BOL: Related items

The Genes That Travel Together: A Genomic Detective Story

BioStar — Fri, 11 Sep 2026 13:00:36 -0500

Imagine looking through thousands of microbial genomes and discovering two genes that repeatedly appear together. The obvious conclusion is that they must somehow be connected—that perhaps they work together, participate in the same pathway, or depend on each other. But evolution has a way of leaving misleading clues. What if these two genes are found together simply because they were inherited from the same ancient ancestor? In that case, their apparent association may have little to do with their biological function; it may simply be a reflection of shared evolutionary history. This is the intriguing problem addressed by CORGIAS (https://github.com/ynishimuraLv/corgias), a computational framework developed to distinguish genuine gene associations from correlations created by common ancestry.

Instead of asking only whether two genes occur together across genomes, CORGIAS asks a deeper question: did these genes actually evolve together, repeatedly gaining or losing their presence in concert, or are they merely travelling together because of their inherited history? The framework introduces two complementary approaches, Ancestral State Adjustment (ASA) and the Simultaneous EVolution test (SEV), which incorporate evolutionary information into the search for gene associations. This distinction becomes increasingly important as genome sequencing continues to uncover enormous numbers of microbial genomes, many from organisms that have never been cultured and whose genes remain functionally mysterious. In this growing genomic landscape, simply finding a gene is no longer enough—we need clues about what that gene might be doing. CORGIAS approaches this problem almost like a genomic detective: rather than treating every association as evidence, it reconstructs the evolutionary story behind the association and asks whether the evidence survives that history. By doing so, it offers a way to separate coincidence from biological connection and potentially uncover functional relationships hidden within the vast microbial genomic landscape. The broader message is beautifully simple: genes do not evolve in isolation, and understanding what they do may require us to look beyond where they are today and reconstruct how they arrived there. Sometimes, the most important clue in a genome is not the gene itself, but the evolutionary journey it has taken.

More at https://academic.oup.com/nargab/article/7/4/lqaf182/8377910?

Yannick Wurm Lab

Thu, 07 Aug 2014 18:02:37 -0500

Evolutionary genomics of social insects. Extensive theoretical work has explained how and why complex societies evolve. However, only little is known about the genes and molecular mechanisms responsible for social phenotypes. We have been identifying genes and mechanisms involved in the evolution of insect societies using modern genomics tools (Illumina, RNAseq, RADseq...). For example we recently:

1. sequenced and analyzed the genome of the invasive red fire ant Solenopsis invicta (PNAS 2011)

2. discovered that a fundamental social trait in this species (how many queens are accepted in the colony) is determined by variants of a social chromosome (Nature 2013).

3. described the gene expression changes that occur in a virgin queen when she is given the opportunity of replacing her mother (Mol Ecol 2010).

Homepage: http://yannick.poulet.org/

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.

Jit — Wed, 20 Dec 2017 18:35:16 -0600

While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects. To address this limitation, we developed the first de Bruijn graph assembler, dipSPAdes, for HP genomes that significantly improves on the state-of-the-art assemblers for HP diploid genomes.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pubmed/25734602

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Shruti Paniwala — Fri, 03 Jan 2020 13:28:19 -0600

DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life.

Address of the bookmark: https://github.com/YoannAnselmetti/DeCoSTAR_pipeline

shovill: Assemble bacterial isolate genomes from Illumina paired-end reads

BioStar — Sat, 02 Jan 2021 07:05:36 -0600

Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.

Address of the bookmark: https://github.com/tseemann/shovill

Recovery of complete genomes from metagenomes

Jit — Wed, 27 Dec 2017 00:04:55 -0600

This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

Address of the bookmark: http://madsalbertsen.github.io/multi-metagenome/

Digest: In silico restriction digest of complete genomes

Jit — Mon, 14 May 2018 04:02:52 -0500

This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated.

A tool for restriction digest of longuser's sequences is available.

Address of the bookmark: http://insilico.ehu.es/digest/

GTDB-Tk: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Rahul Nayak — Wed, 22 Aug 2018 03:21:01 -0500

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

GTDB-Tk is under active development and validation. Please independently confirm the GTDB-Tk predictions by manually inspecting the tree and bringing any discrepencies to our attention. Notifications about GTDB-Tk releases will be available through the ACE Twitter account (https://twitter.com/ace_uq).

Address of the bookmark: https://github.com/Ecogenomics/GTDBTk

MFannot : a program for the annotation of mitochondrial and plastid genomes

Jit — Mon, 26 Aug 2019 11:47:56 -0500

MFannot is a program for the annotation of mitochondrial and plastid genomes

MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.

It makes intense use of RNA/intron detection tools including HMMER, Exonerate, Erpin and others.

http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl

Address of the bookmark: https://github.com/BFL-lab/Mfannot

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Jit — Mon, 18 May 2020 10:53:32 -0500

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately (see Usage).

Address of the bookmark: https://github.com/dutilh/CAT