The Mitochondrial Genome of Chara vulgaris: Insights into the Mitochondrial DNA Architecture of the Last Common Ancestor of Green Algae and Land Plants

Plant mitochondrial genomes exhibit unique evolutionary patterns. They have a high rearrangement but low mutation rate, and a large size. Based on massive mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique evolutionary traits, we propose a “Mitochondrial Fostering” theory where the organelle genome plays an integral role in the arrival and development of orphan genes (genes with no homologs in other lineages). Two approaches were used to test this theory: (1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial originating DNA that migrated to the nucleus) at the genome level, and (2) bioinformatic analysis of particular orphan sequences present in both the mitochondrial genome and the nuclear genome of Arabidopsis thaliana. One study example is given about one orphan sequence that codes for two unique orphan genes: one in the mitochondrial genome and another one in the nuclear genome. DNA alignments show regions of this A. thaliana orphan sequence exist scattered throughout other land plant mitochondrial genomes. This is consistent with the high recombination rates of mitochondrial genomes in land plants. This may also enable the creation of novel coding sequences within the orphan loci, which can then be transferred to the nuclear genome and become exposed to new evolutionary pressures. Our study also reveals a high correlation between the amount of mitochondrial DNA transferred to the nuclear genome and the number of orphan genes in land plants. All the data suggests the mitochondrial genome may play a role in nuclear orphan gene evolution in land plants.

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Precambrian palaeontology in the light of molecular phylogeny – an example: the radiation of the green algae

Biogeosciences Discussions ◽

10.5194/bgd-4-3123-2007 ◽

2007 ◽

Vol 4 (5) ◽

pp. 3123-3142 ◽

Cited By ~ 4

Author(s):

B. Teyssèdre

Keyword(s):

Molecular Phylogeny ◽

Green Algae ◽

Common Ancestor ◽

Heuristic Method ◽

Taxonomic Position ◽

Last Common Ancestor ◽

Critical Method ◽

Shed Light

Abstract. The problem of the antiquity of the radiation of the green algae (phylum Viridiplantae) has been hotly debated and is still controversial today. A method combining Precambrian paleontology and molecular phylogeny is applied to shed light on this topic. As a critical method, molecular phylogeny is essential for avoiding taxonomic mistakes. As a heuristic method, it helps us to discern to what extent the presence of such and such clade is likely at such and such time, and it may even suggest the attribution of some fossil to a clade whose taxonomic position will be distinctly defined even though it has no previously known representative. Some well characterized Precambrian fossils of green algae are Palaeastrum and Proterocladus at Svanbergfjellet (ca. 750 Ma), Tasmanites and Pterospermella at Thule (ca. 1200 Ma), Spiromorpha at Ruyang (ca. 1200 Ma) and Leiosphaeridia crassa at Roper (ca. 1450 Ma). The position of these fossils in the taxonomy and the phylogeny of the Viriplantae is discussed. The conclusions are that the Chlorophyceae and the Ulvophyceae were separated long before 750 Ma, that the Chlorophyta and the Streptophyta were separated long before 1200 Ma and that the last common ancestor of the Viridiplantae and the Rhodophyta was possibly two billion years old.

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Transcriptional responses to arbuscular mycorrhizal symbiosis development are conserved in the early divergent Marchantia paleacea

10.1101/2020.12.14.422721 ◽

2020 ◽

Author(s):

Mara Sgroi ◽

Uta Paszkowski

Keyword(s):

Common Ancestor ◽

Arbuscular Mycorrhizal ◽

Land Plants ◽

Arbuscular Mycorrhizal Symbiosis ◽

Mycorrhizal Symbiosis ◽

Plant Colonization ◽

Last Common Ancestor ◽

Transcriptional Responses ◽

Evolutionarily Conserved ◽

Marchantia Paleacea

AbstractArbuscular mycorrhizal symbiosis (AMS) arose in land plants more than 400 million years ago, perhaps acting as a major contributor to plant terrestrialization. The ability to engage in AMS is evolutionarily conserved across most clades of extant land plants, including early diverging bryophytes. Despite its broad taxonomic distribution, little is known about the molecular components that underpin AMS in early diverging land plants as the mechanisms regulating the symbiosis were primarily characterized in angiosperms. Several AMS associated genes were recently shown to be conserved in liverworts and hornworts, but evidence of them being associated with symbiosis in bryophytes is scarce. In this study, we characterised the dynamic response of the liverwort Marchantia paleacea to Rhizophagus irregularis colonization by time-resolved transcriptomics across progressive stages of symbiosis development. Gene orthology inference and comparative analysis of the M. paleacea transcriptional profile with a well characterised legume model -Medicago truncatula - revealed a deep conservation of transcriptional responses to AMS across distantly related species. We identified evolutionarily conserved patterns of expression of genes required for pre-symbiotic signalling, intracellular colonization and symbiotic nutrient exchange. Our study demonstrates that the genetic machinery regulating key aspects of symbiosis in plant hosts is largely conserved and coregulated across distantly related land plants. If bryophytes are confirmed to be monophyletic, our analysis provides novel insights on the first molecular pathways associated with symbiosis at the dawn of plant colonization of land.Significance StatementArbuscular mycorrhizal symbiosis (AMS) between plants and soil fungi was proposed as one of the key adaptations enabling land colonization by plants. The symbiosis is widespread across most extant plant clades, including early-diverging bryophytes, suggesting that it evolved before the last common ancestor of land plants. Recent phylogenetic analyses uncovered that genes regulating AMS in angiosperms are present in the genomes of bryophytes. Our work shows that a set of these genes are transcriptionally induced during AMS in liverworts. Based on the conservation of their transcriptional profiles across land plants, we propose that these genes acquired an AMS-associated function before the last common ancestor of land plants.

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Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated PHAS loci

10.1101/409417 ◽

2018 ◽

Author(s):

Seth Polydore ◽

Alice Lunardon ◽

Michael J. Axtell

Keyword(s):

Arabidopsis Thaliana ◽

Small Rnas ◽

Cleavage Site ◽

Common Ancestor ◽

Land Plants ◽

Last Common Ancestor ◽

Repetitive Region ◽

Pol Ii ◽

Starting Point ◽

Rna Transcript

AbstractSmall RNAs regulate key physiological functions in land plants. Small RNAs can be divided into two categories: microRNAs (miRNAs) and short interfering RNAs (siRNAs); siRNAs are further sub-divided into transposon/repetitive region-localized heterochromatic siRNAs and phased siRNAs (phasiRNAs). PhasiRNAs are produced from the miRNA-mediated cleavage of a Pol II RNA transcript; the miRNA cleavage site provides a defined starting point from which phasiRNAs are produced in a distinctly phased pattern. 21-22 nucleotide (nt)-dominated phasiRNA-producing loci (PHAS) are well represented in all land plants to date. In contrast, 24 nt-dominated PHAS loci are known to be encoded only in monocots and are generally restricted to male reproductive tissues. Currently, only one miRNA (miR2275) is known to trigger the production of these 24 nt-dominated PHAS loci. In this study, we use stringent methodologies in order to examine whether or not 24 nt-dominated PHAS loci also exist in Arabidopsis thaliana. We find that highly expressed heterochromatic siRNAs were consistently mis-identified as 24 nt-dominated PHAS loci using multiple PHAS-detecting algorithms. We also find that MIR2275 is not found in A. thaliana, and it seems to have been lost in the last common ancestor of Brassicales. Altogether, our research highlights the potential issues with widely used PHAS-detecting algorithms which may lead to false positives when trying to annotate new PHAS, especially 24 nt-dominated loci.

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Mitochondrial fostering: the mitochondrial genome may play a role in plant orphan gene evolution

10.1101/2020.01.02.884874 ◽

2020 ◽

Cited By ~ 1

Author(s):

Seth O’Conner ◽

Ling Li

Keyword(s):

Mitochondrial Dna ◽

Mitochondrial Genome ◽

Gene Evolution ◽

Nuclear Genome ◽

Bioinformatic Analysis ◽

Land Plants ◽

Mitochondrial Genomes ◽

Recombination Rates ◽

Orphan Genes ◽

Orphan Gene

AbstractPlant mitochondrial genomes exhibit odd evolutionary patterns. They have a high rearrangement but low mutation rate, and a large size. Based on massive mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique evolutionary traits, we propose a “Mitochondrial Fostering” theory where the organelle genome plays an integral role in the arrival and development of orphan genes (genes with no homologues in other lineages). Two approaches were used to test this theory: 1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial originating DNA that has migrated to the nucleus) at the genome level, and 2) bioinformatic analysis of particular orphan sequences present in both the mitochondrial genome and the nuclear genome of Arabidopsis thaliana. One study example is given about one orphan sequence that codes for two unique orphan genes: one in the mitochondrial genome and another one in the nuclear genome. DNA alignments show regions of this A. thaliana orphan sequence exist scattered throughout other land plant mitochondrial genomes. This is consistent with the high recombination rates of mitochondrial genomes in land plants. This may also enable the creation of novel coding sequences within the orphan loci, which can then be transferred to the nuclear genome and become exposed to new evolutionary pressures. Our study also reveals a high correlation between mitochondrial DNA rate transferred to the nuclear genome and number of orphan genes in land plants. All the data suggests the mitochondrial genome may play a role in nuclear orphan gene evolution in land plants.

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Faculty Opinions recommendation of Stable transformation and reverse genetic analysis of Penium margaritaceum: a platform for studies of charophyte green algae, the immediate ancestors of land plants.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718258389.793496508 ◽

2014 ◽

Author(s):

Staffan Persson ◽

Clara Sanchez-Rodriguez

Keyword(s):

Genetic Analysis ◽

Green Algae ◽

Stable Transformation ◽

Land Plants ◽

Reverse Genetic

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Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

Scientific Reports ◽

10.1038/s41598-020-79160-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Evy van Berlo ◽

Alejandra P. Díaz-Loyo ◽

Oscar E. Juárez-Mora ◽

Mariska E. Kret ◽

Jorg J. M. Massen

Keyword(s):

Experimental Evidence ◽

Common Ancestor ◽

Great Apes ◽

Pongo Pygmaeus ◽

Last Common Ancestor ◽

Contagious Yawning ◽

Proximate Mechanism ◽

Social Species ◽

Ultimate Causation

AbstractYawning is highly contagious, yet both its proximate mechanism(s) and its ultimate causation remain poorly understood. Scholars have suggested a link between contagious yawning (CY) and sociality due to its appearance in mostly social species. Nevertheless, as findings are inconsistent, CY’s function and evolution remains heavily debated. One way to understand the evolution of CY is by studying it in hominids. Although CY has been found in chimpanzees and bonobos, but is absent in gorillas, data on orangutans are missing despite them being the least social hominid. Orangutans are thus interesting for understanding CY’s phylogeny. Here, we experimentally tested whether orangutans yawn contagiously in response to videos of conspecifics yawning. Furthermore, we investigated whether CY was affected by familiarity with the yawning individual (i.e. a familiar or unfamiliar conspecific and a 3D orangutan avatar). In 700 trials across 8 individuals, we found that orangutans are more likely to yawn in response to yawn videos compared to control videos of conspecifics, but not to yawn videos of the avatar. Interestingly, CY occurred regardless of whether a conspecific was familiar or unfamiliar. We conclude that CY was likely already present in the last common ancestor of humans and great apes, though more converging evidence is needed.

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Ancient origin of fucosylated xyloglucan in charophycean green algae

Communications Biology ◽

10.1038/s42003-021-02277-w ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Maria Dalgaard Mikkelsen ◽

Jesper Harholt ◽

Bjørge Westereng ◽

David Domozych ◽

Stephen C. Fry ◽

...

Keyword(s):

Green Algae ◽

Structural Component ◽

Cell Walls ◽

Uronic Acid ◽

Structural Elucidation ◽

Land Plants ◽

Evolutionary Significance ◽

Biosynthetic Enzymes ◽

Major Structural Component ◽

Mesotaenium Caldariorum

AbstractThe charophycean green algae (CGA or basal streptophytes) are of particular evolutionary significance because their ancestors gave rise to land plants. One outstanding feature of these algae is that their cell walls exhibit remarkable similarities to those of land plants. Xyloglucan (XyG) is a major structural component of the cell walls of most land plants and was originally thought to be absent in CGA. This study presents evidence that XyG evolved in the CGA. This is based on a) the identification of orthologs of the genetic machinery to produce XyG, b) the identification of XyG in a range of CGA and, c) the structural elucidation of XyG, including uronic acid-containing XyG, in selected CGA. Most notably, XyG fucosylation, a feature considered as a late evolutionary elaboration of the basic XyG structure and orthologs to the corresponding biosynthetic enzymes are shown to be present in Mesotaenium caldariorum.

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