Phylogenomics, divergence time estimation and trait evolution provide a new look into the Gracilariales (Rhodophyta)

Lyra, Goia de Mattos; Iha, Cíntia; Grassa, Christopher J.; Cai, Liming; Zhang, Hongrui; Lane, Christopher E.; Blouin, Nicolas A.; Oliveira, Mariana Cabral de; Nunes, José Marcos de Castro; Davis, Charles C.

doi:10.1016/j.ympev.2021.107294

Cited by 23 publications

(25 citation statements)

References 78 publications

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“…The genus has been split into several new genera (most recently in Gurgel et al 2018) based on diagnostic morphological differences and molecularly supported clades. It has been shown though that the diagnostic morphological characters do not correspond to the new genera, and all the recently recognized new genera have been placed back into the original genus Gracilaria (Lyra et al 2021). This has led to a genus that is more easily distinguishable, has a set of exclusive characters, is genetically quite divergent, and is reciprocally monophyletic.…”

Section: Introductionmentioning

confidence: 99%

Splitting blades: why genera need to be more carefully defined; the case for <italic>Pyropia</italic> (Bangiales, Rhodophyta)

Zuccarello¹,

Wen²,

Kim³

2022

Algae

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The trend in naming genera based almost exclusively on molecular data, and not on morphological diagnostic characters, is increasing. In bifurcating phylogenetic trees generic cut-offs are arbitrary, but at the bare minimum nomenclatural changes should be supported by multiple phylogenetic methodologies using appropriate models for all the various gene partitions, strong support with all branch support methods, and should also result in adding to our knowledge of the interrelationships of taxa. We believe that a recent taxonomic treatment of the genus Pyropia (Yang et al. 2020) into several genera is unwarranted. We reanalysed the data presented in the recent article, using additional phylogenetic methods. Our results show that many of the newly established genera are not well supported by all methods, and the new circumscription of the genus Pyropia renders it unsupported. We also tested additional outgroups, which were previously suggested as sister to Pyropia, but this did not substantially change our conclusions. These generic nomenclatural changes of the previously strongly supported genus Pyropia, do not shed light on the evolution of this group and have serious consequences in these commercially important algae, that are also governed by a plethora of regulation and by-laws that now need to be amended. We suggest that the over-splitting of groups based only on poorly produced and modestly supported phylogenies should not be accepted and that the genus Pyropia sensu Sutherland et al. (2011) be restored.

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Section: Introductionmentioning

confidence: 99%

Splitting blades: why genera need to be more carefully defined; the case for <italic>Pyropia</italic> (Bangiales, Rhodophyta)

Zuccarello¹,

Wen²,

Kim³

2022

Algae

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“…The red seaweed Gracilaria vermiculophylla (synonym: Agarophyton vermiculophyllum, Lyra et al, 2021) is native to the Northwest Pacific.…”

Section: Introductionmentioning

confidence: 99%

Genome‐scale signatures of adaptive gene expression changes in an invasive seaweed Gracilaria vermiculophylla

et al. 2022

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Invasive species can successfully and rapidly colonize new niches and expand ranges via founder effects and enhanced tolerance towards environmental stresses. However, the underpinning molecular mechanisms (i.e., gene expression changes) facilitating rapid adaptation to harsh environments are still poorly understood. The red seaweed Gracilaria vermiculophylla, which is native to the northwest Pacific but invaded North American and European coastal habitats over the last 100 years, provides an excellent model to examine whether enhanced tolerance at the level of gene expression contributed to its invasion success. We collected G. vermiculophylla from its native range in Japan and from two non‐native regions along the Delmarva Peninsula (Eastern United States) and in Germany. Thalli were reared in a common garden for 4 months at which time we performed comparative transcriptome (mRNA) and microRNA (miRNA) sequencing. MRNA‐expression profiling identified 59 genes that were differently expressed between native and non‐native thalli. Of these genes, most were involved in metabolic pathways, including photosynthesis, abiotic stress, and biosynthesis of products and hormones in all four non‐native sites. MiRNA‐based target‐gene correlation analysis in native/non‐native pairs revealed that some target genes are positively or negatively regulated via epigenetic mechanisms. Importantly, these genes are mostly associated with metabolism and defence capability (e.g., metal transporter Nramp5, senescence‐associated protein, cell wall‐associated hydrolase, ycf68 protein and cytochrome P450‐like TBP). Thus, our gene expression results indicate that resource reallocation to metabolic processes is most likely a predominant mechanism contributing to the range‐wide persistence and adaptation of G. vermiculophylla in the invaded range. This study, therefore, provides molecular insight into the speed and nature of invasion‐mediated rapid adaption.

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“…It is especially designed to work with lower‐quality assemblies such as those derived from sequencing older herbarium specimens or mining “off‐target” reads from hybrid enrichment data (Granados Mendoza et al, 2020 ). Our lab has been applying this tool to assemble phylogenetic data sets for published and ongoing systematic studies in flowering plants and algae (Marinho et al, 2019 ; Lyra et al, 2021 ; C. C. Davis, personal observation). These published and ongoing data sets include more than 1500 species with a median base coverage of 21.9× for the plastid genome.…”

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confidence: 99%

PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data

2022

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Premise: The application of high-throughput sequencing, especially to herbarium specimens, is rapidly accelerating biodiversity research. Low-coverage sequencing of total genomic DNA (genome skimming) is particularly promising and can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb, a bioinformatic pipeline to efficiently assemble phylogenomic data sets derived from genome skimming. Methods and Results: PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences from all three genomes using a BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/. Conclusions: We demonstrate that PhyloHerb can accurately identify genes using a published data set from Clusiaceae. We also show via simulations that our approach is effective for highly fragmented assemblies from herbarium specimens and is scalable to thousands of species.

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Phylogenomics, divergence time estimation and trait evolution provide a new look into the Gracilariales (Rhodophyta)

Cited by 23 publications

References 78 publications

Splitting blades: why genera need to be more carefully defined; the case for <italic>Pyropia</italic> (Bangiales, Rhodophyta)

Splitting blades: why genera need to be more carefully defined; the case for <italic>Pyropia</italic> (Bangiales, Rhodophyta)

Genome‐scale signatures of adaptive gene expression changes in an invasive seaweed Gracilaria vermiculophylla

PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data

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