MOTIVATION Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. RESULTS We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP...

Ceratocystis fimbriata sensu lato represents a complex of cryptic and commonly plant pathogenic species that are morphologically similar. Species in this complex have been described using morphological characteristics, intersterility tests and phylogenetics. Microsatellite markers have been useful to study the population structure and origin of some species in the complex. In this study we sequ...

The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection ha...

A polyphasic approach to bacterial taxonomy attempts to integrate phylogenetic relationships with phenotypic marker analysis. This study describes the application of membrane fatty acids as a phenotypic marker for methylotrophs. Detailed phospholipid, ester-linked fatty acid (PLFA) profiles are reported for 17 methylotrophic eubacterial strains. These profiles included verification of double bo...

Two cichlid populations each found on separate islands in the Bocas del Toro archipelago, Panama were identified as members the genus Astatheros. DNA from each population was isolated and purified and the mitochondrial gene cytochrome b was used as a molecular marker. Resulting sequences were compared with already published cytochrome b sequences of Astatheros from an internet database. Phyloge...

SYNOPSIS. TWO fundamentally opposed theories have been proposed to account for the origin of the body plan of the flatworms. Each theory relates to a different concept of the evolution of the early metazoans. For the defenders of the classical planuloid/acoeloi'd theory, the simple organization of the flatworms is reminiscent of an hypothetical acoelomate worm-like ancestor of all bilaterians. ...

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker...

Traditional rice (Oryza sativa L.) landraces provide many essential genes for improving yield, disease resistance, abiotic stress tolerance, and other parameters future breeding. This study aimed to analyze the genetic diversity determine phylogenetic position of traditional from tidal swamp areas South Kalimantan, Indonesia, compared germplasm, including wild relatives, obtained GenBank databa...

Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexoni...