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Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage.

ABSTRACT: The chromophyte algae are a large and biologically diverse assemblage of brown seaweeds, diatoms, and other golden algae classified in 13 taxonomic classes. One subgroup (diatoms, pedinellids, pelagophytes, silicoflagellates, and certain enigmatic genera) is characterized by a highly reduced flagellar apparatus. The flagellar apparatus lacks microtubular and fibrous roots, and the flagellum basal body is attached directly to the nucleus. We hypothesize that the flagellar reduction is the result of a single evolutionary series of events. Cladistic analysis of ultrastructural and biochemical data reveals a monophyletic group that unites all taxa with a reduced flagellar apparatus, supporting our hypothesis. Phylogenetic analyses of 18S rRNA gene sequence data provide strong resolution within most of the major groups of chromophytes but only weakly resolve relationships among those groups. Some of the molecularly based most parsimonious trees, however, also unite the taxa with a reduced flagellar apparatus, although the diatoms are not included in this lineage. This grouping is further supported by a posteriori character weighting of the molecular data, suggesting that flagellar reduction occurred at least twice in parallel evolutionary series of events. To further test our hypothesis of a single evolutionary reduction in the flagellar apparatus, we combine the two data sets and subject the hybrid data matrix to parsimony analysis. The resulting trees unite the diatoms with the other reduced flagellar apparatus algae in a monophyletic group. This result supports our hypothesis of a single evolutionary reduction and indicates the existence of a previously unrecognized lineage of algae characterized by a highly reduced flagellar apparatus. Further, this study suggests that the traditional classification of the diatoms with the chrysophytes and xanthophytes in the division (= phylum) Chrysophyta, as presented in most textbooks, is unsatisfactory and that a significantly different classification should be employed.

SUBMITTER: Saunders GW

PROVIDER: S-EPMC42854 | biostudies-other | 1995 Jan

REPOSITORIES: biostudies-other

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Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage.

Saunders G W GW Potter D D Paskind M P MP Andersen R A RA

Proceedings of the National Academy of Sciences of the United States of America 19950101 1

The chromophyte algae are a large and biologically diverse assemblage of brown seaweeds, diatoms, and other golden algae classified in 13 taxonomic classes. One subgroup (diatoms, pedinellids, pelagophytes, silicoflagellates, and certain enigmatic genera) is characterized by a highly reduced flagellar apparatus. The flagellar apparatus lacks microtubular and fibrous roots, and the flagellum basal body is attached directly to the nucleus. We hypothesize that the flagellar reduction is the result ...[more]

PMID: 7816825

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Project description:Gliomas are among the most common intracranial tumors which originated from neuroepithelial cells. Increasing evidence has revealed that long noncoding RNA (lncRNA)-microRNA (miRNA)-mRNA module regulation and tumor-infiltrating immune cells play important regulatory roles in the occurrence and progression of gliomas. However, the precise underlying molecular mechanisms remain largely unknown. Data on gliomas in The Cancer Genome Atlas lack normal control samples; to overcome this limitation, we combined 665 The Cancer Genome Atlas glioma RNA sequence datasets with 188 Genotype-Tissue Expression normal brain RNA sequences to construct an expression matrix profile after normalization. We systematically analyzed the expression of mRNAs, lncRNAs, and miRNAs between gliomas and normal brain tissues. Kaplan-Meier survival analyses were conducted to screen differentially expressed mRNAs, lncRNAs, and miRNAs. A prognostic miRNA-related competitive endogenous RNA network was constructed, and the core subnetworks were filtered using 6 miRNAs, 3 lncRNAs, and 11 mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to investigate the biological functions of significantly dysregulated mRNAs. Co-expression network analysis was performed to analyze and screen the core genes. Furthermore, single-sample Gene Set Enrichment Analysis and immune checkpoint gene expression analysis were performed, as co-expression analysis indicated immune gene dysregulation in glioma. Finally, the expression of representative dysregulated genes was validated in U87 cells at the transcriptional level, establishing a foundation for further research. We identified 7017 mRNAs, 437 lncRNAs, and 9 miRNAs that were differentially expressed in gliomas. Kaplan-Meier survival analysis revealed 5684 mRNAs, 61 lncRNAs, and 7 miRNAs with potential as prognostic signatures in patients with glioma. The hub subnetwork of the competing endogenous RNA network between PART1-hsa-mir-25-SLC12A5/TACC2/BSN/TLN2/ZDHHC8 was screened out. Gene co-expression network, single-sample Gene Set Enrichment Analysis, and immune checkpoint expression analysis demonstrated that tumor-infiltrating immune cells are closely related to gliomas. We identified novel potential biomarkers to predict survival and therapeutic targets for patients with gliomas based on a large-scale sample. Importantly, we filtered pivotal genes that provide valuable information for further exploration of the molecular mechanisms underlying glioma tumorigenesis and progression.

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Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage.

Publications

Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage.

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