Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mitochondrial and plastid genome analysis of the heteromorphic red alga Mastocarpus papillatus (C. Agardh) Kutzing (Phyllophoraceae, Rhodophyta) reveals two characteristic florideophyte organellar genomes.

ABSTRACT: Analysis of the marine red algal species Mastocarpus papillatus (C. Agardh) Kützing using paired-end 36?bp Illumina sequences resulted in the assembly of its complete mitochondrial and plastid genomes. The mitogenome is 25,906?bp in length and contains 50 genes, and the plastid genome is 184,382?bp with 234 genes. The mitochondrial and plastid genomes show high gene synteny with published Florideophyceae.

SUBMITTER: Sissini MN

PROVIDER: S-EPMC7800575 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Mitochondrial and plastid genome analysis of the heteromorphic red alga Mastocarpus papillatus (C. Agardh) Kützing (Phyllophoraceae, Rhodophyta) reveals two characteristic florideophyte organellar genomes.

Sissini Marina Nasri MN Navarrete-Fernández Teresa M TM Murray Erin M C EMC Freese Jillian M JM Gentilhomme Anais S AS Huber Soren R SR Mumford Thomas F TF Hughey Jeffery R JR

Mitochondrial DNA. Part B, Resources 20160903 1

Analysis of the marine red algal species Mastocarpus papillatus (C. Agardh) Kützing using paired-end 36 bp Illumina sequences resulted in the assembly of its complete mitochondrial and plastid genomes. The mitogenome is 25,906 bp in length and contains 50 genes, and the plastid genome is 184,382 bp with 234 genes. The mitochondrial and plastid genomes show high gene synteny with published Florideophyceae. ...[more]

PMID: 33473594

Similar Datasets

Mitochondrial and plastid genome analysis of the marine red alga Coeloseira compressa (Champiaceae, Rhodophyta).

Project description:The classification of species originally assigned to the marine red algal genus Coeloseira G.J. Hollenberg remains univestigated using molecular data. Paired-end 36?bp Illumina sequences (Illumina Inc, San Diego, CA) were generated from a specimen of Coeloseira compressa G. J. Hollenberg and used to assemble the partial mitochondrial and complete plastid genomes. The mitogenome is 25,391?bp in length and contains 46 genes, and the plastome is 176,291?bp with 233 genes. Both organellar genomes show high gene synteny with previously published Florideophyceae. Comparison of organellar and nuclear phylogenetic markers (rbcL, CO1, LSU) of C. compressa to other genera in the Champiaceae supports its removal from Gastroclonium Kützing and the reinstatement of the name Coeloseira compressa.

| S-EPMC7800148 | biostudies-literature

The complete mitochondrial and plastid genomes of the invasive marine red alga Caulacanthus okamurae (Caulacanthaceae, Rhodophyta) from Moss Landing, California, USA.

Project description:Caulacanthus okamurae is an invasive red alga that forms extensive mats in sheltered marine habitats around the world. To determine its genomic structure and genetic relationship to native and other non-native populations of C. okamurae, high-throughput sequencing analysis was performed on an introduced specimen from Bennett Slough, Moss Landing, California, USA. Assembly of 23,146,595 filtered 150 bp paired-end Illumina sequencing reads yielded its complete mitogenome (GenBank accession MT193839) and plastid genome (GenBank accession MT193838). The mitogenome is 25,995 bp in length and contains 50 genes. The plastid genome is 173,516 bp and contains 234 genes. Comparison of the organellar chromosomes to other Gigartinales revealed a high-level of gene synteny. BLAST analysis of marker sequences (rbcL, cox1, cox2) of C. okamurae from Moss Landing identified four identical DNA sequences: one from a specimen from a native population of C. okamurae from South Korea and three from specimens representing invasive populations from France, Spain, and the USA. These genetic results confirm the presence of C. okamurae in central California, USA, and represent the first complete mitogenome and plastid genome from the Caulacanthaceae.

| S-EPMC7782071 | biostudies-literature

Organellar genome analysis of the marine red alga Dasya binghamiae (Dasyaceae, Rhodophyta) reveals an uncharacteristic florideophyte mitogenome structure.

Project description:Analysis of the marine red algal species Dasya binghamiae A.J.K. Millar using paired-end 36?bp Illumina sequences resulted in the assembly of its complete mitochondrial and plastid genomes. The mitogenome is 26,052?bp in length and contains 46 genes, and the plastome is 177,213?bp with 228 genes. The plastid genome shows high gene synteny with previously published Florideophyceae; however, the mitogenome contains several multigene rearrangements. These organellar data confirm the placement of D. binghamiae in Dasya C. Agardh.

| S-EPMC7800281 | biostudies-literature

Sesquiterpenes from the Brazilian red alga Laurencia dendroidea J. Agardh.

Project description:Two new chamigrane sesquiterpenes 1-2 and three known compounds 3-5 were isolated from a lipophilic extract of the red alga Laurencia dendroidea collected from the Southeastern Brazilian coast. Dendroidone (1) and dendroidiol (2) were isolated from samples collected at Biscaia Inlet, Angra dos Reis, Rio de Janeiro and at Manguinhos Beach, Serra, Espírito Santo, respectively. Debromoelatol (3), obtusane (4) and (1S*,2S*,3S*,5S*,8S*,9S*)-2,3,5,9-tetramethyltricyclo[6.3.0.0¹·?]undecan-2-ol (5) were obtained from specimens collected at Vermelha Beach, Parati, Rio de Janeiro. The structures of new compounds were elucidated by extensive NMR (¹H-, ¹³C-, COSY, HSQC, HMBC and NOESY) and high resolution mass spectrometry analysis. Additionally, the absolute configuration of compound 2 was assigned by X-ray analysis. Full spectroscopic data is described for the first time for compound 3. Anti-inflammatory and antimycobacterial activities of compounds 2-5 were evaluated. Compounds 3-5 inhibited the release of inflammatory mediator NO while TNF-? levels were only affected by 3. All compounds tested displayed moderate antimycobacterial action.

| S-EPMC6271906 | biostudies-other

Complete mitochondrial genome of the freshwater red alga Lympha mucosa (Rhodophyta).

Project description:We present the complete mitochondrial genome of a newly described freshwater red alga Lympha mucosa. The genome was sequenced using the Illumina MiSeq platform. The circular mitochondrial genome is 25,191?bp, contains 46 genes (24 CDS, 20 tRNA, and 2 rRNA), and has an overall GC content of 27.5%. Phylogenetic analyses of the cox1 gene show the placement of Lympha mucosa within the strictly freshwater order Batrachospermales. The four mitochondrial genomes within the subclass Nemaliophycidae sequenced to date are highly conserved in terms of genome size, gene content, and gene synteny.

| S-EPMC7800998 | biostudies-literature

Complete mitochondrial genome of the geniculate calcified red alga, Corallina officinalis (Corallinales, Rhodophyta).

Project description:We present the first mitochondrial genome of the calcified, geniculate coralline red alga Corallina officinalis (Corallinales). The circular genome consists of 26,504?bp and has a gene content consisting of 23 protein-coding genes, 26 transfer RNA genes and two ribosomal RNA genes, with an overall GC content of 30.1%.

| S-EPMC7871867 | biostudies-literature

Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes.

Project description:Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4 × 4 mm(2) of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19(th) and early 20(th) century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method.

| S-EPMC4044621 | biostudies-literature

Complete mitochondrial genomes of six species of the freshwater red algal order Batrachospermales (Rhodophyta).

Project description:Only two mitochondrial (mt) genomes had been reported in members of the red algal order Batrachospermales, which are confined to freshwater habitats. Additional mt genomes of six representative members (Batrachospermum macrosporum, Kumanoa ambigua, K. mahlacensis, Paralemanea sp., Sheathia arcuata, and Sirodotia delicatula) were sequenced aiming to gain insights on the evolution of their mt genomes from a comparative analysis with other red algal groups. Mt genomes sequenced had the following characteristics: lengths ranging between 24,864 nt and 29,785 nt, 22 to 26 protein-coding genes, G + C contents of 21.3 to 30.7%, number of tRNA of 16 to 37, non-coding DNA from 3.8% to 14.8%. Comparative analysis revealed that mt genomes in Batrachospermales are highly conserved in terms of genome size and gene content and synteny. Phylogenetic analyses based on COI nucleotide data revealed high bootstrap support only for the genera usually recovered in the phylogenetic analyses but no support for supra-generic groups. The insertion of a group II intron carrying an ORF coding for the corresponding intron maturase interrupting the COI gene was observed in Paralamenea sp. and accounted for its larger genome in comparison to the other Batrachospermales mt genomes.

| S-EPMC7799738 | biostudies-literature

Assessment of four molecular markers as potential DNA barcodes for red algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta).

Project description:DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.

| S-EPMC3527623 | biostudies-literature

Mitochondrial and Plastid Genomes from Coralline Red Algae Provide Insights into the Incongruent Evolutionary Histories of Organelles.

Project description:Mitochondria and plastids are generally uniparentally inherited and have a conserved gene content over hundreds of millions of years, which makes them potentially useful phylogenetic markers. Organelle single gene-based trees have long been the basis for elucidating interspecies relationships that inform taxonomy. More recently, high-throughput genome sequencing has enabled the construction of massive organelle genome databases from diverse eukaryotes, and these have been used to infer species relationships in deep evolutionary time. Here, we test the idea that despite their expected utility, conflicting phylogenetic signal may exist in mitochondrial and plastid genomes from the anciently diverged coralline red algae (Rhodophyta). We generated complete organelle genome data from five coralline red algae (Lithothamnion sp., Neogoniolithon spectabile, Renouxia sp., Rhodogorgon sp., and Synarthrophyton chejuensis) for comparative analysis with existing organelle genome data from two other species (Calliarthron tuberculosum and Sporolithon durum). We find strong evidence for incongruent phylogenetic signal from both organelle genomes that may be explained by incomplete lineage sorting that has maintained anciently derived gene copies or other molecular evolutionary processes such as hybridization or gene flow during the evolutionary history of coralline red algae.

| S-EPMC6279150 | biostudies-literature