Comparative Analyses of Chloroplast Genome Provide Effective Molecular Markers for Species and Cultivar Identification in Bougainvillea.

Bougainvillea is popular in ornamental horticulture for its colorful bracts and excellent adaptability, but the complex genetic relationship among this genus is fuzzy due to limited genomic data. To reveal more genomic resources of Bougainvillea, we sequenced and assembled the complete chloroplast (cp) genome sequences of Bougainvillea spectabilis 'Splendens'. The cp genome size was 154,869 bp in length, containing 86 protein-coding genes, 38 tRNAs, and eight rRNAs. Cp genome comparison across 12 Bougainvillea species (B. spectabilis, B. glabra, B. peruviana, B. arborea, B. praecox, B. stipitata, B. campanulata, B. berberidifolia, B. infesta, B. modesta, B. spinosa, and B. pachyphylla) revealed five mutational hotspots. Phylogenetic analysis suggested that B. spectabilis published previously and B. glabra clustered into one subclade as two distinct groups, sister to the subclade of B. spectabilis 'Splendens'. We considered the phylogeny relationships between B. spectabilis and B. glabra to be controversial. Based on two hypervariable regions and three common plastid regions, we developed five molecular markers for species identification in Bougainvillea and applied them to classify 53 ornamental Bougainvillea cultivars. This study provides a valuable genetic resource for Bougainvillea breeding and offers effective molecular markers to distinguish the representative ornamental species of Bougainvillea.

Balancing selection on an MYB transcription factor maintains the twig trichome color variation in Melastoma normale.

BACKGROUND: The factors that maintain phenotypic and genetic variation within a population have received long-term attention in evolutionary biology. Here the genetic basis and evolution of the geographically widespread variation in twig trichome color (from red to white) in a shrub Melastoma normale was investigated using Pool-seq and evolutionary analyses. RESULTS: The results show that the twig trichome coloration is under selection in different light environments and that a 6-kb region containing an R2R3 MYB transcription factor gene is the major region of divergence between the extreme red and white morphs. This gene has two highly divergent groups of alleles, one of which likely originated from introgression from another species in this genus and has risen to high frequency (> 0.6) within each of the three populations under investigation. In contrast, polymorphisms in other regions of the genome show no sign of differentiation between the two morphs, suggesting that genomic patterns of diversity have been shaped by homogenizing gene flow. Population genetics analysis reveals signals of balancing selection acting on this gene, and it is suggested that spatially varying selection is the most likely mechanism of balancing selection in this case. CONCLUSIONS: This study demonstrate that polymorphisms on a single transcription factor gene largely confer the twig trichome color variation in M. normale, while also explaining how adaptive divergence can occur and be maintained in the face of gene flow.

Chromosomal-level genome assembly of Melastoma candidum provides insights into trichome evolution.

Melastoma, consisting of ~100 species diversified in tropical Asia and Oceania in the past 1-2 million years, represents an excellent example of rapid speciation in flowering plants. Trichomes on hypanthia, twigs and leaves vary markedly among species of this genus and are the most important diagnostic traits for species identification. These traits also play critical roles in contributing to differential adaptation of these species to their own habitats. Here we sequenced the genome of M. candidum, a common, erect-growing species from southern China, with the aim to provide genomic insights into trichome evolution in this genus. We generated a high-quality, chromosome-level genome assembly of M. candidum, with the genome size of 256.2 Mb and protein-coding gene number of 40,938. The gene families specific to, and significantly expanded in Melastoma are enriched for GO terms related to trichome initiation and differentiation. We provide evidence that Melastoma and its sister genus Osbeckia have undergone two whole genome duplications (WGDs) after the triplication event (γ) shared by all core eudicots. Preferential retention of trichome development-related transcription factor genes such as C2H2, bHLH, HD-ZIP, WRKY, and MYB after both WGDs might provide raw materials for trichome evolution and thus contribute to rapid species diversification in Melastoma. Our study provides candidate transcription factor genes related to trichome evolution in Melastoma, which can be used to evolutionary and functional studies of trichome diversification among species of this genus.

The complete chloroplast genome of Petunia exserta (Solanaceae: Petunioideae), an endangered ornamental species.

Petunia exserta is an ornamental species on the brink of extinction in the wild. We report here the complete chloroplast genome of P. exserta, which is 156,598 bp in size consisting of a large single-copy region (87,095 bp), a small single-copy region (18,643 bp), and a pair of inverted repeats (25,430 bp for each). The chloroplast (used 'cp' hereafter) genome contains 132 genes, including 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. Phylogenetic analysis demonstrated that P. exserta was most closely related to P. hybrida, and they together were closer to Calibrachoa hybrida than other taxa in the Solanaceae family.

Comparative Analysis of the Complete Chloroplast Genomes of Nine Paphiopedilum Species.

Paphiopedilum is known as "lady's or Venus" slipper orchids due to its prominent shoe-shaped labellum, with high ornamental value. Phylogenetic relationships among some species in Paphiopedilum genus cannot be effectively determined by morphological features alone or through the analysis of nuclear or chloroplast DNA fragments. In order to provide aid in understanding the evolutionary and phylogenetic relationship in Paphiopedilum at chloroplast (cp) genome-scale level, the complete cp genomes of six Paphiopedilum species were newly sequenced in this study, and three other published cp genome sequences of Paphiopedilum were included in the comparative analyses. The cp genomes of the six Paphiopedilum species ranged from 154,908 bp (P. hirsutissimum) to 161,300 bp (P. victoria-mariae) in size, all constituting four-part annular structures. Analyses of the nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes were conducted. Ten highly variable regions that could serve as potential DNA barcodes or phylogenetic markers for this diverse genus were identified. Sequence variations in the non-coding regions were greater than that in the conserved protein-coding regions, as well as in the large single copy (LSC) and small single copy (SSC) regions than in the inverted repeat (IR) regions. Phylogenetic analysis revealed that all Paphiopedilum species clustered in one monophyletic clade in the Cypripedioideae subfamily and then subdivided into seven smaller branches corresponding to different subgenus or sections of the genus, with high bootstrap supports, indicate that cp genome sequencing can be an effective means in resolving the complex relationship in Paphiopedilum.

Characterization of the complete chloroplast genome sequence of Sarcandra glabra (Chloranthales).

Sarcandra glabra is a perennial evergreen subshrub, with high ornamental and medicinal value. Using the Illumina high-throughput sequencing data, its chloroplast genome is well assembled and characterized. The complete chloroplast genome is 158,872 bp in length with a typical quadripartite structure: a pair of inverted repeats (IRs) of 26,122 bp for each, an 88,182 bp large single-copy (LSC) region and an 18,445 bp small single-copy (SSC) region. It was composed of 128 genes and they were identified 84 coding genes, 8 rRNA genes, 36 tRNA genes. Phylogenetic analysis confirmed that the position of S. glabra lay within the order Chloranthales instead of Piperales simply according to classical morphological taxonomy.

Examination of different definitions of snacking frequency and associations with weight status among U.S. adults.

Snacks, while widely consumed in the United States (U.S.), do not have a standard definition, complicating research to understand associations, if any, with weight status. Therefore, the purpose of this study was to examine the association between snacking frequency and weight status using various snacking definitions that exist in the scientific literature among U.S. adults (NHANES 2013-2016; ≥20y n = 9,711). Four event-based snacking definitions were operationalized including participant-defined snacks, eating events outside of meals, and operationally defined snacks based on absolute thresholds of energy consumed (>50 kcal). Weight status was examined using body mass index (BMI), waist circumference, and sagittal abdominal diameter risk. Logistic regression models examined snacking frequency and associations with weight status. Outcomes varied by the definition of a snack employed, but the majority of findings were null. Mean energy from snacks was significantly higher among women with obesity compared to women with normal weight when a snack was defined as any event outside of a typical mealtime (i.e. other than breakfast, lunch, dinner, super, brunch), regardless of whether or not it contributed ≥50 kcal. Further investigation into ingestive behaviors that may influence the relationship between snacking frequency and weight status is needed.

Dairy intake is not associated with improvements in bone mineral density or risk of fractures across the menopause transition: data from the Study of Women's Health Across the Nation.

OBJECTIVE: Menopause represents a period in which bone deterioration is accelerated; thus, primary prevention strategies to address age-related bone loss are crucial. Dairy products contain more than a dozen essential nutrients, including calcium, phosphorus, vitamin D, and high-quality protein, as well as bioactive compounds that may promote bone mineralization. However, the relationship between dairy consumption and bone health across the menopause transition remains largely unknown. The purpose of this analysis was to estimate the change in lumbar spine and femoral neck bone mineral density and the risk of bone fracture by the frequency of dairy intakes among women across the menopausal transition using the publicly available data from the Study of Women's Health Across the Nation. METHODS: We analyzed total dairy foods in four categories of <0.5, 0.5 to <1.5, 1.5 to <2.5, and ≥2.5 servings/d or <1.5 and ≥1.5 servings/d. A general linear model was used to estimate the association of dairy intake with the 10-year bone mineral density loss rate and a linear mixed model was used to estimate the annualized bone mineral density loss rate of the femoral neck and lumbar spine. A Cox proportional hazard model was applied to calculate hazard ratios and 95% confidence intervals of the nontraumatic fractures. Poisson regression was used to determine the relative risks and 95% confidence intervals of the nontraumatic fractures. The models were controlled for race/ethnicity, age, height, weight, smoking status, physical activity, alcohol consumption, calcium use, menopausal status, and total caloric intake. RESULTS: No significant differences in bone mineral density change were observed, regardless of baseline menopausal status. No significant differences in the risk of nontraumatic fracture were observed. CONCLUSIONS: In this group of US women undergoing the menopausal transition, dairy food intake was neither associated with femoral and spine bone mineral density loss nor the risk of fractures.

Redesigning an Undergraduate Nutrition Course through Active Learning and Team-Based Projects Enhances Student Performance.

Team-based active learning has been associated with enhanced communication and critical thinking skills, and improved clinical competency in other allied-health disciplines, but little is known about this pedagogical technique in nutrition. This study compared content retention and perceptions of a team-based, active learning course redesign intervention in an undergraduate nutrition class pre- (n = 32) and post- (n = 43) intervention. Assessment scores improved overall (69% to 75%; P < 0.01) and within 3 content domains: dietary guidelines (75% to 84%; P = 0.03), the exchange system (38% to 49%; P < 0.01), and dietary assessment (59% to 73%; P < 0.01). Thus, incorporation of team-based active learning was effective in improving content knowledge in undergraduate nutrition students as assessed by performance on exam questions overall and in some but not all content domains. Nonsignificant changes in student evaluations suggest that this is an acceptable, noninferior strategy to facilitate learning in undergraduate courses.

Calcium Supplement Use Is Associated With Less Bone Mineral Density Loss, But Does Not Lessen the Risk of Bone Fracture Across the Menopause Transition: Data From the Study of Women's Health Across the Nation.

Diet is a modifiable factor that is related to bone mass and risk for fractures; however, the use of calcium supplements for bone health is controversial, with little scientific agreement. The purpose of this analysis was to estimate the change in lumbar spine and femoral neck BMD and the risk of bone fracture by the use of calcium supplements among the Study of Women's Health Across the Nation (SWAN) participants. SWAN is a multicenter, multiethnic, community-based longitudinal cohort designed to examine the health of women across the menopause transition (n = 1490; aged 42 to 52 years at baseline in 1996 to 1997 and followed annually until 2006 to 2008). A mixed-effect model for repeated measures was used to estimate annualized BMD change across time between supplement users and nonusers, unadjusted or fully adjusted (age, race, height, weight, menopausal status [pre-, early peri-, late peri-, and postmenopausal], DXA scanner mode, alcohol intake, vitamin D supplement use, smoking, and physical activity) and a log-linear model with repeated measures was used to estimate the relative risk of fracture by calcium supplement use. All models were also stratified by baseline menopausal status. In fully adjusted models, calcium supplement use was associated with less annualized loss of femoral neck BMD (-0.0032 versus -0.0040 g/cm2/year; p < .001) and lumbar spine BMD (-0.0046 versus -0.0053 g/cm2/year, p = 0.021) in the complete cohort. However, this protective association of calcium supplement use with BMD loss was significant only among premenopausal women (femoral neck: -0.0032 versus -0.0042 g/cm2/year; p = 0.002; lumbar spine: -0.0038 versus -0.0050 g/cm2/year, p = 0.001); no significant differences in BMD were observed among women who were early perimenopausal by calcium supplement use at baseline. No significant differences in the relative risk of fracture were observed, regardless of baseline menopausal status. The use of calcium supplements was associated with less BMD loss over more than a decade, but was not related to the risk of incident bone fracture across the menopause transition. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

The complete chloroplast genome sequence of a popular ornamental plant Calibrachoa hybrida (Solanaceae: Petunioideae).

Calibrachoa hybrida is a popular ornamental plant with colorful flowers. We present here the complete chloroplast genome sequence of C. hybrida. With a total length of 156,099 bp, it is comprised of a large single-copy (LSC) region of 86,695 bp and a small single-copy (SSC) region of 18,694 bp separated by two inverted repeats (IRs) of 25,355 bp for each. A total of 132 genes were identified, consisting of 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis using complete chloroplast genomes clustered C. hybrida together with petunia into the subfamily Petunioideae within the family Solanaceae.

Molecular identification of natural hybridization between Melastoma malabathricum and Melastoama beccarianum in Sarawak, Malaysia.

Hybridization is very common in flowering plants and it plays a significant role in plant evolution and adaptation. Melastoma L. (Melastomataceae) comprises about 80-90 species in tropical Asia and Oceania, among which 41 species occur in Borneo. Natural hybridization is frequently reported in Melastoma in China, but so far there have been no confirmed cases of hybridization in Southeast Asia (including Borneo), where most species occur. Here, we identified a case of natural hybridization between Melastoma malabathricum L. and Melastoma beccarianum Cogn. in Sarawak, Malaysia, by using sequence data of three nuclear genes and one chloroplast intergenic spacer. Melastoma malabathricum is the most widespread species of this genus, occurring in almost the whole range of this genus, while M. beccarianum is a local species endemic to northern Borneo. Our results showed that natural hybridization and introgression occur between M. malabathricum and M. beccarianum, and the introgression was asymmetrical, mainly from M. malabathricum to M. beccarianum. As adaptive traits can be transferred by introgression, our study suggests that natural hybridization should be a significant mechanism for the evolution and adaptation of Melastoma in Southeast Asia. However, introgression from the common species M. malabathricum to the relatively rare species M. beccarianum may cause the decline of M. beccarianum, incurring conservation concern. With a large number of species of Melastoma and almost year-around flowering in Southeast Asia, more cases of natural hybridization are expected to be found and identified in near future.

Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F1 hybrid.

Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.

The complete chloroplast genome of Laurocerasus zippeliana (Rosaceae).

Laurocerasus zippeliana is a widely known landscape plant with high adaptability. We report herein the complete chloroplast genome sequence of L. zippeliana assembled from Illumina high-throughput sequencing data. With a total length of 158,940 bp, the complete chloroplast genome was a typical quadripartite circle: two inverted repeats (IRs) of 26,339 bp for each, a large single-copy (LSC) region of 87,339 bp, and a small single-copy (SSC) region of 18,923 bp. A total of 110 unique genes were identified, consisting of 78 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. Phylogenetic analysis confirmed the position of L. zippeliana within the order Rosales.

The complete chloroplast genome of Reevesia thyrsoidea (Malvaceae).

Reevesia thyrsoidea Lindl. is an important ornamental plant with horticultural, industrial, and timber usages. In this study, we reported a complete chloroplast genome of R. thyrsoidea, which was quadripartite and 161,786 bp in size, including two inverted repeats (25,466 bp for each) that separated one large single-copy (90,565 bp) and one small single-copy (20,289 bp) regions. The chloroplast genome contained 131 unique genes (86 protein-coding, 37 tRNA, and 8 rRNA), and 17 of them were double copies. Phylogenetic analysis using the chloroplast genome data indicated that R. thyrsoidea was sister to the species in the family Malvaceae.

Similar Morphologies but Different Origins: Hybrid Status of Two More Semi-creeping Taxa of Melastoma.

Inferring the origins of hybrid taxa based on morphology alone is difficult because morphologically similar hybrids can arise from hybridization between different populations of the same parental species or be produced by hybridization of different parental species. In this study, we investigated the origins of two semi-creeping taxa in Melastoma, which are morphologically similar to a natural hybrid, M. intermedium, by sequencing a chloroplast intergenic spacer, nuclear ribosomal internal transcribed spacer and two low-copy nuclear genes (tpi and cam) in these taxa and their putative parental species. Our sequence analysis provides compelling evidence for the hybrid status of the two semi-creeping taxa: one originating from hybridization between M. dodecandrum and M. malabathricum, and the other between M. dodecandrum and M. normale. The origins of these hybrids are therefore clearly different from M. intermedium, and morphological similarity for the three hybrids is most likely due to their origins from hybridization between the same creeping species M. dodecandrum and a different erect species in each of the three cases. We also observed low rate of introgression from M. normale to M. dodecandrum, and genetic exchange between them may transfer adaptive traits to M. dodecandrum. Rare occurrence of these two hybrids may be due to small range overlaps between parental species in one case, and different flowering periods between parental species in the other.