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)

Phylogenetic Relationships Among the One-Flowered, Determinate Genera of Bambuseae (Poaceae: Bambusoideae)

Bambuseae (woody bamboos), one of two tribes recognized within Bambusoideae (true bamboos), comprise over 90% of the diversity of the subfamily, yet monophyly of the tribe is generally only moderately supported, and phylogenetic relationships within the tribe are poorly understood. In addition, there appears to be some level of conflict between morphological and molecular data within the tribe. We conducted a parsimony analysis of 43 species of Bambuseae, three of Olyreae (herbaceous bamboos), and two outgroup taxa using morphological and plastid rpl16 intron sequence data to (1) further test the monophyly of Bambuseae, (2) test the monophyly of Chusqueinae and Hickelinae (the two one-flowered, determinate subtribes), and (3) examine the apparent conflict between molecular and morphological data sets in the determinate, one-flowered genera of Bambuseae. We recovered a monophyletic Bambusoideae, Bambuseae, Olyreae, and Chusqueinae, although support for Bambuseae remained moderate. Our results suggest that the morphological similarities between Chusqueinae and Hickelinae are homoplasious, but robust resolution of relationships among the major lineages of woody bamboos is still wanting

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

Phylogenetic relationships among the temperate bamboos (Poaceae: Bambusoideae) with an emphasis on Arundinaria and allies

The temperate clade is a diverse but poorly understood major lineage of woody bamboos (Poaceae: Bambusoideae: Bambuseae). Ongoing work is needed to reconstruct evolutionary relationships and establish nomenclatural stability for this difficult but ecologically and economically important group. We present the first robust multilocus plastid phylogeny for the temperate bamboos, assess relationships among key genera with an emphasis on Arundinaria and its allies, and discuss evolutionary phenomena potentially responsible for the taxonomic complexity of this group. Utilizing a total of twelve cp DNA regions (1 coding, 10 intergenic spacers, 1 intron), the temperate bamboos were resolved to include six major lineages: the Bergbamboes Lineage, the African Alpine Bamboo Clade, the Chimonocalamus Clade, the Shibataea Clade, the Phyllostachys Clade, and the Arundinaria Clade. The resulting chloroplast phylogeny is incongruent with current morphological classifications, rendering subtribes and many genera poly- or paraphyletic. Within the Arundinaria Clade, several lineages were identified including the Sasa Clade, the Pleioblastus s.s. Clade, and a clade containing Chinese species currently classified in Acidosasa, Indosasa, Pleioblastus sect. Amari, and Pseudosasa subg. Sinicae (the Sinicae Clade). The analysis also recovered a monophyletic Arundinaria sensu stricto and indicated Sasa and Sasamorpha as possible close relatives of the North America species, although results were equivocal.;We also report the results of a molecular phylogenetic analysis of Arundinaria in North America, including estimates of genetic variation and evidence of natural hybridization and introgression among all three native species. The study involved a comparative analysis of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA sequences representing diversity within and among all three species of Arundinaria sensu stricto plus accessions with intermediate or unusual morphological characteristics (putative hybrids). Molecular evidence demonstrates that A. tecta and A. appalachiana are sister species, forming a clade that is significantly divergent from A. gigantea. All three species retain the potential for cross-fertilization, albeit presumably rare due to allopatry and infrequent flowering. Detected patterns of hybridization were relatively shallow, with the majority of hybrids being the apparent direct (F1) product of crosses between A. gigantea and A. tecta.Several unusual genotypes were identified, presumably representing posthybridizational recombination and/or introgression. In conjunction with this molecular analysis, the newly recognized species from the southern Appalachian Mountains, Arundinaria appalachiana, is described, illustrated, and compared with the related species A. gigantea and A. tecta. This new species is distinguished by a combination of vegetative morphological characters including features of branching and leaf morphology, leaf anatomy, and ecology. A key for the identification of Arundinaria species in North America is included along with a comparative table based on morphology, leaf anatomy, and ecology.;Phylogenetic relationships among Arundinaria and its allies in East Asia were further explored using AFLP data in conjunction with a four-region plastid framework phylogeny, with an emphasis on species-level relationships in the genus Pleioblastus sensu stricto. Hybridization and introgression were detected both within and among genera, highlighting the significant role of reticulate evolution in temperate bamboo diversity. Molecular data confirmed the hybrid origin of Hibanobambusa, Semiarundinaria, and Sasaella, and also revealed the type species of Pseudosasa to be an intergeneric hybrid. Moreover, cryptic links were detected between Sasa and Sasamorpha, resulting in nothotaxa that have obscured the distinction between these genera. AFLP and chloroplast sequence data support the monophyly of Pleioblastus s.s. and reveal species-level resolution in section Pleioblastus, low genetic diversity among populations of the widespread P. simonii (section Medakea), and cryptic reticulation among species in sections Nezasa and Medakea. This analysis also provided additional evidence for the monophyly of North American genus Arundinaria, but failed to reveal its closest relative. A significant conclusion of this research is that reticulate evolution has had an important role in the evolution of the temperate bamboos, in spite of the rarity of flowering.</p

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

Kuruna debilis Attigala, Kaththriarachchi & L. G. Clark 2014, comb. nov.

1. Kuruna debilis (Thwaites) Attigala, Kaththriarachchi & L. G. Clark, comb. nov. Basionym:— Arundinaria debilis Thwaites (1864: 375).Published as part of Attigala, Lakshmi, Triplett, Jimmy K., Kathriarachchi, Hashendra-Suvini & Clark, Lynn G., 2014, A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny, pp. 187-205 in Phytotaxa 174 (1) on page 200, DOI: 10.11646/phytotaxa.174.4.1, http://zenodo.org/record/515231

Kuruna densifolia Attigala, Kaththriarachchi & L. G. Clark 2014, comb. nov.

2. Kuruna densifolia (Munro) Attigala, Kaththriarachchi & L. G. Clark, comb. nov. Basionym:— Arundinaria densifolia Munro (1868: 32).Published as part of Attigala, Lakshmi, Triplett, Jimmy K., Kathriarachchi, Hashendra-Suvini & Clark, Lynn G., 2014, A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny, pp. 187-205 in Phytotaxa 174 (1) on page 200, DOI: 10.11646/phytotaxa.174.4.1, http://zenodo.org/record/515231