Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding

<p>Abstract</p> <p>Background</p> <p>Bottle gourd [<it>Lagenaria siceraria </it>(Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the earliest plants cultivated by man. In spite of its widespread importance and long history of cultivation almost nothing has been known about the genome of this species thus far.</p> <p>Results</p> <p>We report here the partial sequencing of bottle gourd genome using the 454 GS-FLX Titanium sequencing platform. A total of 150,253 sequence reads, which were assembled into 3,994 contigs and 82,522 singletons were generated. The total length of the non-redundant singletons/assemblies is 32 Mb, theoretically covering ~ 10% of the bottle gourd genome. Functional annotation of the sequences revealed a broad range of functional types, covering all the three top-level ontologies. Comparison of the gene sequences between bottle gourd and the model cucurbit cucumber (<it>Cucumis sativus</it>) revealed a 90% sequence similarity on average. Using the sequence information, 4395 microsatellite-containing sequences were identified and 400 SSR markers were developed, of which 94% amplified bands of anticipated sizes. Transferability of these markers to four other cucurbit species showed obvious decline with increasing phylogenetic distance. From analyzing polymorphisms of a subset of 14 SSR markers assayed on 44 representative China bottle gourd varieties/landraces, a principal coordinates (PCo) analysis output and a UPGMA-based dendrogram were constructed. Bottle gourd accessions tended to group by fruit shape rather than geographic origin, although in certain subclades the lines from the same or close origin did tend to cluster.</p> <p>Conclusions</p> <p>This work provides an initial basis for genome characterization, gene isolation and comparative genomics analysis in bottle gourd. The SSR markers developed would facilitate marker assisted breeding schemes for efficient introduction of desired traits.</p

A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers

<p>Abstract</p> <p>Background</p> <p>Sweetpotato (<it>Ipomoea batatas </it>(L.) Lam.), a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpotato is in striking contrast to its importance for human nutrition. Previously existing sequence data were restricted to around 22,000 expressed sequence tag (EST) sequences and ~ 1,500 GenBank sequences. We have used 454 pyrosequencing to augment the available gene sequence information to enhance functional genomics and marker design for this plant species.</p> <p>Results</p> <p>Two quarter 454 pyrosequencing runs used two normalized cDNA collections from stems and leaves from drought-stressed sweetpotato clone <it>Tanzania </it>and yielded 524,209 reads, which were assembled together with 22,094 publically available expressed sequence tags into 31,685 sets of overlapping DNA segments and 34,733 unassembled sequences. Blastx comparisons with the UniRef100 database allowed annotation of 23,957 contigs and 15,342 singletons resulting in 24,657 putatively unique genes. Further, 27,119 sequences had no match to protein sequences of UniRef100database. On the basis of this gene index, we have identified 1,661 gene-based microsatellite sequences, of which 223 were selected for testing and 195 were successfully amplified in a test panel of 6 hexaploid (<it>I. batatas</it>) and 2 diploid (<it>I. trifida</it>) accessions.</p> <p>Conclusions</p> <p>The sweetpotato gene index is a useful source for functionally annotated sweetpotato gene sequences that contains three times more gene sequence information for sweetpotato than previous EST assemblies. A searchable version of the gene index, including a blastn function, is available at <url>http://www.cipotato.org/sweetpotato_gene_index</url>.</p

Genetic diversity of carotenoid-rich bananas evaluated by Diversity Arrays Technology (DArT)

The aim of this work was to evaluate the carotenoid content and genetic variability of banana accessions from the Musa germplasm collection held at Embrapa Cassava and Tropical Fruits, Brazil. Forty-two samples were analyzed, including 21 diploids, 19 triploids and two tetraploids. The carotenoid content was analyzed spectrophotometrically and genetic variability was estimated using 653 DArT markers. The average carotenoid content was 4.73 μg.g -1 , and ranged from 1.06 μg.g -1 for the triploid Nanica (Cavendish group) to 19.24 μg.g -1 for the triploid Saney. The diploids Modok Gier and NBA-14 and the triploid Saney had a carotenoid content that was, respectively, 7-fold, 6-fold and 9-fold greater than that of cultivars from the Cavendish group (2.19 μg.g -1). The mean similarity among the 42 accessions was 0.63 (range: 0.24 to 1.00). DArT analysis revealed extensive genetic variability in accessions from the Embrapa Musa germplasm bank

Análise comparativa da função respiratória de indivíduos hígidos em solo e na água

A mensuração da função respiratória oferece informações essenciais para caracterizar anormalidades pulmonares. A pressão hidrostática da água atua no tórax submerso de diversas formas, causando alterações no sistema respiratório. O objetivo deste estudo foi analisar comparativamente variáveis que avaliam a função respiratória - volume minuto (Vmin), volume corrente (Vc), capacidade vital (Cvital) e frequência respiratória (FR) - de voluntárias no solo e com o tórax submerso em piscina terapêutica aquecida. A função respiratória de 30 voluntárias saudáveis (20,9±2,1 anos; 1,64±0,07 m; 58,8±9,2 kg; índice de massa corporal 21,78±2,63 kg/m²) foi avaliada por meio de ventilômetro em solo e aos 1 e 20 minutos de imersão, com água ao nível dos ombros, em posição sentada. Após 20 minutos de imersão, foi registrado aumento estatisticamente significativo no Vmin (p=0,015) e Vc (p=0,027); e uma redução estatisticamente significativa (p=0,016) na Cvital 1 minuto após imersão, em relação aos valores obtidos em solo. O maior tempo de imersão alterou assim os valores obtidos em solo, com exceção da Cvital, que sofreu alteração significativa desde o primeiro minuto de imersão. Não foram encontradas diferenças significativas entre os valores obtidos após 1 e 20 minutos na água. O estudo permite concluir que a imersão do tórax em piscina aquecida provocou aumento no Vmin e Vc e diminuição na Cvital de voluntárias saudáveis.Measuring respiratory function provides essential information to assess pulmonary changes. Effects of water hydrostatic pressure on the submerged chest cause changes in the respiratory system. The purpose here was to compare respiratory function variables - minute volume (MV), tidal volume (TV), vital capacity (Vitalc), and respiratory rate (RR) - on the ground and with chest submerged in water. Respiratory function of 30 healthy female volunteers (mean age 20.93 ± 2.11; weight 58.8±9.2 kg; body mass index 21.78±2.63 kg/m²) was assessed by spirometry on the ground, and 1 and 20 minutes after immersion in warm water at shoulder level in the sitting position. As compared to ground levels, statistically significant increases were found in MV (p=0.015) and TV (p=0.027) 20 minutes after immersion, as well as a significant decrease (p=0.016) in Vitalc one minute after immersion. Longer time immersion has thus altered values obtained on ground, except for Vitalc, which showed significant reduction on the first minute after chest immersion. Comparison between variable values obtained 1 and 20 minutes in water showed no significant difference. It may thus be said that chest submersion in warm water caused an increase in MV and VT and a decrease in Vitalc of healthy subjects

Discovery and characterization of sweetpotato’s closest tetraploid relative

The origin of sweetpotato, a hexaploid species, is poorly understood, partly because the identity of its tetraploid progenitor remains unknown. In this study, we identify, describe and characterize a new species of Ipomoea that is sweetpotato’s closest tetraploid relative known to date and probably a direct descendant of its tetraploid progenitor. We integrate morphological, phylogenetic, and genomic analyses of herbarium and germplasm accessions of the hexaploid sweetpotato, its closest known diploid relative Ipomoea trifida, and various tetraploid plants closely related to them from across the American continent. We identify wild autotetraploid plants from Ecuador that are morphologically distinct from Ipomoea batatas and I. trifida, but monophyletic and sister to I. batatas in phylogenetic analysis of nuclear data. We describe this new species as Ipomoea aequatoriensis T. Wells & P. Muñoz sp. nov., distinguish it from hybrid tetraploid material collected in Mexico; and show that it likely played a direct role in the origin of sweetpotato’s hexaploid genome. This discovery transforms our understanding of sweetpotato’s origin