RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants

Summary• While photosynthesis is the most notable trait of plants, several lineages of plants (so-called holo-heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels.• Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related holo-heterotrophic plants.• In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of both Epipogium species accumulated mutations twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed in H.monotropa.• Holo-heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants.

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A transcriptome-based phylogenetic study of hard ticks (Ixodidae)

Scientific Reports ◽

10.1038/s41598-019-49641-9 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 6

Author(s):

N. Pierre Charrier ◽

Axelle Hermouet ◽

Caroline Hervet ◽

Albert Agoulon ◽

Stephen C. Barker ◽

...

Keyword(s):

Evolutionary History ◽

Nuclear Genome ◽

Single Copy ◽

Phylogenetic Study ◽

Data Sets ◽

Hard Tick ◽

Rna Seq ◽

Hard Ticks ◽

History Of ◽

Mitochondrial Sequences

Abstract Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different Ixodes species. We combined this new data with 18 data sets obtained from public databases, both for Ixodes and non-Ixodes hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the Ixodes genus is monophyletic and clarify the relationships among Ixodes sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of Rhipicephalus, which we relate with patterns of genome architecture and changes of life-cycle, respectively.

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Genome of a Giant (Trevally): Caranx ignobilis

10.1101/2021.09.11.459923 ◽

2021 ◽

Author(s):

Brandon D. Pickett ◽

Jessica R. Glass ◽

Perry G. Ridge ◽

John S. K. Kauwe

Keyword(s):

Comparative Genomics ◽

Genome Assembly ◽

Nuclear Genome ◽

Apex Predator ◽

Rna Seq ◽

Distinct Population ◽

High Quality ◽

Pacific Biosciences ◽

Long Reads ◽

Significant Interest

ABSTRACTCaranx ignobilis, commonly known as the kingfish or giant trevally, is a large, reef-associated apex predator. It is a prized sportfish, targeted heavily throughout its tropical and subtropical range in the Indian and Pacific Oceans, and it has drawn significant interest in aquaculture due to an unusual tolerance for freshwater. In this study, we present a high-quality nuclear genome assembly of a C. ignobilis individual from Hawaiian waters, which have recently been shown to host a genetically distinct population. The assembly has a contig NG50 of 7.3Mbp and scaffold NG50 of 46.3Mbp. Twenty-five of the 203 scaffolds contain 90% of the genome. We also present the raw Pacific Biosciences continuous long-reads from which the assembly was created. A Hi-C dataset (Dovetail Genomics Omni-C) and Illumina-based RNA-seq from eight tissues are also presented; the latter of which can be particularly useful for annotation and studies of freshwater tolerance. Overall, this genome assembly and supporting data is a valuable tool for ecological and comparative genomics studies of kingfish and other carangoid fishes.

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Malignancy and NF-κB signalling strengthen coordination between expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes

Genome Biology ◽

10.1186/s13059-021-02541-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Marcos Francisco Perez ◽

Peter Sarkies

Keyword(s):

Gene Expression ◽

Mitochondrial Genome ◽

Correlation Analysis ◽

Mitochondrial Gene ◽

Nuclear Genome ◽

Mitochondrial Proteins ◽

Rna Seq ◽

Healthy Human ◽

Oxphos Gene ◽

Cancer Types

Abstract Background Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. The mammalian mitochondrial genome encodes for 13 mitochondrial proteins, and the remaining mitochondrial proteins are encoded by the nuclear genome. Little is known about how coordination between the expression of the two sets of genes is achieved. Results Correlation analysis of RNA-seq expression data from large publicly available datasets is a common method to leverage genetic diversity to infer gene co-expression modules. Here we use this method to investigate nuclear-mitochondrial gene expression coordination. We identify a pitfall in correlation analysis that results from the large variation in the proportion of transcripts from the mitochondrial genome in RNA-seq data. Commonly used normalisation techniques based on total read counts, such as FPKM or TPM, produce artefactual negative correlations between mitochondrial- and nuclear-encoded transcripts. This also results in artefactual correlations between pairs of nuclear-encoded genes, with important consequences for inferring co-expression modules beyond mitochondria. We show that these effects can be overcome by normalizing using the median-ratio normalisation (MRN) or trimmed mean of M values (TMM) methods. Using these normalisations, we find only weak and inconsistent correlations between mitochondrial and nuclear-encoded mitochondrial genes in the majority of healthy human tissues from the GTEx database. Conclusions We show that a subset of healthy tissues with high expression of NF-κB show significant coordination, suggesting a role for NF-κB in ensuring balanced expression between mitochondrial and nuclear genes. Contrastingly, most cancer types show robust coordination of nuclear and mitochondrial OXPHOS gene expression, identifying this as a feature of gene regulation in cancer.

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Malignancy and NF-kB signalling strengthen coordination between the expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes

10.1101/2021.06.30.450588 ◽

2021 ◽

Author(s):

Marcos Francisco Perez ◽

Peter Sarkies

Keyword(s):

Gene Expression ◽

Correlation Analysis ◽

Mitochondrial Gene ◽

Nuclear Genome ◽

Rna Seq ◽

Healthy Human ◽

Protein Coding ◽

Oxphos Gene ◽

Mammalian Mitochondria ◽

Cancer Types

Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. Mammalian mitochondria carry a small genome containing thirteen protein-coding genes with the remaining mitochondrial proteins encoded by the nuclear genome. Little is known about how coordination between the two sets of genes is achieved. Correlation analysis of RNA-seq expression data from large publicly-available datasets is a common method to leverage genetic diversity to infer gene co-expression modules. Here we use this method to investigate nuclear-mitochondrial gene expression coordination. We identify a pitfall in correlation analysis that results from the large variation in the proportion of transcripts from the mitochondrial genome in RNA-seq data. Commonly used normalization techniques based on total read count (such as FPKM or TPM) produce artefactual negative correlations between mitochondrial- and nuclear-encoded transcripts. This also results in artefactual correlations between pairs of nuclear-encoded genes, thus having important consequences for inferring co-expression modules beyond mitochondria. We show that these effects can be overcome by normalizing using the median-ratio normalization (MRN) or trimmed mean of M values (TMM) methods. Using these normalizations, we find only weak and inconsistent correlations between mitochondrial and nuclear-encoded mitochondrial genes in the majority of healthy human tissues from the GTEx database. However, a subset of healthy tissues with high expression of NFkB show significant coordination supporting a role for NFkB in retrograde signalling. Contrastingly, most cancer types show robust coordination of nuclear and mitochondrial OXPHOS gene expression, identifying this as a feature of gene regulation in cancer.

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