DOI: 10.5061/dryad.xksn02vc6
title: Data from: Gene function rather than reproductive mode drives the evolution of RNA helicases in sexual and apomictic Boechera

description: 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.
description: 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 <em>CENTROMERIC HISTONE H3</em> 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 <em>Boechera
 stricta</em> reference genome (Lee et al.,
 2017), <i>freebayes</i> 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 <em>Boechera
 </em>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
 <em>Arabidopsis thalina</em> in the format
 ATxGyyyy.mafft.fa. Alignments of coding regions of
 Boechera accessions and the closest homolog in <em>Arabidopsis
 lyrata</em> downloaded from Phytozome (phytozome.org). Files are in
 fasta format. Filenames are consistent of the gene identifier of the
 closest homolog in <em>Arabidopsis thalina</em> in the format
 ATxGyyyy.mafft.cds.fa. Alignments of protein sequences
 from selected RNA helicases related to AT1G72730 from <em>Boechera
 stricta</em>, <em>Arabidopsis lyrata</em>, and
 <em>Arabidopsis thaliana</em> downloaded from Phytozome
 v.12. For further details please refer to associated
 publication.  
 <em>References</em> 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.