Complete Genome Sequence Data of Pseudomonas bijieensis SP1 Associated with Root Soft Rot of Yam Bean.

Pseudomonas bijieensis is a newly established species with antifungal activity. Here, we report the high-quality and complete genome sequence for P. bijieensis strain SP1, created by hybrid assembly using both short reads and long reads. The length of the circular chromosome is about 6.67 Mb, with a GC content of 60.89%. Bioinformatic analyses revealed gene clusters for the biosynthesis of antimicrobial metabolites 2,4-diacetylphloroglucinol as well as bacterial secretion systems (type I to III and type V to VI). Interestingly, this strain can cause soft rot symptoms in the roots of yam bean, showing the potential to be a plant pathogen. The genomic data will be a valuable resource for exploring the virulence mechanism and antifungal activity of this strain.

Structural insights into the RNA interaction with Yam bean Mosaic virus (coat protein) from Pachyrhizus erosus using bioinformatics approach.

Plants are constantly threatened by a virus infection, i.e., Potyviruses, the second largest genus of plant viruses which results in several million-dollar losses in various essential crops globally. Yam bean (Pachyrhizus erosus) is considered to be one of the essential tuberous legume crops holding a great potential source of starch. Yam Bean Mosaic Virus (YBMV) of Potyvirus group belonging to the family potyviridae affects Yam bean and several angiosperms both in the tropical and sub-tropical regions causing large economical losses in crops. In this study, we attempted to understand the sequence-structure relationship and mode of RNA binding mechanism in YBMV CP using in silico integrative modeling and all-atoms molecular dynamics (MD) simulations. The assembly of coat protein (CP) subunits from YBMV and the plausible mode of RNA binding were compared with the experimental structure of CP from Watermelon mosaic virus potyvirus (5ODV). The transmembrane helix region is present in the YBMV CP sequence ranging from 76 to 91 amino acids. Like the close structural-homolog, 24 CPs monomeric sub-units formed YBMV a conserved fold. Our computational study showed that ARG124, ARG155, and TYR151 orient towards the inner side of the virion, while, THR122, GLN125, SER92, ASP94 reside towards the outer side of the virion. Despite sharing very low sequence similarity with CPs from other plant viruses, the strongly conserved residues Ser, Arg, and Asp within the RNA binding pocket of YBMV CP indicate the presence of a highly conserved RNA binding site in CPs from different families. Using several bioinformatics tools and comprehensive analysis from MD simulation, our study has provided novel insights into the RNA binding mechanism in YBMV CP. Thus, we anticipate that our findings from this study will be useful for the development of new therapeutic agents against the pathogen, paving the way for researchers to better control this destructive plant virus.

Diversity of yam bean ( Pachyrhizus spp. Fabaceae) based on morphoagronomic traits in the Brazilian Amazon / Diversidade de feijão-macuco ( Pachyrhizus spp. Fabaceae) baseada em caracteres morfoagronômicos na amazônia brasileira

Yam bean is a non-conventional horticultural crop adapted to the Amazon region. It presents edible roots, yet, its seeds contain cytotoxic components such as rotenone and pachyrhizin. The Instituto Nacional de Pesquisas da Amazonia has 64 yam bean genotypes in its germplasm bank, however, their diversity is unknown. The aim of this study was to assess the diversity of these genotypes using 10 morphoagronomic traits, plant height, number of secondary branches, shoot biomass, stem diameter, root biomass, number, length, diameter, length/diameter ratio (L/D), and shape. The accessions were planted on non-flooded land, Manaus, Amazonas (02º 59'48.2''S and 60º 01' 22.4''W) in completely randomized design with three replicates and three plants per plot spaced 0.5 x 1 m. The results showed significant diversity for all characters except for stem diameter and visual assessment of root shape. Biplot graphic explained 60% of the total variation, which identified that genotypes P44, P22 and P18 have high values for root yield (80-108 t ha-1), number of secondary branches (15-31) and shoot biomass (0.5-0.8 kg plant-1). Cluster analysis, considering 50% of relative Euclidean distance, revealed 15 major groups. We conclude that the genotypes assessed have wide diversity and some of them high root yield potential. This suggests that a yam bean breeding program can be successful for the yield of roots and seeds in the Amazonian region.

O feijão-macuco é uma hortaliça não convencional da Amazônia. Suas raízes são comestíveis e suas sementes tóxicas por conter rotenona e paquirizina. O Instituto Nacional de Pesquisas da Amazônia (INPA) tem conservado 64 genótipos de feijão-macuco em seu banco de germoplasma, mas a diversidade genética destes é desconhecida. O objetivo deste trabalho foi avaliar estes acessos utilizando 10 descritores morfoagronômicos tais como: altura de planta, número de ramas secundárias, massa da parte aérea, diâmetro de caule, massa, número, comprimento, diâmetro, relação comprimento/diâmetro e formato de raízes. O experimento foi conduzido em terra firme no município de Manaus (02º 59'48.2''LS e 60º 01' 22.4''LO), em delineamento de blocos ao acaso com três repetições e três plantas por parcela. Os resultados mostraram diversidade significativa para todos os caracteres, exceto para diâmetro do caule e avaliação visual do formato da raiz. O Biplot explicou 60% da variação total o qual mostrou que os genótipos P44, P22 e P18 tem elevada produtividade de raízes (80-108 t ha-1), número de ramificações secundarias (15-31) e massa da parte aérea (0.5-0.8 kg/planta). A análise de agrupamento considerando 50% da distancia euclidiana relativa mostrou 15 grupos principais. Por tanto, concluímos haver ampla diversidade nos genótipos especialmente para produtividade de raízes. Isto indica que o melhoramento de feijão-macuco, na região Amazônica, pode ter sucesso para aumentar a produtividade de raízes e sementes.

Fast method for the simultaneous quantification of toxic polyphenols applied to the selection of genotypes of yam bean (Pachyrhizus sp.) seeds.

The purpose of the research was to develop and validate a rapid quantification method able to screen many samples of yam bean seeds to determine the content of two toxic polyphenols, namely pachyrrhizine and rotenone. The analytical procedure described is based on the use of an internal standard (dihydrorotenone) and is divided in three steps: microwave assisted extraction, purification by solid phase extraction and assay by ultra high performance liquid chromatography (UHPLC). Each step was included in the validation protocol and the accuracy profiles methodology was used to fully validate the method. The method was fully validated between 0.25 mg and 5 mg pachyrrhizin per gram of seeds and between 0.58 mg/g and 4 mg/g for rotenone. More than one hundred samples from different accessions, locations of growth and harvest dates were screened. Pachyrrhizine concentrations ranged from 3.29 mg/g to lower than 0.25 mg/g while rotenone concentrations ranged from 3.53 mg/g to lower than 0.58 mg/g. This screening along with principal component analysis (PCA) and discriminant analysis (DA) analyses allowed the selection of the more interesting genotypes in terms of low concentrations of these two toxic polyphenols.

The origin and functional transition of P34.

P34, a storage protein and major soybean allergen, has undergone a functional transition from a cysteine peptidase to a syringolide receptor. An exploration of the evolutionary mechanism of this functional transition is made. To identify homologous genes of P34, syntenic network was constructed using syntenic relationships from the Plant Genome Duplication Database. The collected homologous genes, along with SPE31, a highly homologous protein to P34 from the seeds of Pachyrhizus erosus, were used to construct a phylogenetic tree. The results show that multiple gene duplications, exon shuffling and following granulin domain loss and some critical point mutations are associated with the functional transition. Although some tests suggested the existence of positive selection, the possibility that random fixation under relaxation of purifying selection results in the functional transition is also supported. In addition, the genes Glyma08g12340 and Medtr8g086470 may belong to a new group within the papain family.

cDNA cloning, functional expression and antifungal activities of a dimeric plant defensin SPE10 from Pachyrrhizus erosus seeds.

SPE10 is an antifungal protein isolated from the seeds of Pachyrrhizus erosus. cDNA encoding a 47 amino acid peptide was cloned by RT-PCR and the gene sequence proved SPE10 to be a new member of plant defensin family. The synthetic cDNA with codons preferred in yeast was cloned into the pPIC9 plasmid directly in-frame with the secretion signal alpha-mating factor, and highly expressed in methylotrophic Pichia pastoris. Activity assays showed the recombinant SPE10 inhibited specifically the growth of several pathogenic fungi as native SPE10. Circular dichroism and fluorescence spectroscopy analysis indicated that the native and recombinant protein should have same folding, though there are eight cystein residues in the sequence. Several evidence suggested SPE10 should be the first dimeric plant defensin reported so far.

cDNA cloning, expression, and mutagenesis of a PR-10 protein SPE-16 from the seeds of Pachyrrhizus erosus.

SPE-16 is a new 16kDa protein that has been purified from the seeds of Pachyrrhizus erosus. It's N-terminal amino acid sequence shows significant sequence homology to pathogenesis-related class 10 proteins. cDNA encoding 150 amino acids was cloned by RT-PCR and the gene sequence proved SPE-16 to be a new member of PR-10 family. The cDNA was cloned into pET15b plasmid and expressed in Escherichia coli. The bacterially expressed SPE-16 also demonstrated ribonuclease-like activity in vitro. Site-directed mutation of three conserved amino acids E95A, E147A, Y150A, and a P-loop truncated form were constructed and their different effects on ribonuclease activities were observed. SPE-16 is also able to bind the fluorescent probe 8-anilino-1-naphthalenesulfonate (ANS) in the native state. The ANS anion is a much-utilized "hydrophobic probe" for proteins. This binding activity indicated another biological function of SPE-16.