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The subclass Corallinophycidae is the only group of red algae characterized by the presence of calcite crystals in their cell walls. Except for the Rhodogorgonales, the remaining orders - collectively called corallines - are diverse and widely distributed, having calcified cell walls and highly variable morphology. Corallines constitute the group with the richest fossil record among marine algae. In the present study, we investigate the evolutionary history of the subclass Corallinophycidae and provide a time-calibrated phylogeny to date the radiation of the crown group and its main lineages. We use a multi-locus dataset with an extensive taxon sampling and comprehensive collection of fossil records, carefully assigned to corallines, to reconstruct a time-calibrated phylogeny of this subclass. Our molecular clock analyses suggest that the onset of crown group diversification of Corallinophycidae started in the Lower Jurassic and sped up in the Lower Cretaceous. The divergence time of the oldest order Sporolithales is estimated in the Lower Cretaceous followed by the remaining orders. We discuss the long period of more than 300 million years between the early Paleozoic records attributed to the stem group of Corallinophycidae and the radiation of the crown group. Our inferred phylogeny yields three highly-supported suprageneric lineages for the order Corallinales; we confirm the family Mastophoraceae and amend circumscription of the families Corallinaceae and Lithophyllaceae. These three families are distinguished by a combination of vegetative and reproductive features. In light of the phylogeny, we discuss the evolutionary trends of eleven morphological characters. In addition, we also highlight homoplasious characters and selected autapomorphies emerging in particular taxa., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Background: The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles., Results: We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms., Conclusions: Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages.

454 GS FLX Titanium sequencing data were used to obtain the complete mitochondrial genome of Calliarthron tuberculosum (26,469 bp). The mitogenome contains 44 genes, including 2 ribosomal RNA, 19 transfer RNA, 5 ribosomal proteins, 1 ymf, 2 open reading frames (ORFs) and 16 genes involved in cellular respiration. The secY and rps12 are overlapped by 69 bp. rps3 and rpl16 also have a 45 bp overlapped region. Except for open reading frames near stem-loop region, the results show Calliarthron tuberculosum mtDNA has a high similarity with other Florideophyceae algae mitogenomes in gene synteny, structure and gene content. Phylogeny analysis indicates a close genetic relationship of Calliarthron tuberculosum with Sporolithon durum.

Two red algal classes, the Florideophyceae (approximately 7,100 spp.) and Bangiophyceae (approximately 193 spp.), comprise 98% of red algal diversity in marine and freshwater habitats. These two classes form well-supported monophyletic groups in most phylogenetic analyses. Nonetheless, the interordinal relationships remain largely unresolved, in particular in the largest subclass Rhodymeniophycidae that includes 70% of all species. To elucidate red algal phylogenetic relationships and study organelle evolution, we determined the sequence of 11 mitochondrial genomes (mtDNA) from 5 florideophycean subclasses. These mtDNAs were combined with existing data, resulting in a database of 25 florideophytes and 12 bangiophytes (including cyanidiophycean species). A concatenated alignment of mt proteins was used to resolve ordinal relationships in the Rhodymeniophycidae. Red algal mtDNA genome comparisons showed 47 instances of gene rearrangement including 12 that distinguish Bangiophyceae from Hildenbrandiophycidae, and 5 that distinguish Hildenbrandiophycidae from Nemaliophycidae. These organelle data support a rapid radiation and surprisingly high conservation of mtDNA gene syntheny among the morphologically divergent multicellular lineages of Rhodymeniophycidae. In contrast, we find extensive mitochondrial gene rearrangements when comparing Bangiophyceae and Florideophyceae and multiple examples of gene loss among the different red algal lineages., (© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Abstract We sequenced the complete mitochondrial genome of Gracilariopsis chorda (Gracilariales, Rhodophyta), which is an agar-producing economic red algal species distributed in the northwest Pacific. The mitogenome is 26,534 bp in length with 27.7% GC content that consists of 52 genes including 26 protein-coding, 2 rRNA and 24 tRNA genes. We compared G. chorda mitogenome with that of recently published G. lemaneiformis. Nucleotide sequence similarity between these two mitogenomes was 99.82%, however, there was significant difference in length caused by trnR trnS and trnY genes missing in G. lemaneiformis.

The first complete mitochondrial genome (27,943 bp) of the halymenialean red alga, Grateloupia angusta, was sequenced. The circular mitogenome contains 47 genes, including 26 protein-coding, 19 tRNA and 2 rRNA genes. The rps3 and rpl16 genes are overlapped by 7 bp. The majority of protein-coding genes (17 of 26 genes) use typical ATG start codon, however, 9 genes use alternative start codons such as ATT, AAT, TTA and TTG. The G. angusta mitogenome shows a significant difference to that of Chondrus crispus (Gigartinales) in gene synteny and tRNA compositions.

We sequenced and characterized the first complete mitochondrial genome of the sublittoral red alga Rhodymenia pseudopalmata (Rhodymeniales, Rhodophyta). The mitogenome is 26,166 bp in length with 29.5% GC content. The circular mitogenome contains 47 genes, including 24 protein-coding, 2 rRNA and 21 tRNA genes including two copies of trnG, trnL, trnM and trnS. There are two cases of gene-overlapping, found between sdhD and nad4, and between secY and rps12. The R. pseudopalmata mitochondria genome differs from that of Gracilariopsis lemaneiformis by three missing genes (orf60, rpl20 and trnH).

We describe the first complete mitochondrial genome of Gelidium vagum (Gelidiales) (24,901 bp, 30.4% GC content), an agar-producing red alga. The circular mitochondrial genome contains 43 genes, including 23 protein-coding, 18 tRNA and 2 rRNA genes. All the protein-coding genes have a typical ATG start codon. No introns were found. Two genes, secY and rps12, were overlapped by 41 bp.

Systematics of the red algal order Rhodymeniales was investigated using combined large-subunit nuclear ribosomal DNA (LSU) and elongation factor 2 (EF2) analyses. These data were subjected to distance, parsimony, and Bayesian analyses, and the resulting phylogenies were largely congruent with previously published SSU results in that the four currently recognized rhodymenialean families (Champiaceae, Faucheaceae, Lomentariaceae, and Rhodymeniaceae) were resolved as monophyletic lineages (with the exception of Coelothrix, which is here transferred to the Champiaceae from the Rhodymeniaceae). In addition, taxa presently considered as incertae sedis consisted of two lineages (Fryeella lineage and Hymenocladia lineage). Based on these results, two new families are proposed: (i) the Fryeellaceae fam. nov. to accommodate the genera Fryeella, Hymenocladiopsis, and a new taxon from Tasmania, Australia; and (ii) the Hymenocladiaceae fam. nov., to accommodate Asteromenia, Hymenocladia, and Erythrymenia. In addition to resolving familial relationships, these analyses resolved some novel interspecific affinities, and we propose a new genus, Neogastroclonium gen. nov., for Gastroclonium subarticulatum, a species that differs significantly in both morphology and molecular data from genuine species of Gastroclonium. Relationships among additional faucheacean and lomentariacean taxa were investigated using LSU data only, and these results are discussed. The familial classification of the Rhodymeniales proposed herein is discussed in light of vegetative and reproductive anatomy, most notably the ontogeny of the tetrasporangia., (© 2008 Phycological Society of America.)