EVOLUTION OF MORPHOLOGICAL NOVELTY: A PHYLOGENETIC ANALYSIS OF GROWTH PATTERNS IN STREPTOCARPUS (GESNERIACEAE)

Abstract.— Streptocarpus shows great variation in vegetative architecture. In some species a normal shoot apical meristem never forms and the entire vegetative plant body may consist of a single giant cotyledon, which may measure up to 0.75 m (the unifoliate type) or with further leaves arising from this structure (the rosulate type). A molecular phylogeny of 87 taxa (77 Streptocarpus species, seven related species, and three outgroup species) using the internal transcribed spacers and 5.8S region of nuclear ribosomal DNA suggests that Streptocarpus can be divided into two major clades. One of these broadly corresponds to the caulescent group (with conventional shoot architecture) classified as subgenus Streptocarpella, whereas the other is mainly composed of acaulescent species with unusual architecture (subgenus Streptocarpus). Some caulescent species (such as S. papangae) are anomalously placed with the acaulescent clade. Available cytological data are, however, completely congruent with the two major clades: the caulescent clade is x = 15 and the acaulescent clade (including the caulescent S. papangae) is x = 16 (or polyploid multiples of 16). The genera Linnaeopsis, Saintpaulia, and Schizoboea are nested within Streptocarpus. The sequenced region has evolved, on average, 2.44 times faster in the caulescent clade than in the acaulescent clade and this is associated with the more rapid life cycle of the caulescents. Morphological variation in plant architecture within the acaulescent clade is homoplastic and does not appear to have arisen by unique abrupt changes. Instead, rosulate and unifoliate growth forms have evolved several times, reversals have occurred, and intermediate architectures are found. An underlying developmental plasticity seems to be a characteristic of the acaulescent clade and is reflected in a great lability of form.     

The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole‐genome shotgun sequencing of the nuclear genome of flax. Seven paired‐end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep‐coverage (approximately 94× raw, approximately 69× filtered) short‐sequence reads (44–100 bp), produced a set of scaffolds with N₅₀ = 694 kb, including contigs with N₅₀ = 20.1 kb. The contig assembly contained 302 Mb of non‐redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole‐genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis‐assembly of regions at the genome scale. A total of 43 384 protein‐coding genes were predicted in the whole‐genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K_s) observed within duplicate gene pairs was consistent with a recent (5–9 MYA) whole‐genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam‐A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole‐genome shotgun short‐sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.     

Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes

Background  

Inteins are self-splicing protein elements. They are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins) with a peptide bond. They are encoded as in-frame insertions within the genes for the host proteins. Inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. Only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these are from ascomycete or basidiomycete fungi.     

Floral phenology of an Andean bellflower and pollination by buff‐tailed sicklebill hummingbird

The Andean bellflowers comprise an explosive radiation correlated with shifts to specialized pollination. One diverse clade has evolved with extremely curved floral tubes and is predicted to be pollinated exclusively by one of two parapatric species of sicklebill hummingbirds (Eutoxeres). In this study, we focused on the floral biology of Centropogon granulosus, a bellflower thought to be specialized for pollination by Eutoxeres condamini, in a montane cloud forest site in southeastern Peru. Using camera traps and a pollination exclusion experiment, we documented E. condamini as the sole pollinator of C. granulosus. Visitation by E. condamini was necessary for fruit development. Flowering rates were unequivocally linear and conformed to the “steady‐state” phenological type. Over the course of >1800 h of monitoring, we recorded 12 E. condamini visits totaling 42 s, indicating traplining behavior. As predicted by its curved flowers, C. granulosus is exclusively pollinated by buff‐tailed sicklebill within our study area. We present evidence for the congruence of phenology and visitation as a driver of specialization in this highly diverse clade of Andean bellflowers.     

Longitudinal trends in subcutaneous fat thickness during adolescence

Longitudinal principal components (LPC) analysis is used to summarize adolescent trends in subcutaneous fat thickness at three sites (biceps, suprailiac, and abdominal). For each site, component 1 (C1) represents fatness level, and component 2 (C2) represents an increase followed by a decrease (fat wave) in fatness. Components 3-5 (retained for girls only) represent more complicated patterns of change (multiple increases and decreases). Correlations among scores for C1 for each site and among scores for C2 for each site indicate a high correspondence of fatness level and the magnitude of the fat wave. Associations between components and other indicators of maturity are apparent, indicating that serial fat patterns are controlled to some degree by influences affecting other pubescent events. Continuity between childhood fatness levels and adolescent patterns of fatness are relatively weak. Continuity between adolescent and adulthood fatness is somewhat greater.     

Complex origin of Trinitario-type Theobroma cacao (Malvaceae) from Trinidad and Tobago revealed using plastid genomics

Trinidad and Tobago has a long history of producing high-quality cacao (Theobroma cacao L.). Cacao genotypes in Trinidad and Tobago are of a highly distinctive kind, the so-called “Trinitario” cultivar group, widely considered to be of elite quality. The origin of Trinitario cacao is unclear, although it is generally considered to be of hybrid origin. We used massive parallel sequencing to identify polymorphic plastidic single nucleotide polymorphisms (cpSNPs) and polymorphic plastidic simple sequence repeats (cpSSRs) in order to determine the origin of the Trinitario cultivar group by comparing patterns of polymorphism to a reference set of ten completely sequenced chloroplast genomes (nine T. cacao and one outgroup, T. grandiflorum (Willd. ex Spreng.) Schum). Only three cpSNP haplotypes were present in the Trinitario cultivars sampled, each highly distinctive and corresponding to reference genotypes for the Criollo (CRI), Upper Amazon Forastero (UAF) and Lower Amazon Forastero (LAF) varietal groups. These three cpSNP haplotypes likely represent the founding lineages of cacao to Trinidad and Tobago. The cpSSRs were more variable with eight haplotypes, but these clustered into three groups corresponding to the three cpSNP haplotypes. The most common haplotype found in farms of Trinidad and Tobago was LAF, followed by UAF and then CRI. We conclude that the Trinitario cultivar group is of complex hybrid origin and has derived from at least three original introduction events.     

Single Nucleotide Polymorphisms in the Coding Region of the Developmental Gene Gcyc in Natural Populations of the Relict Ramonda myconi (Gesneriaceae)

Abstract: Gcyc is a developmental gene, present in the Gesneriaceae family, that has both highly conserved and highly variable regions. Ramonda myconi (Gesneriaceae) is a paleoendemic plant restricted to mountainous areas of NE Spain. In this study we examine the population variation in the coding region of Gcyc in R. myconi. The fast-evolving nature of the coding regions of the Gcyc gene plus the ancient history of R. myconi together provide an appropriate background to obtain the first insights into population-level variation in developmental genes of flowering plants. One locus of Gcyc was specifically amplified and sequenced. Four single nucleotide polymorphisms (SNPs) were detected in the 420 sequenced bases of the gene in two R. myconi populations. The Pyrenean population had only one SNP while all four SNPs were present in the southern population. Three out of four SNPs were non-synonymous. Such novel results indicate that the detection of SNPs in R. myconi over its entire distribution area could be used as an aid to reconstructing the population history of the species, as well as to investigate the relationship between developmental genes and morphological traits.