Santa Cruz) in the Boliviano-Tucumano Forest, is morphologically most similar to another Bolivian endemic species C. minutiflorum Rusby (Hunz.), and is closely related to C. caballeroi. Complete descriptions, illustrations, distributions and conservation assessments of all new species are given. Chromosome numbers for C. piuranum and C. longifolium are also provided. Three of the new species were included in a new phylogenetic analysis for Capsicum; their positions were strongly resolved within clades previously recognized in the genus.