Statistical Databases

Hypervirulent K. pneumoniae (hvKp) is an evolving pathotype that is more virulent than classical K. pneumoniae (cKp). hvKp usually infects individuals from the community, who are often healthy. Infections are more common in the Asian Pacific Rim but are occurring globally. hvKp infection frequently presents at multiple sites or subsequently metastatically spreads, often requiring source control. hvKp has an increased ability to cause central nervous system infection and endophthalmitis, which require rapid recognition and site-specific treatment. The genetic factors that confer hvKp's hypervirulent phenotype are present on a large virulence plasmid and perhaps integrative conjugal elements. Increased capsule production and aerobactin production are established hvKp-specific virulence factors. Similar to cKp, hvKp strains are becoming increasingly resistant to antimicrobials via acquisition of mobile elements carrying resistance determinants, and new hvKp strains emerge when extensively drug-resistant cKp strains acquire hvKp-specific virulence determinants, resulting in nosocomial infection. Presently, clinical laboratories are unable to differentiate cKp from hvKp, but recently, several biomarkers and quantitative siderophore production have been shown to accurately predict hvKp strains, which could lead to the development of a diagnostic test for use by clinical laboratories for optimal patient care and for use in epidemiologic surveillance and research studies.

Hypervirulent Klebsiella pneumoniae

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal feed. Fabaceae, the third largest family of flowering plants, has traditionally been divided into the following three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae, all together with 800 genera and 20,000 species. The latter subfamily contains most of the major cultivated food and feed crops. Among the grain legumes are some of mankind's earliest crop plants, whose domestication parallelled that of cereals: Soybean in China; faba bean, lentil, chickpea and pea in the Fertile Crescent of the Near East; cowpeas and bambara groundnut in Africa; soybean and mungbeans in East Asia; pigeonpea and the grams in South Asia; and common bean, lima bean, scarlet runner bean, tepary bean and lupin in Central and South America. The importance of legumes is evidenced by their high representation in ex situ germplasm collections, with more than 1,000,000 accessions worldwide. A detailed knowledge of the phylogenetic relationships of the Fabaceae is essential for understanding the origin and diversification of this economically and ecologically important family of angiosperms. This review aims to combine the phylogenetic and genetic diversity approaches to better illustrate the origin, domestication history and preserved germplasm of major legume crops from 13 genera of six tribes and to indicate further potential both for science and agriculture.

/pdf/legume-crops-phylogeny-and-genetic-diversity-for-science-and-1lvkdujjsr.pdf

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

La arveja (Pisum sativum L.) es uno de los cultivos domesticados mas antiguos, altamente valorados y ampliamente cultivados en todo el mundo. Sin embargo, en Colombia esta especie carece de estudios geneticos que permitan establecer la variabilidad total. Se estudio la estructura y diversidad genetica en una coleccion de 50 introducciones de arveja arbustiva provenientes del departamento de Narino con 16 marcadores de repeticion de secuencia simple (SSR). El promedio del contenido de informacion polimorfica (PIC) fue 0,62 con un total de 28 alelos y un promedio de 4 alelos por locus, siendo el locus AB71 y D21 los que amplificaron el mayor numero de alelos (6). La Heterocigosidad observada (Ho) fue 0.09± 0.08 y la esperada (He) 0.42± 0.33, indicando un alto nivel de endogamia (Fis= 0.60) demostrando la naturaleza homocigota de P. sativum. Se infirieron las relaciones geneticas por medio de un analisis de similitud y un analisis Bayesiano (STRUCTURE) detectando dos agrupaciones para los genotipos de arveja analizados, con una alta similitud con las caracteristicas agromorfologicas de cada genotipo. A pesar de la baja heterocigosis, los valores de heterocigosidad espera de la poblacion total (He = 0.60) y de la agrupacion 2 (He = 0.70) asi como la presencia de alelos unicos y raros, muestran un nivel de variabilidad genetica en la coleccion. Los resultados del presente estudio seran utiles para programas de pre - mejoramiento de la misma.

Caracterización molecular de arveja arbustiva (Pisum sativum L) en la zona cerealista del departamento de Nariño, Colombia

Single and low copy nuclear genes offer a larger number of, and more rapidly evolving, characters than the chloroplast and nuclear ribosomal gene sequences that have dominated plant phylogenetic studies to date. Until recently, only one or a few low copy nuclear gene markers were included in such studies. Now, the rapid adoption of “next generation sequencing” (NGS) techniques offers simpler and cheaper access to hundreds of, and not just tens of, coding and noncoding DNA regions. In this review, we describe the most commonly-used NGS methods available for accessing nuclear genes and discuss many NGS case studies that have been published in the last two to three years. These approaches include whole genome sequencing to target microsatellites, transcriptome sequencing, Exon-Primed Intron-Crossing sequencing (EPIC), targeted enrichment (or sequence capture), RAD sequencing (RAD-Seq, including genotyping-by-sequencing or GBS), and genome skimming. We also discuss some of the challenges to, and posed by, the NGS approaches.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/jse.12174

Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next-gen approaches

Faba bean (Vicia faba L.) is an important food legume crop, grown for human consumption globally including in China, Turkey, Egypt and Ethiopia. Although genetic gain has been made through conventional selection and breeding efforts, this could be substantially improved through the application of molecular methods. For this, a set of reliable molecular markers representative of the entire genome is required. A library with 125,559 putative SSR sequences was constructed and characterized for repeat type and length from a mixed genome of 247 spring and winter sown faba bean genotypes using 454 sequencing. A suit of 28,503 primer pair sequences were designed and 150 were randomly selected for validation. Of these, 94 produced reproducible amplicons that were polymorphic among 32 faba bean genotypes selected from diverse geographical locations. The number of alleles per locus ranged from 2 to 8, the expected heterozygocities ranged from 0.0000 to 1.0000, and the observed heterozygosities ranged from 0.0908 to 0.8410. The validation by UPGMA cluster analysis of 32 genotypes based on Nei's genetic distance, showed high quality and effectiveness of those novel SSR markers developed via next generation sequencing technology. Large scale SSR marker development was successfully achieved using next generation sequencing of the V. faba genome. These novel markers are valuable for constructing genetic linkage maps, future QTL mapping, and marker-assisted trait selection in faba bean breeding efforts.

/pdf/high-throughput-novel-microsatellite-marker-of-faba-bean-via-u5radvv03n.pdf

High-throughput novel microsatellite marker of faba bean via next generation sequencing.

Vegetables harboring bacteria resistant to antibiotics are a growing food safety issue. However, data concerning carbapenem-resistant Enterobacteriaceae (CRE) in ready-to-eat fresh vegetables is still rare. In this study, 411 vegetable samples from 36 supermarkets or farmer's markets in 18 cities in China, were analyzed for CRE. Carbapenemase-encoding genes and other resistance genes were analyzed among the CRE isolates. Plasmids carrying carbapenemase genes were studied by conjugation, replicon typing, S1-PFGE southern blot, restriction fragment length polymorphism (RFLP), and sequencing. CRE isolates were also analyzed by pulsed-field gel electrophoresis (PFGE). Ten vegetable samples yielded one or more CRE isolates. The highest detection rate of CRE (14.3%, 4/28) was found in curly endive. Twelve CRE isolates were obtained and all showed multidrug resistance: Escherichia coli, 5; Citrobacter freundii, 5; and Klebsiella pneumoniae, 2. All E. coli and C. freundii carried blaNDM, while K. pneumoniae harbored blaKPC-2. Notably, E. coli with blaNDM and ST23 hypervirulent Klebsiella pneumoniae (hvKP) carrying blaKPC-2 were found in the same cucumber sample and clonal spread of E. coli, C. freundii, and K. pneumoniae isolates were all observed between vegetable types and/or cities. IncX3 plasmids carrying blaNDM from E. coli and C. freundii showed identical or highly similar RFLP patterns, and the sequenced IncX3 plasmid from cucumber was also identical or highly similar (99%) to the IncX3 plasmids from clinical patients reported in other countries, while blaKPC-2 in K. pneumoniae was mediated by similar F35:A-:B1 plasmids. Our results suggest that both clonal expansion and horizontal transmission of IncX3- or F35:A-:B1-type plasmids may mediate the spread of CRE in ready-to-eat vegetables in China. The presence of CRE in ready-to-eat vegetables is alarming and constitutes a food safety issue. To our knowledge, this is the first report of either the C. freundii carrying blaNDM, or K. pneumoniae harboring blaKPC-2 in vegetables. This is also the first report of ST23 carbapenem-resistant hvKP strain in vegetables.

/pdf/characteristics-of-carbapenem-resistant-enterobacteriaceae-4msjnaqcwk.pdf

Characteristics of Carbapenem-Resistant Enterobacteriaceae in Ready-to-Eat Vegetables in China

Pea (Pisum sativum L.) is an important food legume globally, and is the plant species that J.G. Mendel used to lay the foundation of modern genetics. However, genomics resources of pea are limited comparing to other crop species. Application of marker assisted selection (MAS) in pea breeding has lagged behind many other crops. Development of a large number of novel and reliable SSR (simple sequence repeat) or microsatellite markers will help both basic and applied genomics research of this crop. The Illumina HiSeq 2500 System was used to uncover 8,899 putative SSR containing sequences, and 3,275 non-redundant primers were designed to amplify these SSRs. Among the 1,644 SSRs that were randomly selected for primer validation, 841 yielded reliable amplifications of detectable polymorphisms among 24 genotypes of cultivated pea (Pisum sativum L.) and wild relatives (P. fulvum Sm.) originated from diverse geographical locations. The dataset indicated that the allele number per locus ranged from 2 to 10, and that the polymorphism information content (PIC) ranged from 0.08 to 0.82 with an average of 0.38. These 1,644 novel SSR markers were also tested for polymorphism between genotypes G0003973 and G0005527. Finally, 33 polymorphic SSR markers were anchored on the genetic linkage map of G0003973 × G0005527 F2 population.

/pdf/high-throughput-development-of-ssr-markers-from-pea-pisum-317091eg6q.pdf

High-Throughput Development of SSR Markers from Pea (Pisum sativum L.) Based on Next Generation Sequencing of a Purified Chinese Commercial Variety

Simple sequence repeat (SSR) markers have previously been applied to linkage mapping of the pea (Pisum sativum L.) genome. However, the transferability of existing loci to the molecularly distinct Chinese winter pea gene pool was limited. A novel set of pea SSR markers was accordingly developed. Together with existing SSR sequences, the genome of the G0003973 (winter hardy) × G0005527 (cold sensitive) cross was mapped using 190 F2 individuals. In total, 157 SSR markers were placed in 11 linkage groups with an average interval of 9.7 cM and total coverage of 1518 cM. The novel markers and genetic linkage map will be useful for marker-assisted pea breeding.

SSR genetic linkage map construction of pea (Pisum sativum L.) based on Chinese native varieties

Frost stress is one of the major abiotic stresses causing seedling death and yield reduction in winter pea. To improve the frost tolerance of pea, field evaluation of frost tolerance was conducted on 672 diverse pea accessions at three locations in Northern China in three growing seasons from 2013 to 2016 and marker-trait association analysis of frost tolerance were performed with 267 informative SSR markers in this study. Sixteen accessions were identified as the most winter-hardy for their ability to survive in all nine field experiments with a mean survival rate of 0.57, ranging from 0.41 to 0.75. Population structure analysis revealed a structured population of two sub-populations plus some admixtures in the 672 accessions. Association analysis detected seven markers that repeatedly had associations with frost tolerance in at least two different environments with two different statistical models. One of the markers is the functional marker EST1109 on LG VI which was predicted to co-localize with a gene involved in the metabolism of glycoproteins in response to chilling stress and may provide a novel mechanism of frost tolerance in pea. These winter-hardy germplasms and frost tolerance associated markers will play a vital role in marker-assisted breeding for winter-hardy pea cultivar.

Hao Junjie

Papers

High-throughput novel microsatellite marker of faba bean via next generation sequencing.

Characteristics of Carbapenem-Resistant Enterobacteriaceae in Ready-to-Eat Vegetables in China

High-Throughput Development of SSR Markers from Pea (Pisum sativum L.) Based on Next Generation Sequencing of a Purified Chinese Commercial Variety

SSR genetic linkage map construction of pea (Pisum sativum L.) based on Chinese native varieties

Marker-trait association analysis of frost tolerance of 672 worldwide pea ( Pisum sativum L.) collections