Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer <i>Pinus sylvestris</i>

Cervantes, Sandra; Vuosku, Jaana; Pyhäjärvi, Tanja

doi:10.7717/peerj.11781

Cited by 8 publications

(12 citation statements)

References 80 publications

(121 reference statements)

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“…For her study, she focused on the haploid conifer megagametophyte. While here results indicated that purifying selection is more effective in haploid tissue, she could not detect the expected reduced diversity of genes predominantly expressed in the megagametophyte (Cervantes et al 2021).…”

Section: Innovative Methods and Approachescontrasting

confidence: 80%

Genomics and adaptation in forest ecosystems

Neophytou

Heer

Milesi

et al. 2022

Tree Genetics & Genomes

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Rapid human-induced environmental changes like climate warming represent a challenge for forest ecosystems. Due to their biological complexity and the long generation time of their keystone tree species, genetic adaptation in these ecosystems might not be fast enough to keep track with conditions changing at such a fast pace. The study of adaptation to environmental change and its genetic mechanisms is therefore key for ensuring a sustainable support and management of forests. The 4-day conference of the European Research Group EvolTree (https://www.evoltree.eu) on the topic of “Genomics and Adaptation in Forest Ecosystems” brought together over 130 scientists to present and discuss the latest developments and findings in forest evolutionary research. Genomic studies in forest trees have long been hampered by the lack of high-quality genomics resources and affordable genotyping methods. This has dramatically changed in the last few years; the conference impressively showed how such tools are now being applied to study past demography, adaptation and interactions with associated organisms. Moreover, genomic studies are now finally also entering the world of conservation and forest management, for example by measuring the value or cost of interspecific hybridization and introgression, assessing the vulnerability of species and populations to future change, or accurately delineating evolutionary significant units. The newly launched conference series of EvolTree will hopefully play a key role in the exchange and synthesis of such important investigations.

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Section: Innovative Methods and Approachescontrasting

confidence: 80%

Genomics and adaptation in forest ecosystems

Neophytou

Heer

Milesi

et al. 2022

Tree Genetics & Genomes

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“…To assess the influence of purifying selection on the nucleotide diversity of the tissue-specifically expressed genes we genotyped 20 megagametophytes from unrelated trees of a single population using exome capture (Kesälahti R. unpublished data). We identify tissue-specific genes based on a previousl study (Cervantes et al 2021). Analyses were done in six datasets, one for each tissue-specific set of genes, plus a dataset used as reference point which included all variable sites (hereafter refer as all-sites dataset).…”

Section: Resultsmentioning

confidence: 99%

“…For each gene, we obtained the tissue-specificity and gene expression level information across five tissues (megagametophyte, haploid, and four diploid tissues vegetative bud, embryo, needle, and phloem) from the TMM matrix reported in Cervantes et al 2021. We considered genes with a tau index score of 0.8 and up as tissue-specific (Yanai et al 2005).…”

Section: Identification Of Genes With Tissue-specific Expressionmentioning

confidence: 99%

Strong purifying selection in haploid tissue-specific genes of Scots pine supports the masking theory

Cervantes

Kesälahti

Kumpula

et al. 2023

Preprint

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The masking theory states that genes expressed in haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploidorganisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intra-specific competition. Evidence from other plant groups is scarce and results show no support for the masking theory. Here we have used a gymnosperm Scots pine megagametophyte, a maternally-derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects (DFE) of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue, and that this signal of strong selection is not an artifact driven by high expression levels

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“…We considered 1 349 291 SNPs obtained by mapping RNA‐seq reads to the Scots pine reference transcriptome ( https://www.ncbi.nlm.nih.gov/nuccore/GILO00000000.1 ). From this initial set, we first excluded markers identified in contigs associated with potential contaminants (fungi or microbes; Cervantes et al., 2021 ; Ojeda et al., 2019 ; https://figshare.com/articles/dataset/Pinus_sylvestris_assembly_Trinity_guided_gene_level_information/13109492/1 ). Second, we removed heterozygous SNPs in haploid samples.…”

Section: Methodsmentioning

confidence: 99%

“…For the UOULU RNA‐seq set, we provide information about the predicted multicopy status, orthologous genes identified in P . taeda (Zimin et al., 2014 ) and Pinus lambertiana (Stevens et al., 2016 ) based on BLASTN results (see details in Ojeda et al., 2019 ), and expression levels and tissue specificity in five tissues (Cervantes et al., 2021 ). This information is available in Data S1 .…”

Section: Methodsmentioning

confidence: 99%

Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

et al. 2022

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Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissuespecific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.

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Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

Cited by 8 publications

References 80 publications

Genomics and adaptation in forest ecosystems

Genomics and adaptation in forest ecosystems

Strong purifying selection in haploid tissue-specific genes of Scots pine supports the masking theory

Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

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