MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes

Premise of the study: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. Methods and Results: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. Conclusions: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.

ThaleMine (https://apps.araport.org/thalemine/) is a comprehensive data warehouse that integrates a wide array of genomic information of the model plant Arabidopsis thaliana. The data collection currently includes the latest structural and functional annotation from the Araport11 update, the Col-0 genome sequence, RNA-seq and array expression, co-expression, protein interactions, homologs, pathways, publications, alleles, germplasm and phenotypes. The data are collected from a wide variety of public resources. Users can browse gene-specific data through Gene Report pages, identify and create gene lists based on experiments or indexed keywords, and run GO enrichment analysis to investigate the biological significance of selected gene sets. Developed by the Arabidopsis Information Portal project (Araport, https://www.araport.org/), ThaleMine uses the InterMine software framework, which builds well-structured data, and provides powerful data query and analysis functionality. The warehoused data can be accessed by users via graphical interfaces, as well as programmatically via web-services. Here we describe recent developments in ThaleMine including new features and extensions, and discuss future improvements. InterMine has been broadly adopted by the model organism research community including nematode, rat, mouse, zebrafish, budding yeast, the modENCODE project, as well as being used for human data. ThaleMine is the first InterMine developed for a plant model. As additional new plant InterMines are developed by the legume and other plant research communities, the potential of cross-organism integrative data analysis will be further enabled

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymenas germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.</p

Araport: Data Integration for the Arabidopsis Research Community

<p>Poster presented at the 2015 UMD Minisymposium</p

jcvi: jcvi v0.6.6

What's new Wrappers for DNA aligners available: NUCMER, LAST Batch Ks calculations Misc bug fixes for ALLMAPS Calculate DUST and TRF bed Imputation, liftover and STR predictio

tanghaibao/jcvi: JCVI v0.6.9

What's new GRABSEEDS now imports Pillow Documentation for karyotype synteny plot Short tandem repeat (STR) caller Copy number variation (CNV) caller AWS supporting function

Polyribosomal RNA-Seq Reveals the Decreased Complexity and Diversity of the Arabidopsis Translatome

<div><p>Recent RNA-seq studies reveal that the transcriptomes in animals and plants are more complex than previously thought, leading to the inclusion of many more splice isoforms in annotated genomes. However, it is possible that a significant proportion of the transcripts are spurious isoforms that do not contribute to functional proteins. One of the current hypotheses is that commonly used mRNA extraction methods isolate both pre-mature (nuclear) mRNA and mature (cytoplasmic) mRNA, and these incompletely spliced pre-mature mRNAs may contribute to a large proportion of these spurious transcripts. To investigate this, we compared a traditional RNA-seq dataset (total RNA-seq) and a ribosome-bound RNA-seq dataset (polyribosomal RNA-seq) from <i>Arabidopsis thaliana</i>. An integrative framework that combined <i>de novo</i> assembly and genome-guided assembly was applied to reconstruct transcriptomes for the two datasets. Up to 44.8% of the <i>de novo</i> assembled transcripts in total RNA-seq sample were of low abundance, whereas only 0.09% in polyribosomal RNA-seq <i>de novo</i> assembly were of low abundance. The final round of assembly using PASA (Program to Assemble Spliced Alignments) resulted in more transcript assemblies in the total RNA-seq than those in polyribosomal sample. Comparison of alternative splicing (AS) patterns between total and polyribosomal RNA-seq showed a significant difference (G-test, p-value<0.01) in intron retention events: 46.4% of AS events in the total sample were intron retention, whereas only 23.5% showed evidence of intron retention in the polyribosomal sample. It is likely that a large proportion of retained introns in total RNA-seq result from incompletely spliced pre-mature mRNA. Overall, this study demonstrated that polyribosomal RNA-seq technology decreased the complexity and diversity of the coding transcriptome by eliminating pre-mature mRNAs, especially those of low abundance.</p></div

Somatotyping in Adolescents: Stratified by Sex and Physical Activity

Background: Somatotyping is a method for describing the human physique in terms of a number of traits that relate to body shape and composition. Somatotypes of athletes in selected sports are quite different from one another. It is also used to describe changes in physique during growth, ageing and training as well as in relation to physical performance. Somatotyping gives more information than some typical measures of body composition such as body fat percentage and body mass index that is useful in determining what type of sports will be suitable for an individual. Objective: School is a place where any type of intervention can bring about a substantial change in the physique of an individual and it is also a place where children are involved in various types of sports. The objective of the study is to somatotype school children and to find any sex difference if present. Methodology: Somatotyping consists of numerical ratings for adiposity (endomorphy), musculo-skeletal development (mesomorphy), and slenderness (ectomorphy). The anthropometric somatotype can be calculated from a set of 10 measurements: height, weight, four skinfolds (triceps, subscapular, supraspinale and medial calf), two biepicondylar breadths (humerus and femur) and two girths (upper arm flexed and tensed, and calf). The anthropometric measurements and somatotyping was done, based on Heath-Carter anthropometric somatotyping. Results: We have somatotyped children of a residential rural school in Pondicherry. We observed that somatotype of girls and boys were significantly different. Endomorph physique was more in girls, while mesomorph and ectomorph physique was dominant in boys. Conclusion: Somatotyping children in school will help us to identify specific physique deficiency and to help them in choosing the sports of their choice

Alternative splicing of <i>ATGSTF11</i> (A) and <i>AFC2</i> (B) genes.

<p>TAIR10 gene models, Full-length cDNA (FL-cDNA), transcripts assembled and reads alignments in the total RNA-seq and polyribosomal RNA-seq datasets are listed from top to bottom. Retained introns in total RNA-seq are highlighted using red rectangles. The red and blue colors represent forward and reverse reads in the read-alignment part, respectively.</p