Peltigera (Ascomycota) living in open and shady environments depend on different Nostoc photobionts DOI Open Access
Inga Jüriado, Ulla Kaasalainen, Jaan Liira

et al.

Folia Cryptogamica Estonica, Journal Year: 2023, Volume and Issue: 60, P. 75 - 99

Published: Nov. 1, 2023

Species of Peltigera (lichen-forming Ascomycota) establish obligate symbioses with several monophyletic groups (phylogroups) Nostoc cyanobacteria. Some these fungi are strict specialists and only associate one phylogroup throughout their range, while others generalists many different phylogroups. We sampled 20 taxa, mostly representing the section Peltigera, from grassland forest habitats across Europe. Mycobionts’ identities were confirmed using fungal ITS sequences. The cyanobionts identified grouped based on single nucleotide differences in trnL region phylogenetic analysis rbcLX region. Our data that some species clearly prefer open habitats, largely confined to shady habitats. two habitat preferences consistently paired association groups. As a specific example, ecologically versatile species, canina P. didactyla, both growing associated when associations between mycobionts influenced by conditions, diversity taxon should be considered context management conservation planning.

Language: Английский

Common Methods for Phylogenetic Tree Construction and Their Implementation in R DOI Creative Commons

Yue Zou,

Zixuan Zhang, Yujie Zeng

et al.

Bioengineering, Journal Year: 2024, Volume and Issue: 11(5), P. 480 - 480

Published: May 11, 2024

A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing trees, including distance methods, maximum parsimony, likelihood, Bayesian inference, tree-integration (supermatrix supertree). Here discuss advantages, shortcomings, applications of each method offer relevant codes to construct trees from molecular data using packages algorithms R. This review aims provide comprehensive guidance reference researchers seeking while also promoting further development innovation field. By offering clear concise overview different available, hope enable select most appropriate approach their specific research questions datasets.

Language: Английский

Citations

17
Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages DOI Creative Commons
Anna Cho, Gordon Lax, Patrick J. Keeling

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 198, P. 108120 - 108120

Published: June 7, 2024

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one major eukaryotic supergroups. Due to their ecological impact as primary producer, ochrophytes are relatively well-studied compared rest yet evolutionary relationships remain poorly understood. This in part due number missing lineages large-scale multigene analyses, and an apparently rapid radiation leading many short internodes between ochrophyte subgroups tree. These also found across deep-branching stramenopiles with limited signal, leaving controversial overall. We have addressed this issue other recently, now examine whether contentious within may be resolved help filling updated phylogenomic dataset ochrophytes, along exploring various gene filtering criteria identify most phylogenetically informative genes. generated ten new transcriptomes from culture collections single-cell isolation environmental sample, added these existing dataset, examined effects selecting genes high signal or low noise. For some previously relationships, we find variety analyses consistently unite unstable groupings strong statistical support. example, recovered robust grouping Eustigmatophyceae Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed sister-lineage Pinguiophyceae. Selecting data quality more stable topologies. Overall, adding under-represented groups different still crucial resolving discrete properties affect differently. something which explored further our understanding molecular evolution stramenopiles.

Language: Английский

Citations

6
Molecular diversity and evolution of far-red light-acclimated photosystem I DOI Creative Commons
Christopher J. Gisriel, Donald A. Bryant, Gary W. Brudvig

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Nov. 20, 2023

The need to acclimate different environmental conditions is central the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, an acclimation mechanism that enables certain cyanobacteria use FRL drive photosynthesis. During this process, a well-defined gene cluster upregulated, resulting in changes photosystems allow them absorb perform photochemistry. Because FaRLiP widespread, and because it exemplifies cyanobacterial adaptation mechanisms nature, interest understand its molecular evolution. Here, we performed phylogenetic analysis photosystem I subunits encoded analyzed available structural data predict ancestral characteristics FRL-absorbing I. suggests FRL-specific arose relatively late during when compared with some II, order Nodosilineales, which include strains like Halomicronema hongdechloris Synechococcus sp. PCC 7335, could have obtained via horizontal transfer. We show form contained three chlorophyll f -binding sites PsaB2 subunit, rotated molecule A 0B site electron transfer chain. Along our previous study II expressed these studies describe complexes by cluster.

Language: Английский

Citations

8
A Phylogenomic Backbone for Acoelomorpha Inferred from Transcriptomic Data DOI Creative Commons
Samuel Abalde, Ulf Jondelius

Systematic Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 15, 2024

Abstract —Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs—which include three main groups, namely Acoela, Nemertodermatida, and Xenoturbella—have been proposed to be an early diverging Bilateria, sister protostomes deuterostomes, but phylogenomic analyses have recovered this clade nested within the as Ambulacraria. The position Xenacoelomorpha metazoan tree has understandably attracted a lot attention, overshadowing study phylogenetic relationships group. Given that Xenoturbella includes only six species whose well understood, we decided focus on most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, sequenced 29 transcriptomes, doubling number species, infer backbone for based genomic data. topology is congruent with previous studies. important difference recovery Paratomella first off-shoot dramatically changing reconstruction ancestral acoel. Besides, detected incongruence between gene trees tree, likely linked incomplete lineage sorting, some signal introgression families Dakuidae Mecynostomidae, which hampers inferring correct placement family and, particularly, genus Notocelis. We also used dataset time diversification times Acoelomorpha, coincide known bilaterian extinction events. importance morphological data in acoelomorph phylogenetics, tested several partitions models. Although failed recover robust phylogeny, proven suitable alternative when reference phylogeny available.

Language: Английский

Citations

2
The underestimated fraction: diversity, challenges and novel insights into unicellular cyanobionts of lichens DOI Creative Commons
Patrick Jung, Laura Williams, Burkhard Büdel

et al.

ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Abstract Lichens are remarkable and classic examples of symbiotic organisms that have fascinated scientists for centuries. Yet, it has only been a couple decades significant advances focused on the diversity their green algal and/or cyanobacterial photobionts. Cyanolichens, which contain cyanobacteria as photosynthetic partner, include up to 10% all known lichens and, such, studies cyanobionts much rarer compared counterparts. For unicellular cyanobionts, i.e. do not form filaments, these even scarcer. Nonetheless, currently at least 10 different genera in cosmopolitan lichen order Lichinales. An international consortium (International Network CyanoBionts; INCb) will tackle this lack knowledge. In article, we discuss status current cyanobiont research, compare taxonomic resolution photobionts from cyanolichens with those (chlorolichens), give roadmap research how recondition underestimated fraction lichens.

Language: Английский

Citations

1
Biosynthesis and differential spatial distribution of the 3‐deoxyanthocyanidins apigenidin and luteolinidin at the interface of a plant‐cyanobacteria symbiosis exposed to cold DOI Creative Commons
Erbil Güngör, Benjamin Bartels,

Giorgio Bolchi

et al.

Plant Cell & Environment, Journal Year: 2024, Volume and Issue: 47(11), P. 4151 - 4170

Published: June 25, 2024

Aquatic ferns of the genus Azolla (Azolla) form highly productive symbioses with filamentous cyanobacteria fixing N

Language: Английский

Citations

0
Paraphyly and cryptic diversity unveils unexpected challenges in the “naked lichens” (Calvitimela, Lecanoromycetes, Ascomycota) DOI Creative Commons
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 190, P. 107944 - 107944

Published: Oct. 14, 2023

Molecular phylogenetics has revolutionized the taxonomy of crustose lichens and revealed an extensive amount cryptic diversity. Resolving relationships between genera in lichen family Tephromelataceae proven difficult taxon limits within genus Calvitimela are only partly understood. In this study, we tested monophyly investigated phylogenetic at different taxonomic levels using integrative approach. We performed a global sampling all species currently assigned to conducted additional C. melaleuca sensu lato across Norway. included 108 specimens produced more than 300 sequences from five loci (ITS, LSU, MCM7, mtSSU, TEF1-α). inferred estimated divergence times Calvitimela. Moreover, analyzed chemical morphological characters test their diagnostic values genus. Our molecular results show evolutionarily old deeply divergent lineages The overlapping subgenera Chemical characters, however, largely informative level subgenera, but often homoplastic level. subgenus is found include four distinct genetic lineages. Detailed examinations s. lat. reveal differences taxa previously assumed be morphologically cryptic. Furthermore, young evolutionary ages signs gene tree discordance indicate recent possibly incomplete lineage sorting Phylogenetic analysis observations that austrochilensis uniseptata extraneous (Tephromelataceae). also evidence supporting septentrionalis being sister cuprea. Severidea, one new grouping recovered as highly supported aglaea. Lastly, two fertile were phylogenetically nested sorediate discuss need for updated classification evolution species. Through generic circumscription delimitation propose practical

Language: Английский

Citations

0
Peltigera (Ascomycota) living in open and shady environments depend on different Nostoc photobionts DOI Open Access
Inga Jüriado, Ulla Kaasalainen, Jaan Liira

et al.

Folia Cryptogamica Estonica, Journal Year: 2023, Volume and Issue: 60, P. 75 - 99

Published: Nov. 1, 2023

Species of Peltigera (lichen-forming Ascomycota) establish obligate symbioses with several monophyletic groups (phylogroups) Nostoc cyanobacteria. Some these fungi are strict specialists and only associate one phylogroup throughout their range, while others generalists many different phylogroups. We sampled 20 taxa, mostly representing the section Peltigera, from grassland forest habitats across Europe. Mycobionts’ identities were confirmed using fungal ITS sequences. The cyanobionts identified grouped based on single nucleotide differences in trnL region phylogenetic analysis rbcLX region. Our data that some species clearly prefer open habitats, largely confined to shady habitats. two habitat preferences consistently paired association groups. As a specific example, ecologically versatile species, canina P. didactyla, both growing associated when associations between mycobionts influenced by conditions, diversity taxon should be considered context management conservation planning.

Language: Английский

Citations

0