Bioinformatics and Genomics

Article commentary

phylopath: Easy phylogenetic path analysis in R

Section Editor rating: 7 / 10

Elena Papaleo –– A nice R-based tool to perform phylogenetic path analyses.
Gene characteristics of the complete mitochondrial genomes of Paratoxodera polyacantha and Toxodera hauseri (Mantodea: Toxoderidae)

Editor rating: 7 / 10

Antonio Amorim –– This paper contributes significantly to the knowledge of mitogenomes evolution.
Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

Editor rating: 7 / 10

Donovan Parks –– Detailed study showing the limitations of using 16S rRNA and ITS sequences for establishing the taxonomic profiles of environmental samples.
PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

Section Editor rating: 8 / 10

Elena Papaleo –– The authors present a novel tool, PlasmidSeeker, which could be useful for genomic research and also help the time-consuming and tedious assembly steps.
Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica

Editor rating: 8 / 10

Curtis Daehler –– This work provides genetic evidence suggesting the native range of a widely distributed animal that was accidentally spread by humans starting hundreds of years ago.
The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

Editor rating: 8 / 10

Xavier Pochon –– This study provides the first range-wide phylogeographic study of the banded coral shrimp S. hispidus, extending across more than 27,000 km of the globe. Coalescence analysis brings evidence that an isolated Indo-Pacific lineage evolved from a rare dispersal event from the Atlantic around South Africa via the Benguela Current, thereby colonizing the Indian and Pacific Oceans, followed by dispersal across the Indo-Pacific in the last 200,000 years. Surprisingly, this benthic coral reef associated shrimp shows a single haplotype dominating the largest continuous tropical oceanic expanse on the planet.
Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia miltiorrhiza

Editor rating: 7 / 10

Gerrit Beemster –– Epigenetic regulation is rapidly becoming a new regulatory mechanism in developmental processes and this study is a nice contribution to that field using a non model species.
Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula

Editor rating: 7 / 10

Tatiana Vishnivetskaya –– Metal resistant strain from cold environments could be useful for bioremediation at low temperatures
A bibliometric analysis in gene research of myocardial infarction from 2001 to 2015

Editor rating: 7 / 10

Maria Cristina Albertini –– Important information has been disclosed in the paper.
A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora

Editor rating: 8 / 10

Xavier Pochon –– This study developed a simple and cost-effective assay that quickly allows for discrimination amongst coral species in the genus Pocillopora using simple PCR amplification followed by digestion with widely available restriction enzymes. Pocilloporid corals exhibit extreme phenotypic plasticity, making morphological identification of species very challenging. The assay was tested on 691 coral samples collected from across the Hawaiian Archipelago and successfully characterised all six Pocillopora species occurring in Hawaii. Compared to sequence-based identification, this method is simple, rapid and represents a cost saving of nearly 95%. This work will benefit future studies of population structure, ecology, biodiversity, evolution and conservation in this challenging coral genus.

Discussing these articles

The paper for the phylopath package is now published in @PeerJ. It includes a worked example of a study by @AGonzalezVoyer, @MGS_tweets and others. PDF typesetting looks quite good! https://t.co/SGxRcVK4qx

210 days ago
Accuracy of taxonomy prediction https://t.co/f7MjLz3bKf via @thePeerJ

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads https://t.co/ltYMfY300w via @thePeerJ

The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages https://t.co/TXOB7dyxro https://t.co/QkZN9Zfxz0

Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula https://t.co/Pe0VoMrmWT

Zhou H, Tan W, Qiu Z, Song Y, Gao S. (2018) A bibliometric analysis in gene research of myocardial infarction from 2001 to 2015. PeerJ 6:e4354 https://t.co/DLzmzAy7tn #CiteSpace https://t.co/9IFzDlxMK6

New paper to ID Pocillopora corals https://t.co/It92AVvX7X