ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences

The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the way up to the whole-genome level. Homology-based approaches based on related reference sequences are usually the preferred option for gene and transcript prediction in newly sequenced genomes, resulting in the popularity of a variety of BLAST and BLAST-based tools. For organelle genomes, a single-reference–based gene finding tool that uses grouping parameters for BLAST results has been implemented in the Genome Search Plotter (GSP). However, this tool does not accept multiple and user-customized reference sequences required for a broad homology search. Here, we present multiple Reference–based Gene Search and Plot (ReGSP), a simple and convenient web tool that accepts multiple reference sequences for homology-based gene search. The tool incorporates cPlot, a novel dot plot tool, for illustrating nucleotide sequence similarity between the query and the reference sequences. ReGSP has an easy-to-use web interface and is freely accessible at https://ds.mju.ac.kr/regsp.

Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat

Background Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is the main regulator determining the efficiency of lignin synthesis and composition. Although it has been characterized in many plants, to date, the importance of the CCoAOMT family in wheat is not well understood. Results Here, a total of 21 wheat CCoAOMT genes (TaCCoAOMT) were identified through an in silico genome search method and they were classified into four groups based on phylogenetic analysis, with the members of the same group sharing similar gene structures and conserved motif compositions. Furthermore, the expression patterns and co-expression network in which TaCCoAOMT is involved were comprehensively investigated using 48 RNA-seq samples from Fg infected and mock samples of 4 wheat genotypes. Combined with qRT-PCR validation of 11 Fg-responsive TaCCoAOMT genes, potential candidates involved in the FHB response and their regulation modules were preliminarily suggested. Additionally, we investigated the genetic diversity and main haplotypes of these CCoAOMT genes in bread wheat and its relative populations based on resequencing data. Conclusions This study identified and characterized the CCoAOMT family in wheat, which not only provided potential targets for further functional analysis, but also contributed to uncovering the mechanism of lignin biosynthesis and its role in FHB tolerance in wheat and beyond.

Pericardial effusion

Pericardial effusion is classified according to its onset—acute, subacute, or chronic (>3 months)—distribution (circumferential or loculated), and haemodynamic impact. Concerning the size, we propose a simple semiquantitative echocardiographic assessment: mild (<10 mm), moderate (10–20 mm), and large (>20 mm), evaluated as the largest telediastolic echo-free space in two-dimensional mode. Symptoms vary according to the speed of accumulation; slow accumulation may induce no or minor symptoms. In the presence of chronic, large pericardial effusions, appropriate tests for neoplasms, tuberculosis, and hypothyroidism should be considered. Chest computed tomography scanning is helpful in reaching an aetiological diagnosis (neoplasms, lymphomas, pneumonia, tuberculosis). High values of proteins, albumin, and lactate dehydrogenase are usually considered indicative of an exudate, as in pleural fluid, but this may not be true for pericardial fluid, and cytology has a sensitivity of only 50% for neoplasm. Mycobacterium cultures and a genome search for tuberculosis with the polymerase chain reaction in pericardial fluid are mandatory if pericardiocentesis is performed. If inflammatory signs are present, the clinical management should be that of pericarditis and a trial of non-steroidal anti-inflammatory drugs, colchicine, or low-dose corticosteroids, or a combination of these, may be tried. In about 60% of cases, the effusion is associated with a known disease, and the therapy should be targeted. When pericardiocentesis is performed in large effusions, prolonged pericardial drainage of up to 30 mL/24 h has been suggested to prevent recurrences, although evidence to support this is scarce. Prognosis is related to the aetiology, and idiopathic effusions may have a good prognosis especially if the effusion is mild to moderate.

RNA polymerase mapping in plants identifies enhancers enriched in causal variants

Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have been reported to be absent in plants based on a study of Arabidopsis thaliana. Here, our PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally-engaged RNA polymerase II (Pol2) at both 5’ and 3’ ends of genes, consistent with paused or slowly-moving Pol2, and divergent transcription at potential intragenic enhancers. A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many enhancer candidates. These sites show distinct patterns of methylation and nucleotide variation based on genomic evolutionary rate profiling characteristic of active enhancers. Maize GRO-Seq data showed RNA polymerase occupancy at promoters and enhancers consistent with cassava but not Arabidopsis. Furthermore, putative enhancers in maize identified by dREG significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation. We show that SNPs within these divergently transcribed intergenic regions predict significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution, suggesting a functional importance of these sites on cassava. The findings shed new light on plant transcription regulation and its impact on development and plasticity.

Pericardial effusion

Pericardial effusion is classified according to its onset—acute, subacute, or chronic (>3 months)—distribution (circumferential or loculated), and haemodynamic impact. Concerning the size, we propose a simple semiquantitative echocardiographic assessment: mild (<10 mm), moderate (10–20 mm), and large (>20 mm), evaluated as the largest telediastolic echo-free space in two-dimensional mode. Symptoms vary according to the speed of accumulation; slow accumulation may induce no or minor symptoms. In the presence of chronic, large pericardial effusions, appropriate tests for neoplasms, tuberculosis, and hypothyroidism should be considered. Chest computed tomography scanning is helpful in reaching an aetiological diagnosis (neoplasms, lymphomas, pneumonia, tuberculosis). High values of proteins, albumin, and lactate dehydrogenase are usually considered indicative of an exudate, as in pleural fluid, but this may not be true for pericardial fluid, and cytology has a sensitivity of only 50% for neoplasm. Mycobacterium cultures and a genome search for tuberculosis with the polymerase chain reaction in pericardial fluid are mandatory if pericardiocentesis is performed. If inflammatory signs are present, the clinical management should be that of pericarditis and a trial of non-steroidal anti-inflammatory drugs, colchicine, or low-dose corticosteroids, or a combination of these, may be tried. In about 60% of cases, the effusion is associated with a known disease, and the therapy should be targeted. When pericardiocentesis is performed in large effusions, prolonged pericardial drainage of up to 30 mL/24 h has been suggested to prevent recurrences, although evidence to support this is scarce. Prognosis is related to the aetiology, and idiopathic effusions may have a good prognosis especially if the effusion is mild to moderate.

A Computational Framework for Tracing the Origins of Genomic Islands in Prokaryotes

Genomic islands (GIs) are chunks of genomic fragments that are acquired from nongenealogical organisms through horizontal gene transfer (HGT). Current researches on studying donor-recipient relationships for HGT are limited at a gene level. As more GIs have been identified and verified, the way of studying donor-recipient relationships can be better modeled by using GIs rather than individual genes. In this paper, we report the development of a computational framework for detecting origins of GIs. The main idea of our computational framework is to identify GIs in a query genome, search candidate genomes that contain genomic regions similar to those GIs in the query genome by BLAST search, and then filter out some candidate genomes if those similar genomic regions are also alien (detected by GI detection tools). We have applied our framework in finding the GI origins for Mycobacterium tuberculosis H37Rv, Herminiimonas arsenicoxydans, and three Thermoanaerobacter species. The predicted results were used to establish the donor-recipient network relationships and visualized by Gephi. Our studies have shown that donor genomes detected by our computational approach were mainly consistent with previous studies. Our framework was implemented with Perl and executed on Windows operating system.

Genetic Dissection of Complex Genetic Factor Involved in NIDDM of OLETF Rat

The Otsuka Long-Evans Tokushima Fatty (OLETF) rat is an animal model for obese-type, noninsulin-dependent diabetes mellitus (NIDDM) in humans. NIDDM in this rat model was shown to be regulated by multiple genes. We have identified 14 quantitative trait loci (QTLs) responsible for NIDDM (Nidd1-14/of) on chromosomes 1, 5, 7, 8, 9, 11, 12, 14, 16, and 17 by a whole genome search in 160 F2 progenies obtained by mating the OLETF and the F344 rats. Among these loci, two QTLs,Nidd1and2/of, were declared significant loci at a genome-wide level.Nidd3, 8, 9,and13/ofexhibited heterosis: heterozygotes showing significantly higher glucose levels than OLETF or F344 homozygotes. We also found evidence for interaction (epistasis) betweenNidd1/ofandNidd2/of, betweenNidd1/ofandNidd10/of, betweenNidd2/ofandNidd8/of, and betweenNidd2/ofandNidd14/of. Furthermore,Nidd6and11/ofshowed linkage with body weight, andNidd1, 2, 8, 9, 10,and12/ofhad an interaction with body weight. These indicated that NIDDM in the OLETF would have a higher degree of genetic complexity. We suggest several interesting candidate genes located in rat genomic regions forNidd1-14/ofor the syntenic regions in human genome.