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Sequence database for the single-copy, nuclear-encoded, core photosynthetic gene psbO

ABSTRACT: We have compiled a psbO sequence database for its use as phytoplankton marker gene (see Pierella Karlusich et al 2023 Molecular Ecology Resources doi:10.1111/1755-0998.13592). psbO is nuclear-encoded and only present in photosynthetic organisms (both cyanobacteria and eukaryotic phototrophs), mainly in one copy per genome. The database contains >18,000 unique psbO sequences covering cyanobacteria, photosynthetic protists, macroalgae and land plants. It includes sequences retrieved from IMG, NCBI, MMETSP and other sequenced genomes and transcriptomes, as well as from the environmental sequence catalogs of Global Ocean Sampling and Tara Oceans. The taxonomic assignment of environmental sequences of psbO was determined by the placement of their translated sequences on a PsbO protein reference phylogeny. This reference phylogeny was built in the following way. The sequences were retrieved using HMMer version 3.2.1 with gathering threshold option (http://hmmer.org/) for the corresponding Pfam domain (MSP; PF01716) against the translated sequenced genomes and transcriptomes from the literature and from PhycoCosm, MMETSP and IMG databases. The translated Pfam region of each sequence was retrieved and the redundancy of the dataset was reduced using CDHIT version 4.6.4 (W. Li & Godzik, 2006) at a 80% identity cut-off. These translated sequences were then aligned with MAFFT version 6 using the G-INS-I strategy (Katoh & Toh, 2008). The reference phylogenetic trees was generated with PhyML version 3.0 using the LG substitution model plus gamma-distributed rates and four substitution rate categories (Guindon et al., 2010). The starting tree was a BIONJ tree and the type of tree improvement was subtree pruning and regrafting. Branch support was calculated using the approximate likelihood ratio test (aLRT) with a Shimodaira–Hasegawa-like (SH-like) procedure. Contaminant sequences were carefully removed based on phylogenetic incongruence. The corresponding curated final alignment was used as reference. For parallelization of the taxonomic annotation task, a set of 50 environmental sequences were translated and the PsbO specific Pfam region (PF01716) were retrieved for the following analysis. First, they were aligned against the reference alignment using the option --add of MAFFT version 6 with the G-INS-I strategy (Katoh and Toh 2008 Brief Bioinformatics 9:286-298). Second, the resulting alignment was used for building a phylogeny as described above. Finally, the sequences were classified according to their grouping in monophyletic branches of statistical support >0.7 with reference sequences of the same taxonomic group.

ORGANISM(S): cyanobacteria phytoplankton algae land plants

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PROVIDER: S-BSST659 | biostudies-other |

REPOSITORIES: biostudies-other

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Project description:BACKGROUND: Recent genomic studies have drastically altered our knowledge of polyploid evolution. Wild potatoes (Solanum section Petota) are a highly diverse and economically important group of about 100 species widely distributed throughout the Americas. Thirty-six percent of the species in section Petota are polyploid or with diploid and polyploid cytotypes. However, the group is poorly understood at the genomic level and the series is ideal to study polyploid evolution. Two separate studies using the nuclear orthologs GBSSI and nitrate reductase confirmed prior hypotheses of polyploid origins in potato and have shown new origins not proposed before. These studies have been limited, however, by the use of few accessions per polyploid species and by low taxonomic resolution, providing clade-specific, but not species-specific origins within clades. The purpose of the present study is to use six nuclear orthologs, within 54 accessions of 11 polyploid species, 34 accessions of 29 diploid species of section Petota representing their putative progenitors, and two outgroups, to see if phenomena typical of other polyploid groups occur within wild potatoes, to include multiple origins, loss of alleles, or gain of new alleles. RESULTS: Our results increase resolution within clades, giving better ideas of diploid progenitors, and show unexpected complexity of allele sharing within clades. While some species have little diversity among accessions and concur with the GBSSI and nitrate reductase results, such as S. agrimonifolium, S. colombianum, S. hjertingii, and S. moscopanum, the results give much better resolution of species-specific progenitors. Seven other species, however, show variant patterns of allele distributions suggesting multiple origins and allele loss. Complex three-genome origins are supported for S. hougasii, and S. schenckii, and one of the ten accessions of S. stoloniferum. A very unexpected shared presence of alleles occurs within one clade of S. verrucosum from Central America, and S. berthaultii from South America in six polyploid species S. demissum, S. hjertingii, S. hougasii, S. iopetalum, S. schenckii, and S. stoloniferum. CONCLUSIONS: Our results document considerable genomic complexity of some wild potato polyploids. These can be explained by multiple hybrid origins and allele losses that provide a clear biological explanation for the taxonomic complexity in wild potato polyploids. These results are of theoretical and practical benefit to potato breeders, and add to a growing body of evidence showing considerable complexity in polyploid plants in general.

Project description:BackgroundMolecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales.Principal findingsWe present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group.ConclusionsThe 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.

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Sequence database for the single-copy, nuclear-encoded, core photosynthetic gene psbO

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