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Although red algae are economically highly valuable for their gelatinous cell wall compounds as well as being integral parts of marine benthic habitats, very little genome data are currently available. We present mitochondrial genome sequence data from the red alga Grateloupia taiwanensis S.-M. Lin & H.-Y. Liang. Comprising 28,906 nucleotide positi...
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... genomes of G. taiwanensis and G. angusta are highly similar with no rearrangements (Fig. 2); full bars represent higher similarity between the two genomes, and lower or absence of bars represents lower or absent similiarity be- tween the G. taiwanensis and G. angusta mitocondrial ge- nomes. Sequence similarity is consistent throughout, but a region of reduced similarity can be observed roughly be- tween positions 1800 and ...
Citations
... (Porphyridiophyceae; Kim et al., 2022). Additionally, other groups I and II introns in different regions of the mitogenome have been reported in other members of red algae (Depriest et al., 2014;Hancock et al., 2010;Harden et al., 2016;Kim et al., 2022;Seo et al., 2023;Yang et al., 2016). The analysis of group II introns in Porphyridium mitogenomes by Kim et al. (2022) demonstrated the dynamic nature of group II intron evolution, supporting the occurrence of lateral movement of group II introns among diverse eukaryotes, and revealed their ability to proliferate, once integrated in mitochondrial DNA. ...
Data on genome characteristics and phylogenomics are becoming more readily available for the
Rhodophyta, especially from organelles. However, for the freshwater red algal order
Batrachospermales, information is still scarce with only nine organellar genomes available from six
genera. A total of 22 new mitochondrial genomes representing 13 genera were generated and combined
with the previously published data. Based on this large mitogenome data set, this study aimed to:
(i) describe the structural characteristics of the mitogenomes across the Batrachospermales and compare
with other red algal mitogenomes; (ii) infer phylogenetic relationships among the Batrachospermales
using a broad dataset of taxa and genes. We determined that structure of the mitogenomes showed
little variation, particularly genome size (22,863–29,785 bp), total number of genes (39–49), proteincoding
genes (22–27), and GC content (25.3–32.4%). The largest genomes were observed in three
species of Paralemanea, which also had larger intergenic regions. Synteny among members of
Batrachospermales was highly conserved with the exceptions of three species of Paralemanea having
a group II intron in the cox1 gene and the five Kumanoa species having a small divergent region. Only
three gene losses were detected in the mitogenomes of members of Batrachospermales and the gene
content was otherwise similar to other orders of Nemaliophycidae. The phylogenomic analysis based on
17 concatenated genes showed two large groups within the Batrachospermales, which were also
recovered in previous studies of single or multigene phylogenetic analyses. The existence of two groups
can have taxonomic implications to be considered in future studies.
... angusta, G. asiatica, G. elliptica, G. filicina, G. taiwanensis, and G. turuturu). In the family Halymeniaceae with a total of 227 species, complete mitochondrial genomes have been reported only for nine species (six Grateloupia, two Polyopes, and the single Pachymeniopsis species) (DePriest et al. 2014;Kim et al. 2014bKim et al. , 2021Lee et al. 2015;Guiry and Guiry 2017;Li et al. 2018;Kozhenkova 2020;Schoch et al. 2020;Patil et al. 2022Patil et al. , 2023a. Recent developments in molecular methods are resulting in a golden era for seaweed biodiversity research, including discoveries and descriptions of novel species at various phylogenetic levels (Salomaki and Lane 2017). ...
... Table 2 in electronic supplementary material displays that the mitochondrial genome of G. cornea encodes 51 genes, including 25 PCGs, 23 tRNA genes, and three rRNA genes. Similar mitochondrial properties, including AT composition, gene content and organization were also observed in other red algae (DePriest et al. 2014;Kim et al. 2014bKim et al. , 2021Li et al. 2018;Patil et al. 2022Patil et al. , 2023a. ...
... They share a core set of three rRNA, 23 tRNA, and 25 PCGs, as well as 14 respiratory chain elements (complexes I to IV), four ATP synthase subunits, four ribosomal proteins (two SSU and one LSU), one protein translocase (TatC), and two hypothetical protein genes (orf173 and orf632) (table 2 in electronic supplementary material). The ribosomal protein L20 (rpl20) is the gene missing compared to six Grateloupia, two Polyopes and Pachymeniopsis species mitochondrial genomes were analysed in this study (DePriest et al. 2014;Kim et al. 2014bKim et al. , 2021Li et al. 2018;Patil et al. 2022Patil et al. , 2023a. A small subunit of the ribosome, i.e. rrn5 is only observed in the mitogenomes of G. cornea (in this study), G. elliptica (OP479979) (Patil et al. 2023a), G. turuturu (Patil et al. 2023b), P. lanceolata (NC084251) and P. affinis (OM960741) (Patil et al. 2022). ...
The mitogenome is an important tool for taxonomic and evolutionary investigation. Here, a few complete mitogenomes of red algae have been reported. We have reported the complete mitogenome sequences of Grateloupia cornea Okamura, 1913 (Rhodophyta, Halymeniales). The genome is 30,595 bp in circumference, and has a strongly biased [AT] = 66.9%. Like most other Grateloupia species, it has a group II intron in the cox1 gene. Maximum likelihood and maximum parsimony analyses showed that G. cornea is more closely related to G. asiatica. This shows that the group II intron in the cox1 ORF present in most species of Grateloupia was present in their common ancestor, and uniquely lost in G. asiatica. The seven Grateloupia species with known mitogenome sequences remain monophyletic, with the genus Polyopes as sister taxon. The complete mitochondrial genome data will be valuable for future research on comparative mitochondrial genome analysis, an extensive understanding of gene content and organization, evolution of the cox1 intron in Rhodophyta as well as phylogenetic analysis.
... Yamada, 1941), classified under the phylum, Rhodophyta; class, Florideophyceae; subclass, Rhodymeniophycidae; order: Halymeniales; family, Halymeniaceae; and genus, Grateloupia [5]. There are 69 Grateloupia species that have been classified, and 36 species are still unclassified, and out Reference In this study [6] - [7] [8] [9] [10] [11] Note: a Including the intronic ORF and hypothetical protein genes. ...
... In addition, mitogenomes have a specific sequence that gives reliable data for studying the gene order, makeup, contents, and secondary structures of the encoded RNA [14,15], and it is also useful for making molecular kits (barcoding markers) for economically important species identification [16]. The Grateloupia species contain a characteristic intronic cox1 gene (Table 1), and such features are useful to understand evolutionary and phylogenetic studies [3,[6][7][8][9]17]. Algae mitogenomes consist of introns in the genic region, tandem repeats, and large intergenic repeats, which create challenges for assembling complete circular mitogenomes [15] but due to revolutionary advances in sequencing technologies and bioinformatics tools, such issues can be overcome. ...
... Mold/Protozoan Mitochondrial was selected for the genetic code; red algae belonging to the Florideophyceae and Bangiophyceae classes have demonstrated this method of codon translation [3,[6][7][8][9][10][11]. The mitogenome annotation was performed using the MFannot tool (https://megasun.bch.umontreal.ca/apps/mfannot/, ...
The mitochondrial genome (mitogenome) is essential for identifying species and tracing genetic variation, gene patterns, and evolutionary studies. Here, the mitogenome of Grateloupia turuturu was sequenced on the Illumina sequencing platform. This circular mitogenome (28,265 bp) contains 49 genes, including three rRNAs, twenty transfer RNAs (tRNAs), and twenty-six protein-coding genes (PCGs). Nucleotide composition indicates biased AT (68.8%) content. A Group II intronic sequence was identified between two exons of the cox1 gene, and this sequence comprises an open reading frame (ORF) that encodes a hypothetical protein. The gene content, annotation, and genetic makeup are identical to those of Halymeniaceae members. The complete mitogenome sequences of the Grateloupia and Polyopes species were used in a phylogenetic analysis, which revealed that these two genera are monophyletic and that G. turuturu and G. elliptica are closely related. This newly constructed mitogenome will help us better understand the general trends in the development of cox1 introns in Halymeniaceae, as well as the evolution of red algal mitogenomes within the Rhodophyta and among diverse algal species.
... Results of agarose gel electrophoresis using total genomic DNA (gDNA) from seven Stylonematophyceae species ( Fig. 1; for species information, see Supplementary Fig. 1 and Supplementary Data 1) demonstrates the presence of multiple low-molecular-weight (LMW) DNA fragments. In addition, complete mitogenomes were not assembled using short-read sequencing data, which is unusual for red algae [28][29][30][31] . Instead, partial linear contigs were identified in the genome assemblies ( Supplementary Fig. 2a). ...
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
... However, only three mitochondrial genomes have been published in the order Halymeniales, i.e. Grateloupia angusta (KC875853; Kim et al. 2014), Grateloupia taiwanensis (KM999231; DePriest et al. 2014), and Grateloupia filicina (MG598532; Li et al. 2018). In this study, we sequenced and analyzed the complete mitochondrial genome of P. lancifolius, which is the first mitochondrial genome of the genus. ...
Polyopes lancifolius is a species of Halymeniales, the fifth species-rich order within Rhodophyta. Using next-generation sequencing techniques, we recovered the complete mitochondrial genome of P. lancifolius, i.e. total 26,142 bp in length with 31% GC contents. A total of 49 functional genes were annotated, including 24 protein-coding, 23 transfer RNA, and 2 ribosomal RNA genes. The gene content and synteny have been highly congruent to those of the other halymenialean species, such as Grateloupia taiwanensis, G. filicina, and Grateloupia angusta. Interestingly, the cox1 intron and intronic Open Reading Frame (ORF) are absent in P. lancifolius, that are existed in the other three halymenialean species.
... With respect to the tendency of mitochondrial genome to higher mutation rate and divergences in gene sequences, mitochondrial genes are valuable markers which can be used to resolve evolutionary relationship among the closely related species and among the population. Using all mitochondrial genes as a phylogenetic marker, the inter-relationship between red algae were resolved (DePriest et al. 2014;Kim et al. 2014;Smith 2015). ...
Chlorosarcinopsis eremi is a member of Chlamydomonadales algae which is isolated from terrestrial environments. In this study, the mitochondrial genome of C. eremi isolated from desert region of Iran, was represented for the first time. Following sequencing, assembly and annotation, comparative analyses of C. eremi and other available Chlamydomonadales algae complete mitochondrial genomes were performed. The mitochondrial genome of C. eremi was circular, had a low number of genes coding in the same strand with a minor amount of repeated sequences; same as other non-Reinhardtinia species of Chlamydomonadales algae. GC content of C. eremi mitochondrial genome was in normal range when compared with non-Chlamydomonadales organisms, but among Chlamydomonadales algae, C. eremi had a low GC content mitochondrial genome. C. eremi had the highest percent of non-coding sequences in comparison with other available Chlamydomonadales mitochondrial genomes which was related to intergenic regions. Identity analysis of protein-coding sequences of Chlamydomonadales mitochondrial genomes showed more divergences and may be related to the high mutation rate of mitochondrial genome reported in microbial eukaryotes.
... Palmaria palmata, Yang et al. 2016;Porphyra purpurea, Burger et al. 1999). Interestingly, while in the mt genomes of the genus Pyropia sequenced so far the COI gene (Harden et al. 2015) is interrupted by two group II introns, both in Paralemanea sp. and in the unrelated species Grateulopia taiwanensis (Depriest et al. 2014) a single group II intron interrupt the COI gene at position 1,159 nt, indicating a favourable disposition for an intron insertion at this position of this gene. ...
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.
... Palmaria palmata, Yang et al. 2016;Porphyra purpurea, Burger et al. 1999). Interestingly, while in the mt genomes of the genus Pyropia sequenced so far the COI gene (Harden et al. 2015) is interrupted by two group II introns, both in Paralemanea sp. and in the unrelated species Grateulopia taiwanensis (Depriest et al. 2014) a single group II intron interrupt the COI gene at position 1,159 nt, indicating a favourable disposition for an intron insertion at this position of this gene. ...
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.
... Indeed, the first microsatellite marker for any coralline alga was only recently reported for the maerl-forming crustose species Phymatolithon calcareum (Pardo et al., 2014). The development of next generation sequencing technologies has led to an increased focus on high throughput sequencing and publication of genomelevel datasets for a number of macroalgal species (DePriest et al., 2014;Kim et al., 2015;Bi et al., 2016;Williamson et al., 2016). Such data have the potential to address many questions relating to taxonomy, phylogeny and evolutionary history in algal genetics (Kim et al., 2014). ...
We present the first population genetics study of the calcifying coralline alga and ecosystem engineer Corallina officinalis. Eleven novel SNP markers were developed and tested using Kompetitive Allele Specific PCR (KASP) genotyping to assess the population structure based on five sites around the NE Atlantic (Iceland, three UK sites and Spain), spanning a wide latitudinal range of the species' distribution. We examined population genetic patterns over the region using discriminate analysis of principal components (DAPC). All populations showed significant genetic differentiation, with a marginally insignificant pattern of isolation by distance (IBD) identified. The Icelandic population was most isolated, but still had genotypes in common with the population in Spain. The SNP markers presented here provide useful tools to assess the population connectivity of C. officinalis. This study is amongst the first to use SNPs on macroalgae and represents a significant step towards understanding the population structure of a widespread, habitat-forming coralline alga in the NE Atlantic.
... The mitogenomes of red algae are conserved in both content and genome structure (Tablizo and Lluisma 2014;DePriest et al. 2014;Gray et al. 2004;Hancock et al. 2010). Our comparative analysis showed that the number and order of mitochondrial DNA genes are similar in G. salicornia, G. vermiculophylla, G. chilensis, and G. changii (Online resource 1: Table S2). ...
Gracilaria changii is an agarophyte that has been used for agar extraction and as salads. Currently, there are only three complete mitochondrial genomes of Gracilaria species available in GenBank. We report here the complete mitogenome of G. changii from Peninsular Malaysia using next-generation sequencing. It had a total length of 25,729 bp, comprising 50 genes (25 protein-coding genes – PCGs, 2 rRNA genes, and 23 tRNA genes). The gene synteny of G. changii was similar to G. salicornia from Peninsular Malaysia with three additional tRNA genes (trnY, trnR, trnS1) in comparison to G. salicornia from Hawaii. G. changii had similar start codons (ATG) for all the PCGs, but three (rps3, rpl20, and secY) had incomplete T-stop codons. Genomic data of G. changii is useful to build a more complete dataset for phylogenetic analyses in Gracilariaceae.
