DOI: 10.5061/dryad.79cnp5j8z
title: Evolution of repetitive genomic content and gene families over geo-climatic gradients in Brassicaceae

description: On temperature gradients such as elevation or latitude, species turnover
 is common and specialists can persist in extreme environments. This is
 likely paralleled by adaptive and possibly also non-adaptive changes on a
 molecular level, from genes to the structure of genomes. Here we
 investigated associations between elevation and latitude, partly
 represented by climate variables, with features of the genome including
 genome size, transposable element (TE) content and gene family expansion
 and contraction by comparative genomics using the plant family
 Brassicaceae. Together, the geo-climatic variables were good predictors of
 TE content and genome size, explaining 40-60% or more of the variation
 among species. The relationship between mean annual temperature and TE
 content was U-shaped, with species of cooler and hotter climates generally
 having more TEs. The relationships with elevation and mean annual
 precipitation (both corrected for temperature) were positive. Patterns
 were most prevalent for the most abundant TE class, long terminal repeat
 elements (LTR). Gene family expansions and contractions in species of high
 elevations highlighted a restructured genomic architecture regarding cell
 wall modeling, the response to temperature stimulus and processes involved
 in posttranslational protein modiﬁcations. Results point to abiotically
 extreme environments either favoring high TE contents or constraining TE
 silencing on the level of species. Furthermore, establishing in distinct
 geo-climatic regions seems associated with considerable parallel evolution
 with overlapping gene families changing copy numbers.
description: The median of elevation, median of latitude, median of mean
 annual temperature (MAT) and mean annual precipitation (MAP) were
 calculated using the WorldClim database (Fick & Hijmans, 2017) per
 species based on the GBIF entries for each species (Tab. S7). GBIF entries
 were first filtered manually for the correct subspecies and the species’
 native distribution range according to Plants of the World Online (2024).
 Then, sampling points were thinned to only keep entries which were at
 least 5km away from each other using the function “geoThin” from the
 package “enmSdmX” (Smith, 2022) in R v4.3.0. For <em>A.
 thaliana</em> and <em>C. hirsuta</em>, 10% of the data
 was randomly taken of all entries from GBIF before thinning, as it had too
 many entries for this step to run with reasonable memory-efficiency
 (original and thinned files will be deposited on Dryad after
 acceptance).
description: # Evolution of repetitive genomic content and gene families over
 geo-climatic gradients in Brassicaceae Dataset DOI:
 [10.5061/dryad.79cnp5j8z](https://doi.org/10.5061/dryad.79cnp5j8z) ##
 Description of the data and file structure Due to different licensing of
 GBIF entries, I provide here the download links for the datasets used and
 the R scripts used to filter and thin the data. *
 gbif_download_links.xlsx: Links used to download the data from GBIF. *
 filter_gbif_downloads.R: R script used to filter the downloaded files from
 GBIF. * thin_gbif_datasets.R: R script to thin the data. abbreviations: |
 A. alpina | aalp | | :--------------- | :------- | | A. thaliana | atha |
 | A. arenosa | aareno | | A. halleri | ahal | | A. lyrata | alyr | | A.
 arenicola | aare | | A. caerulea | acae | | A. ciliata | acil | | B.
 divaricarpa | bdiv | | B. puberula | bpub | | B. retrofracta | bret | | B.
 stricta | bstricta | | B. vulgaris | bvul | | C. himalaica | chim | | C.
 hirsuta | chir | | C. planisiliqua | cpla | | C. rubella | crub | | C.
 hirsuta | chir | | C. resedifolia | cres | | E. heterophyllum | ehet | |
 E. syriacum | esyr | | E. yunnanense | eyun | | E. salsugineum | esal | |
 K. saxatilis | ksax | | L. africanum | lafr | | L. aucheri | lauc | | M.
 erraticum | merr | | N. brachypetala | nbra | | N. rotundifolia | nrot | |
 P. turrita | ptur | | R. bulbosa | rbul | | S. altissimum | salt | | S.
 irio | siri | | T. glabra | tgla | | T. parvula | tpar | ## Access
 information Other publicly accessible locations of the data: * GBIF Data
 was derived from the following sources: * GBIF