Characterization and De Novo Genome Assembly for New Rhizobium Ruizarguesonis Rhizobial Strain Vst36-3 Involved in Symbiosis with Pisum and Vicia Plants.

در راستای توسعه کشاورزی پایدار، آزمایشی به منظور بررسی اثر منابع مختلف کود (کود سبز، کود دامی و کود شیمیایی) بر عملکرد و اجزای عملکرد ذرت دانه ای، تحت تأثیر مدیریت های مختلف خاک ورزی، به صورت کرت های یک بار خرد شده در قالب طرح بلوک های کامل تصادفی با سه تکرار در ایستگاه تحقیقات کشاورزی و منابع طبیعی زهک طی دو سال زراعی 1392-1391 و 1393-1392 به اجرا در آمد. جو به عنوان کود سبز قبل از کشت ذرت در پاییز هر سال کشت شد. سیستم خاک ورزی به عنوان عامل اصلی در دو سطح شامل: خاک ورزی متداول و بدون خاک ورزی و منابع کودی شامل: 1- شاهد ( بدون مصرف کود)، 2- کود سبز جو بدون مصرف کود دامی و شیمیایی،3- کود سبز جو همراه با مصرف کامل کود شیمیایی به جو ، 4- کود سبز جو به همراه دو سوم کود شیمیایی به جو و یک سوم باقی مانده به ذرت، 5- کود سبز جو به همراه یک سوم کود شیمیایی به جو و دو سوم باقی مانده به ذرت، 6- کود سبز جو به همراه مخلوط نصف کود دامی و شیمیایی و 7- کود سبز جو به همراه 40 تن کود دامی به عنوان عامل فرعی بودند. نتایج به دست آمده نشان داد که سال، منابع مختلف کود و سیستم خاک ورزی اثر معنی دار بر ارتفاع بوته، طول بلال، تعداد دانه در ردیف، وزن هزار دانه، شاخص برداشت و عملکرد دانه در هکتار داشت. بیشترین عملکرد دانه در سیستم خاک ورزی متداول با میانگین 85/6057 کیلوگرم در هکتار به دست آمد. بیشترین مقدار عملکرد دانه از تیمار کود سبز جو به همراه مخلوط نصف کود دامی و شیمیایی با میانگین 7019 کیلوگرم در هکتار به دست آمد. برهمکنش سال در سیستم خاک ورزی در منبع کود نشان داد که بیشترین عملکرد در سال دوم در سیستم خاک ورزی متداول و در تیمار 6 با میانگین عملکرد 9400 کیلوگرم در هکتار حاصل شد. بر اساس نتایج به دست آمده از این تحقیق می توان نتیجه گیری کرد که استفاده از کود سبز به همراه مخلوط کردن کود دامی و شیمیایی همراه با سیستم خاک ورزی متداول ضمن دستیابی به عملکرد بالا فوایدی چون کاهش مصرف کود شیمیایی و حفظ محیط زیست را به دنبال خواهد داشت.

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

Next-generation sequencing technologies for whole-genome sequencing of mycobacteria are rapidly becoming an attractive alternative to more traditional sequencing methods. In particular this technology is proving useful for genome-wide identification of mutations in mycobacteria (comparative genomics) as well as for de novo assembly of whole genomes. Next-generation sequencing however generates a vast quantity of data that can only be transformed into a usable and comprehensible form using bioinformatics. Here we describe the methodology one would use to prepare libraries for whole-genome sequencing, and the basic bioinformatics to identify mutations in a genome following Illumina HiSeq or MiSeq sequencing, as well as de novo genome assembly following sequencing using Pacific Biosciences (PacBio).

Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.

Cyanobacteria play a key role in many ecosystems. Cell-environment interaction has been attributed to their metabolite production, allowing cyanobacteria to adapt and survive under extreme conditions. A strain of cyanobacteria (Chlorogloeopsis sp. ULAP01) isolated from a copper mine tailing site in Ampucao, Benguet, the Philippines, was examined in this study. It aimed to construct the whole genome sequence of the cyanobacterium, characterize it, and compare the assembled genome with the sequences available in the National Center for Biotechnology Information (NCBI) database. The whole genome of Chlorogloeopsis sp. ULAP01 was assembled, constructed, and functionally analyzed. Sequence analysis of the Chlorogloeopsis sp. ULAP01 with the C. fritschii genomes available in the NCBI database was also performed. The assembled genome had a total length of 7.9 Mb, 45 contigs, and 41% GC content. The isolate was identified as putatively Chlorogloeopsis sp. ULAP01 by morphological and molecular characterization through GTDB-Tk results and evolutionary analysis. It forms a separate node from the two known clusters of Chlorogloeopsis, indicating that it may be a separate strain or a new, previously uncharacterized strain or species. Chlorogloeopsis sp. ULAP01 shared 2,019 core genes with the other C. fritschii assemblies in the NCBI database but also possessed a total of 4,449 unique genes, 65.24% of its total annotated genes. It was noted that the strain shared the same core genes, but the accessory genes of Chlorogloeopsis sp. ULAP01 varied widely with the other Chlorogloeopsis sp. in the database. Chlorogloeopsis sp. ULAP01 is the first isolate to be added to NCBI that came from a tropical freshwater ecosystem. The unique specialized genes such as copB, entS, yfeA, and ftsP are involved in cellular processes for survival in a metal-stressed condition that may be responsible for its survival in an extreme environment.

Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.

The use of green manures in agriculture can provide nutrients, affect soil microbial communities, and be a more sustainable management practice. The activities of soil microbes can effect crop growth, but the extent of this effect on yield remains unclear. We investigated soil bacterial communities and soil properties under four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) and determined the effects of these regimes on maize growth. Milk vetch showed the greatest potential for improving crop productivity and increased maize yield by 31.3%. This change might be related to changes in soil microbes and soil properties. The entire soil bacterial community and physicochemical properties differed significantly among treatments, and there were significant correlations between soil bacteria, soil properties, and maize yield. In particular, abundance of the phyla Acidobacteria and Verrucomicrobia was positively correlated with maize yield, while Proteobacteria and Chloroflexi were negatively correlated with yield. These data suggest that the variation of maize yield was related to differences in soil bacteria. The results also indicate that soil pH, alkali solution nitrogen, and available potassium were the key environmental factors shaping soil bacterial communities and determining maize yields. Both soil properties and soil microbes might be useful as indicators of soil quality and potential crop yield.

Restoration of soil fertility of arable land is a great challenge in the developing and populous countries like India. The country witnessed the benefits Green Revolution Technologies (GRTs) in boosting of grain yield and the after effect of GRTs during past few decades in terms of deterioration of soil fertility and land degradation, loss of soil flora and fauna, genetic erosion, ecological unbalance, yield plateauing and associated insecurity in livelihood of the farmers. Now maintenance of soil fertility and sustainability of agriculture production are of important concerns. Green manuring can play an important role in this regard as it showed versatile impacts like improvement of soil physico-chemical and biological properties and fertility, nutrient supply to succeeding crops, checking erosion and plant protection. The previous research activities on various aspects of green manures were reviewed here in favour of evergreen agriculture for the future.

Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6–40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources.

Manure is a common source of nitrogen (N) in organic farming. However, manure is not always easily available, while the maximum N amount added as animal manure in organic agriculture is restricted by EU regulations. The present study was designed to test whether green manuring with a warm-season legume and intercropping with a cold-season legume can substitute farm-yard manure or compost as N sources in organic greenhouse tomato crops. To test this hypothesis, a winter-spring (WS) tomato crop was installed in February following the incorporation of crop residues of an autumn-winter (AW) tomato crop intercropped with faba bean, which had been fertilized with cowpea residues as green manure. This treatment, henceforth termed legume treatment (LT), was compared with the use of compost or manure as an N fertilization source in both tomato crops. In addition, a combination of compost and LT was also used as a fourth treatment. The results showed that green manuring with legumes and particularly cowpea can contribute a significant amount of N to the following organic tomato crop, through the biological fixation process. Nevertheless, legumes as green manure, or compost, or their combination cannot efficiently replace farmyard manure as an N fertilization source. Compost exhibited a slow mineralization course.

Complete Genome Sequences of Four Strains ofErwiniatracheiphila: A Resource for Studying aBacterial Plant Pathogen with a Highly Complex Genome.

The last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, the continued development of genome quality metrics is imperative. Using the 2016 Atlantic bottlenose dolphin NCBI RefSeq annotation and mass spectrometry-based proteomic analysis of six tissues, we confirmed 10,402 proteins from 4711 protein groups, constituting nearly one-third of the possible predicted proteins. Since the identification of larger proteins with more identified peptides implies reduced database fragmentation and improved gene annotation accuracy, we propose the metric NP10, which attempts to capture this quality improvement. The NP10 metric is calculated by first stratifying proteomic results by identifying the top decile (or 10th 10-quantile) of identified proteins based on the number of peptides per protein and then returns the median molecular weight of the resulting proteins. When using the 2016 versus 2012 Tursiops truncatus genome annotation to search this proteomic data set, there was a 21% improvement in NP10. This metric was further demonstrated by using a publicly available proteomic data set to compare human genome annotations from 2004, 2013 and 2016, which showed a 33% improvement in NP10. These results demonstrate that proteomics may be a useful metrological tool to benchmark genome accuracy, though there is a need for reference proteomic datasets across species to facilitate the evaluation of new de novo and existing genome.

Phylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) using whole-genome sequencing (WGS) is increasingly used in epidemiological investigations of bacteria. The approach, however, is both resource intensive and time-consuming. Oxford Nanopore Technologies (ONT) sequencing is capable of real-time data analysis but the high error rate hampers its application in cgSNP-based phylogenetic analysis. Here, we developed a cgSNP-independent phylogenetic analysis method using ONT read assemblies by focusing on open reading frame (ORF) content patterns. WGS data of 66 Enterobacter hormaechei strains acquired by both ONT and Illumina sequencing and 162 strains obtained from NCBI database were converted to binary sequences based on the presence or absence of ORFs using BLASTn. Phylogenetic trees calculated from binary sequences (ORF trees) were compared with cgSNP trees derived from Illumina sequences. Clusters of closely related strains in the cgSNP trees formed comparable clusters in the ORF trees built with binary sequences, and the tree topologies between them were similar based on Fowlkes-Mallows index. The ORF-based phylogenetic analysis using ONT sequencing may be useful in epidemiological investigations and offer advantages over the cgSNP-based approach. Conversion of assembled WGS data to binary sequences based on the presence or absence of ORFs circumvents read error concerns with ONT sequencing. Since ONT sequencing generates data in real time and does not require major investment, this ORF-based phylogenetic analysis method has the potential to enable phylogenetic and epidemiological analysis at the point of care.

Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-read de-novo genome assemblies now starting to be publicly available, opening the door for a wide array of ‘omics-based research. Here we present a new de-novo genome assembly for the endangered Caribbean star coral, Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our new de-novo assembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additional O. faveolata fragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affecting O. faveolata, as well as its increasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other ‘omics analyses to aid in the conservation of this species.

O arroz irrigado é uma cultura significativa para o País, do ponto de vista socioeconômico, em especial nas várzeas tropicais do Estado do Tocantins. Muitas vezes, devido ao uso de adubação inadequada, sua produtividade é limitada. Conduziram-se dois experimentos de campo, na Fazenda Xavante, município de Dueré, Estado do Tocantins, durante dois anos consecutivos, para se avaliar a resposta do arroz irrigado à adubação verde e química, cultivado em um Inceptissolo, cujos tratamentos consistiram de oito combinações de adubação: Adubo verde + N0P0K0; Adubo verde + N100P120K100; Adubo verde + N50P60K50; Adubo verde + N75P90K75; Adubo verde + N45P120K100 (aplicação de N, P e K no plantio); Adubo verde + N45P120K100 (aplicação de P e K no plantio e N em cobertura); Adubo verde + N100P120K100 + 4 Mg ha-1 calcário; e Sem adubo verde + N100P120K100. Obteve-se a produtividade máxima (kg ha-1) de grãos com o tratamento adubo verde + N45P120K100 (aplicação de P e K no plantio e N em cobertura). Entre os componentes da produtividade, o comprimento da panícula foi influenciado positiva e significativamente, pelos tratamentos de adubação. Com a prática da adubação verde, a quantidade de fertilizante nitrogenado a ser empregada pode ser reduzida e, em conseqüência, diminuir também o custo de produção do arroz irrigado.