Published November 9, 2023 | Version v2
Dataset Open

Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra

Creators

  • 1. CNRS, UMR EcoFoG (Agroparistech, Cirad, INRAE, Université des Antilles, Université de la Guyane)
  • 2. GenPhySE, INRAE, INP, ENVT, Université de Toulouse
  • 3. Université Bordeaux, INRAE, BIOGECO
  • 4. INRAE, UMR EcoFoG (Agroparistech, CNRS, Cirad, Université des Antilles, Université de la Guyane)

Description

Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to plant somatic mutation remain insufficiently tested. Unlike in most animals, the plant germline is assumed to be set aside late in development, leading to the expectation that plants accumulate somatic mutations along growth. Therefore, several predictions were made on the fate of somatic mutations: mutations have generally low frequency in plant tissues; mutations at high frequency have a higher chance of intergenerational transmission; branching topology of the tree dictates mutation distribution; and, exposure to UV radiation increases mutagenesis. To provide new insights into mutation accumulation and transmission in plants, we produced two high-quality reference genomes and a unique dataset of 60 high-coverage whole-genome sequences of two tropical tree species, Dicorynia guianensis (Fabaceae) and Sextonia rubra (Lauraceae). We identified 15,066 de novo somatic mutations in D. guianensis and  3,208 in S. rubra, surprisingly almost all found at low frequency. We demonstrate that: 1) low-frequency mutations can be transmitted to the next generation; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought.

Notes (English)

This is the backup of all results from TreeMutation. README file are present in every subfolders to help navigate the results. For those who want to quickly navigate the results of mutations detections, the summary below pinpoint to the main files with * representing tree name (angela or sixto).

Heterozygous sites are called for all libraries against the genome (file: 01_genomes/04_hz/*_shared_hz.vcf). Cambial putative mutations are called for all cambial libraries against the genome and masked for heterozygous sites (file: 02_mutations/01_raw/*_cambium_nonhz_mutations.sql). Leaf putative mutations are called for all leaf libraries against the genome and masked for heterozygous sites (file: 02_mutations/01_raw/*_leaf_nonhz_mutations.sql). Leaf mutations are further filtered based on minimum allelic count in the normal sample (MAC=0), sequencing depth of normal and tumour samples (DP) and the existence of at least two biological replicates across the crown (BIO) and masked for putative cambial mutations (file: 02_mutations/02_filtered/*_leaf_mutations.tsv and 02_mutations/02_filtered/*_leaf_mutations.vcf). Leaf mutations are annotated with their spectra (file: 02_mutations/02_filtered/*_leaf_mutations_spectra.tsv) and their phylogeny built (file: 02_mutations/02_filtered/*_leaf_mutations.treefile). A set of candidates for mutation transmission to fruits is selected (file: 02_mutations/02_filtered/*_fruits_candidate_mutations.tsv) and resequenced using amplicon. The resulting libraries are aligned against the genomes and the candidate fruit mutations are called up (file: 02_mutations/04_fruits/*_candidate_fruit_mutations.vcf) before filtering the candidates according to expected mutations, resulting in the transmitted mutations summarised in the table 02_mutations/04_fruits/fruits_mutations.tsv.

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