Reference Genome Sequence of the Model Plant Setaria

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and \u3e95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with \u3e1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum)

Antioxidative Properties of Bitter Gourd (Momordica charantia) and Zucchini (Cucurbita pepo)

The enzymatic and non-enzymatic antioxidative capacities of bitter gourd (Momordica charantia) and zucchini (Cucurbita pepo) were investigated in water extracts and chemical buffer extracts. Bitter gourd and zucchini fruits were purchased from a farmer’s market and homogenized separately in water and in a native enzyme extraction buffer. Total phenolic compounds, free radical DPPH scavenging activity, SOD activity and β- glucosidase activity were assayed in the extracts. The average total phenolic compounds recorded in bitter gourd were 13.28 GAE/g fresh weights while in zucchini, the average was 8.67GAE/g fresh weight. This study also found that bitter gourd was 82.05% as effective as ascorbic acid in inhibiting the free radical DPPH while zucchini was 12.19% as effective. The results indicated that bitter gourd was significantly higher in antioxidant content and in β-glucosidase activities than zucchini (P\u3c0.05). On the other hand, significantly higher SOD activities were recorded in zucchini than in bitter gourd extracts

Allotetraploid Origin and Divergence in Eleusine (Chloridoideae, Poaceae): Evidence from Low-copy Nuclear Gene Phylogenies and a Plastid Gene Chronogram

Background and Aims: Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa. Methods: Two low-copy nuclear (LCN) markers, Pepc4 and EF-1a, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) using the Bayesian dating method. Key Results: The monophyly of Eleusine is strongly supported by sequence data from two LCN markers. In the cpDNA phylogeny, three tetraploid species (E. africana, E. coracana and E. kigeziensis) share a common ancestor with the E. indica–E. tristachya clade, which is considered a source of maternal parents for allotetraploids. Two homoeologous loci are isolated from three tetraploid species in the Pepc4 phylogeny, and the maternal parents receive further support. The A-type EF-1a sequences possess three characters, i.e. a large number of variations of intron 2; clade E-A distantly diverged from clade E-B and other diploid species; and seven deletions in intron 2, implying a possible derivation through a gene duplication event. The crown age of Eleusine and the allotetraploid lineage are 3.89 million years ago (mya) and 1.40 mya, respectively. Conclusions: The molecular data support independent allotetraploid origins for E. kigeziensis and the E. africana–E. coracana clade. Both events may have involved diploids E. indica and E. tristachya as the maternal parents, but the paternal parents remain unidentified. The habitat-specific hypothesis is proposed to explain the divergence of Eleusine and its allotetraploid lineage

Five Nuclear Loci Resolve the Polyploid History of Switchgrass (Panicum virgatum L.) and Relatives

Polyploidy poses challenges for phylogenetic reconstruction because of the need to identify and distinguish between homoeologous loci. This can be addressed by use of low copy nuclear markers. Panicum s.s. is a genus of about 100 species in the grass tribe Paniceae, subfamily Panicoideae, and is divided into five sections. Many of the species are known to be polyploids. The most well-known of the Panicum polyploids are switchgrass (Panicum virgatum) and common or Proso millet (P. miliaceum). Switchgrass is in section Virgata, along with P. tricholaenoides, P. amarum, and P. amarulum, whereas P. miliaceum is in sect. Panicum. We have generated sequence data from five low copy nuclear loci and two chloroplast loci and have clarified the origin of P. virgatum. We find that all members of sects. Virgata and Urvilleana are the result of diversification after a single allopolyploidy event. The closest diploid relatives of switchgrass are in sect. Rudgeana, native to Central and South America. Within sections Virgata and Urvilleana, P. tricholaenoides is sister to the remaining species. Panicum racemosum and P. urvilleanum form a clade, which may be sister to P. chloroleucum. Panicum amarum, P. amarulum, and the lowland and upland ecotypes of P. virgatum together form a clade, within which relationships are complex. Hexaploid and octoploid plants are likely allopolyploids, with P. amarum and P. amarulum sharing genomes with P. virgatum. Octoploid P. virgatum plants are formed via hybridization between disparate tetraploids. We show that polyploidy precedes diversification in a complex set of polyploids; our data thus suggest that polyploidy could provide the raw material for diversification. In addition, we show two rounds of allopolyploidization in the ancestry of switchgrass, and identify additional species that may be part of its broader gene pool. This may be relevant for development of the crop for biofuels

DNA barcoding indicates multiple invasions of the freshwater snail Melanoides tuberculata sensu lato in Florida

Melanoides tuberculata sensu lato (Thiaridae) are polymorphic female-clonal snails of Asian and African origins that have invaded freshwaters worldwide, including those in Florida. Although the snails have been documented in Florida for at least 70 years, no studies have investigated whether the observed distribution is due to a single introduction or multiple independent invasions. Here, cytochrome oxidase I was used to measure genetic diversity within and among sites in Florida and compare genetic diversity between Florida and other regions of the world. We also examined the relationship between shell morphology and haplotype diversity to determine if shell morphs can serve as a proxy for haplotypes. In total, we recovered 8 haplotypes randomly distributed across populations in Florida. Phylogenetic reconstruction supported the hypothesis of multiple invasions by diverse representatives of the M. tuberculata species complex. In contrast, shell morphology was not found to be a useful phylogeographic character, with divergent haplotypes represented by similar shell forms. These results suggest that the observed invasion patterns in Florida are best explained by serial introductions, and that shell morphology cannot be used to predict haplotypes or reconstruct invasion history of Melanoides tuberculata s.l. and that extensive taxonomic revisions are needed to investigate invasion dynamics

New records of digenetic trematodes infecting Melanoides tuberculata (O.F. Müller, 1774) in Florida, USA

Melanoides tuberculata is a well-known invasive, freshwater snail and intermediate host for many species of parasitic trematodes. Despite being well established in Florida’s freshwater systems, little work has been conducted to document the associated trematodes of the snails. Live snails were collected from 11 sites from 25 locations sampled across the state of Florida, USA of which individuals from six sites were found to be infected with trematodes. Gross morphological characters and phylogenetic analysis using 18S rRNA and ITS2 gene regions, were used to identify these trematode taxa. Snails infected with the gill flukes, Centrocestus formosanus and Haplorchis pumilio (Heterophyidae) were found at two and four sites, respectively. While C. formosanus has been documented in this snail species in Florida, H. pumilio has not been documented in Florida before this study. The eye fluke, Philophthalmus sp. (Philophthalmidae) was found in two sites. This parasite was previously reported in Florida in birds but not in any snail hosts. An unidentifiable species of kidney fluke, Renicolidae sp., and an unidentifiable species of bat fluke, Lecithodendriidae sp., were found in one site each. Both Renicolidae sp. and Lecithodendriidae sp. are new North American records of trematodes infecting M. tuberculata, but whether they are they are of native or invasive origin is unknown. These new records of trematode taxa infecting M. tuberculata in Florida emphasizes the critical need for monitoring of invasive snails and their associated parasites

A NEW SPECIES OF CHUSQUEA SECT. VERTICILLATAE (POACEAE: BAMBUSOIDEAE) FROM ECUADOR

Volume: 1Start Page: 847End Page: 85

Cartoon of relationships among the species of sections <i>Virgata</i> and <i>Urvilleana</i> and their close relatives.

<p>Diversification occurred at the diploid level, a hybridization event involving a seed parent with the A genome and a pollen parent with the B genome gave rise to an allotetraploid offspring. Diversification then occurred at the tetraploid level. An AB genome tetraploid crossed with another AB tetraploid to give rise to octoploids and hexaploids. Octoploid <i>P. amarum</i> is omitted for clarity.</p

Bayesian phylogram of the analysis of all accessions of sections <i>Virgata</i> and <i>Urvilleana</i>, using only the B genome of <i>knotted1</i>; topology is that presented in Supplemental Figure S1 for the <i>Virgata</i>-<i>Urvilleana</i> clade, but with sequence names replaced by colored ovals.

<p>The pink oval with the letter c indicates sequences from <i>P</i>. <i>virgatum</i> var. <i>cubense</i>. Unlabeled ovals represent sequences from tetraploids. Ovals labeled with 6x or 8x indicate hexaploid or octoploid plants, respectively, from which only one sequence type was recovered. Slender lines connect sequences from the same plant. Vertices labeled 6x or 8x indicate hexaploid or octoploid plants respectively; unlabeled vertices indicate tetraploids. Numbers above branches are Bayesian posterior probabilities.</p

Statistics and evolutionary models for separate data partitions.

<p>PIC  =  parsimony informative characters. PIC parenthetical indicates the number of parsimony informative characters within the temperate clade. MP  =  maximum parsimony; CI  =  consistency index, excluding uninformative characters; RI  =  retention index. Models are based on the Hierarchical Likelihood Ratio Test implemented in jModelTest. MP tree numbers with asterisks indicate the maximum number that was saved.</p