Long-read RNA-Seq for the discovery of long noncoding and antisense RNAs in plant organelles.

Plant organelle transcription has been studied for decades. As techniques advanced, so did the fields of mitochondrial and plastid transcriptomics. The current view is that organelle genomes are pervasively transcribed, irrespective of their size, content, structure, and taxonomic origin.

Pervasive transcription of plant organelle genomes: functional noncoding transcriptomes?

Plant mitochondrial and plastid genomes typically show pervasive, genome-wide transcription. Little is known, however, about the utility of organelle noncoding RNAs, which often make up most of the transcriptome. Here, we suggest that long-read sequencing data combined with dedicated RNA databases could help identify putative functional organelle noncoding transcripts.

An overview of online resources for intra-species detection of gene duplications.

Gene duplication plays an important role in evolutionary mechanism, which can act as a new source of genetic material in genome evolution. However, detecting duplicate genes from genomic data can be challenging. Various bioinformatics resources have been developed to identify duplicate genes from single and/or multiple species.

HSDFinder: A BLAST-Based Strategy for Identifying Highly Similar Duplicated Genes in Eukaryotic Genomes.

Gene duplication is an important evolutionary mechanism capable of providing new genetic material for adaptive and nonadaptive evolution. However, bioinformatics tools for identifying duplicate genes are often limited to the detection of paralogs in multiple species or to specific types of gene duplicates, such as retrocopies. Here, we present a user-friendly, BLAST-based web tool, called HSDFinder, which can identify, annotate, categorize, and visualize highly similar duplicate genes (HSDs) in eukaryotic nuclear genomes.

HSDatabase-a database of highly similar duplicate genes from plants, animals, and algae.

Gene duplication is an important evolutionary mechanism capable of providing new genetic material, which in some instances can help organisms adapt to various environmental conditions. Recent studies, for example, have indicated that highly similar duplicate genes (HSDs) are aiding adaptation to extreme conditions via gene dosage. However, for most eukaryotic genomes HSDs remain uncharacterized, partly because they can be hard to identify and categorize efficiently and effectively.

Genome evolution: Minicircular mtDNA and unusual heteroplasmy in a parasitic plant.

Minicircular organelle genomes exist in diverse species but have never been observed in plants - that is, until now. The mitochondrial genome of the holoparasite Rhopalocnemis phalloides comprises 21 minicircles, which are extremely heteroplasmic, providing an exceptional example of convergent organelle evolution across disparate lineages.

Simple Matching Using QIIME 2 and RDP Reveals Misidentified Sequences and an Underrepresentation of Fungi in Reference Datasets.

Simple nucleotide matching identification methods are not as accurate as once thought at identifying environmental fungal sequences. This is largely because of incorrect naming and the underrepresentation of various fungal groups in reference datasets. Here, we explore these issues by examining an environmental metabarcoding dataset of partial large subunit rRNA sequences of Basidiomycota and basal fungi.

Mutational Effects of Mobile Introns on the Mitochondrial Genomes of Yeasts.

It has been argued that DNA repair by homologous recombination in the context of endonuclease-mediated cleavage can cause mutations. To better understand this phenomenon, we examined homologous recombination following endonuclease cleavage in a native genomic context: the movement of self-splicing introns in the mitochondrial genomes of yeasts. Self-splicing mitochondrial introns are mobile elements, which can copy and paste themselves at specific insertion sites in mitochondrial DNA using a homing endonuclease in conjunction with homologous recombination.

Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases.

Annotating protein-coding genes can be challenging, especially when searching for the best hits against multiple functional databases. This is partly because of "bad words" appearing as top hits, such as hypothetical or uncharacterized proteins. To help alleviate some of these issues, we designed a bioinformatics tool called NoBadWordsCombiner, which efficiently merges the hits from various databases, strengthening gene definitions by minimizing functional descriptions containing "bad words.

Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes.

Although gene duplications have been documented in many species, the precise numbers of highly similar duplicated genes (HSDs) in eukaryotic nuclear genomes remain largely unknown and can be time-consuming to explore. We developed HSDFinder to identify, categorize, and visualize HSDs in eukaryotic nuclear genomes using protein family domains and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In contrast to existing tools, HSDFinder allows users to compare HSDs among different species and visualize results in different KEGG pathway functional categories via heatmap plotting.

Draft genome sequence of the Antarctic green alga sp. UWO241.

Antarctica is home to an assortment of psychrophilic algae, which have evolved various survival strategies for coping with their frigid environments. Here, we explore Antarctic psychrophily by examining the ∼212 Mb draft nuclear genome of the green alga sp. UWO241, which resides within the water column of a perennially ice-covered, hypersaline lake.

Depositing annotated sequences in GenBank: there needs to be a better way.

Submitting sequences to the National Center for Biotechnology Information (NCBI) is an integral part of research and the publication process for many disciplines within the life sciences, and it will only become more important as sequencing technologies continue to improve. Here, I argue that the available infrastructure and resources for uploading data to NCBI-especially the associated annotations of eukaryotic genomes-are inefficient, hard to use and sometimes just plain bad. This, in turn, is causing some researchers to forgo annotations entirely in their submissions.

The strange mitochondrial genomes of Metschnikowia yeasts.

While sequencing and characterizing the mitochondrial genomes of 71 strains from the yeast genus Metschnikowia [1] (close cousin to the model species Candida albicans), we uncovered one of the most extreme examples of mitochondrial genome architectural diversity observed to date. These Metschnikowia mitochondrial DNAs (mtDNAs) capture nearly the entire known gene-size and intron-content range for cox1 and cob across all eukaryotic life and show remarkable differences in structure and noncoding content. This genomic variation can be seen both among species and between strains of the same species, raising the question: why are Metschnikowia mitogenomes so malleable?

Revisiting Ceriantharian (Anthozoa) Mitochondrial Genomes: Casting Doubts about Their Structure and Size.

Recently, Stampar et al. (2019. Linear mitochondrial genome in Anthozoa (Cnidaria): a case study in.

Common Repeat Elements in the Mitochondrial and Plastid Genomes of Green Algae.

Despite both originating from endosymbiotic bacteria, one does not typically expect mitochondrial DNA (mtDNA) to show strong sequence identity to plastid DNA (ptDNA). Nevertheless, a recent analysis of revealed exactly that. A common repeat element has proliferated throughout the mtDNA and ptDNA of this chlamydomonadalean green alga, resulting in the unprecedented situation whereby these two distinct organelle genomes are largely made up of nearly identical sequences.

Can Green Algal Plastid Genome Size Be Explained by DNA Repair Mechanisms?

A major finding in organelle biology over the past decade is that land plant mitochondrial genomes, which are the largest among eukaryotes, can have a "Jekyll and Hyde" mutational pattern: low for synonymous sites, high for intergenic ones. This has led to the theory that double-strand breaks (DSBs) in the intergenic DNA of plant mitogenomes are repaired by inaccurate mechanisms, such as break-induced replication, which can result in large insertions and, thus, could explain why these genomes are so prone to expansion. But how universal is this theory? Can it apply to other giant organelle DNAs, such as the massive plastid DNAs (ptDNAs) of chlamydomonadalean green algae? Indeed, it can.

Presence and absence of light-independent chlorophyll biosynthesis among green algae in an ice-covered Antarctic lake.

The cold, permanently ice-covered waters of Lake Bonney, Antarctica, may seem like an uninviting place for an alga, but they are home to a diversity of photosynthetic life, including sp. UWO241, a psychrophile residing in the deep photic zone. Recently, we found that UWO241 has lost the genes responsible for light-independent chlorophyll biosynthesis, which is surprising given that this green alga comes from a light-limited environment and experiences extended periods of darkness during the Antarctic winter.

Unparalleled Variation in RNA Editing among Plastomes.

The number and position of C-to-U RNA editing sites in Selaginella plastomes can be extremely variable, to a degree that is currently unparalleled in any other photosynthetic genus.

The mitochondrial and chloroplast genomes of the green alga Haematococcus are made up of nearly identical repetitive sequences.

The chlamydomonadalean green alga Haematococcus lacustris (strain UTEX 2505) has the largest chloroplast genome on record: 1352 kb with ∼90% non-coding DNA [1,2]. But what of the mitochondrial genome? Here we present sequencing, assembly, and analysis of the mitogenome that shows that it, too, is extremely expanded. What's more, the same repetitive elements have spread throughout the mitochondrial and chloroplast (or plastid) DNA (mtDNA and ptDNA, respectively), resulting in the situation whereby these two distinct organelle genomes are made up of nearly identical sequences.

Evolution: A Plant Plastid Genome that Has Forsaken Guanine and Cytosine.

The plastid genomes of the non-photosynthetic plants Balanophora reflexa and B. laxiflora are among the most GC-biased genomes observed to date. A new study shows that ∼80% of the plastid-derived proteome is represented by only six amino acids, and several genes are in excess of 95% AT.

: the makings of a giant-sized chloroplast genome.

Recent work on the chlamydomonadalean green alga uncovered the largest plastid genome on record: a whopping 1.35 Mb with >90 % non-coding DNA. A 500-word description of this genome was published in the journal .