Data from: Gene function rather than reproductive mode drives the evolution of RNA helicases in sexual and apomictic Boechera
Schmidt, Anja et al. (2020), Data from: Gene function rather than reproductive mode drives the evolution of RNA helicases in sexual and apomictic Boechera, Dryad, Dataset, https://doi.org/10.5061/dryad.xksn02vc6
In higher plants sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. Evolutionary advantages leading to coexistence of both reproductive modes are currently not well understood. It is expected that accumulation of deleterious mutations leads to a rapid elimination of apomictic lineages from populations. In this line, apomixis originated repeatedly, likely from deregulation of the sexual pathway, leading to alterations in the development of reproductive lineages (germlines) in apomicts as compared to sexual plants. This potentially involves mutations in genes controlling reproduction.
Increasing evidence suggests that RNA helicases are crucial regulators of germline development. To gain insights into the evolution of 58 members of this diverse gene family in sexual and apomictic plants, we applied target enrichment combined with Next Generation Sequencing to identify allelic variants from 24 accessions of the genus Boechera, comprising sexual, facultative and obligate apomicts. Interestingly, allelic variants from apomicts did not show consistently increased mutation frequency. Either sequences were highly conserved in any accession, or allelic variants preferentially harbored mutations in evolutionary less conserved C- and N-terminal domains, or presented high mutation load independent of the reproductive mode. Only for a few genes allelic variants harboring deleterious mutations were only identified in apomicts. To test if high sequence conservation correlates with roles in fundamental cellular or developmental processes, we analyzed Arabidopsis thaliana mutant lines in VASA-LIKE (VASL), and identified pleiotropic defects during ovule and reproductive development. This indicates that also in apomicts mechanisms of selection are in place based on gene function.
120 bp probes (myBaits custom desing by MYcroarray (Ann Arbor, MI, USA) were designed and used for target pulldown of 58 RNA helicases and the CENTROMERIC HISTONE H3 from 24 Boechera accessions representing 12 species, 3 ploidy levels and sexual and apomictic modes of reproduction. Libraries were sequenced on the Illumina HighSeq 2500 plattform using 125 bp paired end sequencing. After quality control and trimming reads were mapped to the Boechera stricta reference genome (Lee et al., 2017), freebayes v.1.1.0-50 was used for variant calling (Garrison 2012).
Sequences were sorted by genomic loci before alignment with MAFFT v7.271 (Katoh and Standley, 2013). On this database 3 types of alignments are provided:
Alignments of genomic regions of the Boechera variants including upstream regulatory regions, depending on data availabilty. Alignments comprise allelic variants of analysed accessions and the Boechera stricta coding sequence downloaded from Phytozome (phytozome.org). Files are in fasta format. Filenames are consistent of the gene identifier of the closest homolog in Arabidopsis thalina in the format ATxGyyyy.mafft.fa.
Alignments of coding regions of Boechera accessions and the closest homolog in Arabidopsis lyrata downloaded from Phytozome (phytozome.org). Files are in fasta format. Filenames are consistent of the gene identifier of the closest homolog in Arabidopsis thalina in the format ATxGyyyy.mafft.cds.fa.
Alignments of protein sequences from selected RNA helicases related to AT1G72730 from Boechera stricta, Arabidopsis lyrata, and Arabidopsis thaliana downloaded from Phytozome v.12.
For further details please refer to associated publication.
Garrison EM, Gabor. 2012. Haplotype-based variant detection from short-read sequencing. arXiv:1207.3907.
Lee C-R, Wang B, Mojica J, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, et al. 2017. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nat Ecol Evol 1:119-1
Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol 30:772-780.
Deutsche Forschungsgemeinschaft, Award: SCHM2448/2