Evolution of conserved noncoding sequences in Arabidopsis thaliana
Data files
Jan 29, 2021 version files 5.23 GB
-
final_gen_eco_cn_id.txt
1.26 KB
-
README.txt
556 B
-
SRR1945446_bwa_alt_3_masked_maker_tair10.aa
12.09 MB
-
SRR1945446_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945446_bwa_alt_3_masked_maker_tair10.cds
35.38 MB
-
SRR1945446_bwa_alt_3_masked_missing.txt
2.65 KB
-
SRR1945446_bwa_alt_3_masked_moved.txt
13.52 KB
-
SRR1945446_bwa_alt_3_masked_mx_all.bed
5.52 MB
-
SRR1945446_bwa_alt_3_masked.fasta
120.82 MB
-
SRR1945460_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.10 MB
-
SRR1945460_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.09 MB
-
SRR1945460_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.40 MB
-
SRR1945460_bwa_alt_3_pbj_6_rename_missing.txt
2.05 KB
-
SRR1945460_bwa_alt_3_pbj_6_rename_moved.txt
13.32 KB
-
SRR1945460_bwa_alt_3_pbj_6_rename_mx_all.bed
5.62 MB
-
SRR1945460_bwa_alt_3_pbj_6_rename.fasta
119.72 MB
-
SRR1945476_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.10 MB
-
SRR1945476_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.09 MB
-
SRR1945476_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.42 MB
-
SRR1945476_bwa_alt_3_pbj_6_rename_missing.txt
2.26 KB
-
SRR1945476_bwa_alt_3_pbj_6_rename_moved.txt
13.95 KB
-
SRR1945476_bwa_alt_3_pbj_6_rename_mx_all.bed
5.58 MB
-
SRR1945476_bwa_alt_3_pbj_6_rename.fasta
119.74 MB
-
SRR1945575_bwa_alt_3_masked_maker_tair10.aa
12.09 MB
-
SRR1945575_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945575_bwa_alt_3_masked_maker_tair10.cds
35.37 MB
-
SRR1945575_bwa_alt_3_masked_missing.txt
2.36 KB
-
SRR1945575_bwa_alt_3_masked_moved.txt
12.94 KB
-
SRR1945575_bwa_alt_3_masked_mx_all.bed
5.59 MB
-
SRR1945575_bwa_alt_3_masked.fasta
120.81 MB
-
SRR1945600_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.10 MB
-
SRR1945600_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.09 MB
-
SRR1945600_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.39 MB
-
SRR1945600_bwa_alt_3_pbj_6_rename_missing.txt
2.31 KB
-
SRR1945600_bwa_alt_3_pbj_6_rename_moved.txt
13.66 KB
-
SRR1945600_bwa_alt_3_pbj_6_rename_mx_all.bed
5.62 MB
-
SRR1945600_bwa_alt_3_pbj_6_rename.fasta
119.65 MB
-
SRR1945757_bwa_alt_3_masked_maker_tair10.aa
12.39 MB
-
SRR1945757_bwa_alt_3_masked_maker_tair10.bed
1.13 MB
-
SRR1945757_bwa_alt_3_masked_maker_tair10.cds
36.23 MB
-
SRR1945757_bwa_alt_3_masked_missing.txt
414 B
-
SRR1945757_bwa_alt_3_masked_moved.txt
495 B
-
SRR1945757_bwa_alt_3_masked_mx_all.bed
5.39 MB
-
SRR1945757_bwa_alt_3_masked.fasta
120.86 MB
-
SRR1945758_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12 MB
-
SRR1945758_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.08 MB
-
SRR1945758_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.10 MB
-
SRR1945758_bwa_alt_3_pbj_6_rename_missing.txt
3.02 KB
-
SRR1945758_bwa_alt_3_pbj_6_rename_moved.txt
19.42 KB
-
SRR1945758_bwa_alt_3_pbj_6_rename_mx_all.bed
5.63 MB
-
SRR1945758_bwa_alt_3_pbj_6_rename.fasta
119.64 MB
-
SRR1945764_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.09 MB
-
SRR1945764_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.08 MB
-
SRR1945764_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.40 MB
-
SRR1945764_bwa_alt_3_pbj_6_rename_missing.txt
2.12 KB
-
SRR1945764_bwa_alt_3_pbj_6_rename_moved.txt
14.50 KB
-
SRR1945764_bwa_alt_3_pbj_6_rename_mx_all.bed
5.59 MB
-
SRR1945764_bwa_alt_3_pbj_6_rename.fasta
119.65 MB
-
SRR1945773_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.12 MB
-
SRR1945773_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.09 MB
-
SRR1945773_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.45 MB
-
SRR1945773_bwa_alt_3_pbj_6_rename_missing.txt
2.07 KB
-
SRR1945773_bwa_alt_3_pbj_6_rename_moved.txt
14.15 KB
-
SRR1945773_bwa_alt_3_pbj_6_rename_mx_all.bed
5.64 MB
-
SRR1945773_bwa_alt_3_pbj_6_rename.fasta
119.72 MB
-
SRR1945796_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.07 MB
-
SRR1945796_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.09 MB
-
SRR1945796_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.33 MB
-
SRR1945796_bwa_alt_3_pbj_6_rename_missing.txt
2.06 KB
-
SRR1945796_bwa_alt_3_pbj_6_rename_moved.txt
14.76 KB
-
SRR1945796_bwa_alt_3_pbj_6_rename_mx_all.bed
5.57 MB
-
SRR1945796_bwa_alt_3_pbj_6_rename.fasta
119.64 MB
-
SRR1945808_bwa_alt_3_pbj_5_rename_maker_tair10.aa
12.10 MB
-
SRR1945808_bwa_alt_3_pbj_5_rename_maker_tair10.bed
1.09 MB
-
SRR1945808_bwa_alt_3_pbj_5_rename_maker_tair10.cds
35.40 MB
-
SRR1945808_bwa_alt_3_pbj_5_rename_missing.txt
2.07 KB
-
SRR1945808_bwa_alt_3_pbj_5_rename_moved.txt
13.34 KB
-
SRR1945808_bwa_alt_3_pbj_5_rename_mx_all.bed
5.62 MB
-
SRR1945808_bwa_alt_3_pbj_5_rename.fasta
119.62 MB
-
SRR1945811_bwa_alt_3_masked_maker_tair10.aa
12.07 MB
-
SRR1945811_bwa_alt_3_masked_maker_tair10.bed
1.08 MB
-
SRR1945811_bwa_alt_3_masked_maker_tair10.cds
35.32 MB
-
SRR1945811_bwa_alt_3_masked_missing.txt
2.93 KB
-
SRR1945811_bwa_alt_3_masked_moved.txt
15.65 KB
-
SRR1945811_bwa_alt_3_masked_mx_all.bed
5.56 MB
-
SRR1945811_bwa_alt_3_masked.fasta
120.82 MB
-
SRR1945818_bwa_alt_3_pbj_2_rename_maker_tair10.aa
12.12 MB
-
SRR1945818_bwa_alt_3_pbj_2_rename_maker_tair10.bed
1.09 MB
-
SRR1945818_bwa_alt_3_pbj_2_rename_maker_tair10.cds
35.46 MB
-
SRR1945818_bwa_alt_3_pbj_2_rename_missing.txt
1.85 KB
-
SRR1945818_bwa_alt_3_pbj_2_rename_moved.txt
12.17 KB
-
SRR1945818_bwa_alt_3_pbj_2_rename_mx_all.bed
5.56 MB
-
SRR1945818_bwa_alt_3_pbj_2_rename.fasta
119.62 MB
-
SRR1945826_bwa_alt_3_masked_maker_tair10.aa
12.08 MB
-
SRR1945826_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945826_bwa_alt_3_masked_maker_tair10.cds
35.33 MB
-
SRR1945826_bwa_alt_3_masked_missing.txt
2.99 KB
-
SRR1945826_bwa_alt_3_masked_moved.txt
14.39 KB
-
SRR1945826_bwa_alt_3_masked_mx_all.bed
5.54 MB
-
SRR1945826_bwa_alt_3_masked.fasta
120.82 MB
-
SRR1945829_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.01 MB
-
SRR1945829_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.08 MB
-
SRR1945829_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.16 MB
-
SRR1945829_bwa_alt_3_pbj_6_rename_missing.txt
2.30 KB
-
SRR1945829_bwa_alt_3_pbj_6_rename_moved.txt
14.88 KB
-
SRR1945829_bwa_alt_3_pbj_6_rename_mx_all.bed
5.59 MB
-
SRR1945829_bwa_alt_3_pbj_6_rename.fasta
119.62 MB
-
SRR1945844_bwa_alt_3_masked_maker_tair10.aa
12.05 MB
-
SRR1945844_bwa_alt_3_masked_maker_tair10.bed
1.08 MB
-
SRR1945844_bwa_alt_3_masked_maker_tair10.cds
35.27 MB
-
SRR1945844_bwa_alt_3_masked_missing.txt
2.80 KB
-
SRR1945844_bwa_alt_3_masked_moved.txt
13.73 KB
-
SRR1945844_bwa_alt_3_masked_mx_all.bed
5.61 MB
-
SRR1945844_bwa_alt_3_masked.fasta
120.81 MB
-
SRR1945852_bwa_alt_3_pbj_2_rename_maker_tair10.aa
12.03 MB
-
SRR1945852_bwa_alt_3_pbj_2_rename_maker_tair10.bed
1.08 MB
-
SRR1945852_bwa_alt_3_pbj_2_rename_maker_tair10.cds
35.22 MB
-
SRR1945852_bwa_alt_3_pbj_2_rename_missing.txt
4.97 KB
-
SRR1945852_bwa_alt_3_pbj_2_rename_moved.txt
13.96 KB
-
SRR1945852_bwa_alt_3_pbj_2_rename_mx_all.bed
5.52 MB
-
SRR1945852_bwa_alt_3_pbj_2_rename.fasta
119.65 MB
-
SRR1945858_bwa_alt_3_masked_maker_tair10.aa
12.06 MB
-
SRR1945858_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945858_bwa_alt_3_masked_maker_tair10.cds
35.28 MB
-
SRR1945858_bwa_alt_3_masked_missing.txt
3.12 KB
-
SRR1945858_bwa_alt_3_masked_moved.txt
15.32 KB
-
SRR1945858_bwa_alt_3_masked_mx_all.bed
5.61 MB
-
SRR1945858_bwa_alt_3_masked.fasta
120.82 MB
-
SRR1945861_bwa_alt_3_masked_maker_tair10.aa
12.12 MB
-
SRR1945861_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945861_bwa_alt_3_masked_maker_tair10.cds
35.47 MB
-
SRR1945861_bwa_alt_3_masked_missing.txt
2.42 KB
-
SRR1945861_bwa_alt_3_masked_moved.txt
13.56 KB
-
SRR1945861_bwa_alt_3_masked_mx_all.bed
5.56 MB
-
SRR1945861_bwa_alt_3_masked.fasta
120.83 MB
-
SRR1945869_bwa_alt_3_masked_maker_tair10.aa
12.07 MB
-
SRR1945869_bwa_alt_3_masked_maker_tair10.bed
1.08 MB
-
SRR1945869_bwa_alt_3_masked_maker_tair10.cds
35.33 MB
-
SRR1945869_bwa_alt_3_masked_missing.txt
2.16 KB
-
SRR1945869_bwa_alt_3_masked_moved.txt
12.79 KB
-
SRR1945869_bwa_alt_3_masked_mx_all.bed
5.54 MB
-
SRR1945869_bwa_alt_3_masked.fasta
120.83 MB
-
SRR1945879_bwa_alt_3_masked_maker_tair10.aa
12.11 MB
-
SRR1945879_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945879_bwa_alt_3_masked_maker_tair10.cds
35.44 MB
-
SRR1945879_bwa_alt_3_masked_missing.txt
2.57 KB
-
SRR1945879_bwa_alt_3_masked_moved.txt
12.50 KB
-
SRR1945879_bwa_alt_3_masked_mx_all.bed
5.55 MB
-
SRR1945879_bwa_alt_3_masked.fasta
121.63 MB
-
SRR1945881_bwa_alt_3_masked_maker_tair10.aa
12.13 MB
-
SRR1945881_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945881_bwa_alt_3_masked_maker_tair10.cds
35.49 MB
-
SRR1945881_bwa_alt_3_masked_missing.txt
2.30 KB
-
SRR1945881_bwa_alt_3_masked_moved.txt
12.87 KB
-
SRR1945881_bwa_alt_3_masked_mx_all.bed
5.51 MB
-
SRR1945881_bwa_alt_3_masked.fasta
120.83 MB
-
SRR1945883_bwa_alt_3_masked_maker_tair10.aa
12.09 MB
-
SRR1945883_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945883_bwa_alt_3_masked_maker_tair10.cds
35.37 MB
-
SRR1945883_bwa_alt_3_masked_missing.txt
2.33 KB
-
SRR1945883_bwa_alt_3_masked_moved.txt
15.21 KB
-
SRR1945883_bwa_alt_3_masked_mx_all.bed
5.56 MB
-
SRR1945883_bwa_alt_3_masked.fasta
121.61 MB
-
SRR1945916_bwa_alt_3_masked_maker_tair10.aa
12.10 MB
-
SRR1945916_bwa_alt_3_masked_maker_tair10.bed
1.08 MB
-
SRR1945916_bwa_alt_3_masked_maker_tair10.cds
35.43 MB
-
SRR1945916_bwa_alt_3_masked_missing.txt
2.44 KB
-
SRR1945916_bwa_alt_3_masked_moved.txt
12.50 KB
-
SRR1945916_bwa_alt_3_masked_mx_all.bed
5.52 MB
-
SRR1945916_bwa_alt_3_masked.fasta
120.83 MB
-
SRR1945995_bwa_alt_3_masked_maker_tair10.aa
12.09 MB
-
SRR1945995_bwa_alt_3_masked_maker_tair10.bed
1.09 MB
-
SRR1945995_bwa_alt_3_masked_maker_tair10.cds
35.37 MB
-
SRR1945995_bwa_alt_3_masked_missing.txt
2.43 KB
-
SRR1945995_bwa_alt_3_masked_moved.txt
12.86 KB
-
SRR1945995_bwa_alt_3_masked_mx_all.bed
5.60 MB
-
SRR1945995_bwa_alt_3_masked.fasta
120.82 MB
-
SRR1946002_bwa_alt_3_masked_maker_tair10.aa
12.06 MB
-
SRR1946002_bwa_alt_3_masked_maker_tair10.bed
1.08 MB
-
SRR1946002_bwa_alt_3_masked_maker_tair10.cds
35.29 MB
-
SRR1946002_bwa_alt_3_masked_missing.txt
3.31 KB
-
SRR1946002_bwa_alt_3_masked_moved.txt
15.97 KB
-
SRR1946002_bwa_alt_3_masked_mx_all.bed
5.61 MB
-
SRR1946002_bwa_alt_3_masked.fasta
120.82 MB
-
SRR1946036_bwa_alt_3_pbj_5_rename_maker_tair10.aa
12.03 MB
-
SRR1946036_bwa_alt_3_pbj_5_rename_maker_tair10.bed
1.09 MB
-
SRR1946036_bwa_alt_3_pbj_5_rename_maker_tair10.cds
35.19 MB
-
SRR1946036_bwa_alt_3_pbj_5_rename_missing.txt
2.02 KB
-
SRR1946036_bwa_alt_3_pbj_5_rename_moved.txt
14.49 KB
-
SRR1946036_bwa_alt_3_pbj_5_rename_mx_all.bed
5.57 MB
-
SRR1946036_bwa_alt_3_pbj_5_rename.fasta
119.63 MB
-
SRR1946047_bwa_alt_3_pbj_5_rename_maker_tair10.aa
12.07 MB
-
SRR1946047_bwa_alt_3_pbj_5_rename_maker_tair10.bed
1.08 MB
-
SRR1946047_bwa_alt_3_pbj_5_rename_maker_tair10.cds
35.32 MB
-
SRR1946047_bwa_alt_3_pbj_5_rename_missing.txt
2.52 KB
-
SRR1946047_bwa_alt_3_pbj_5_rename_moved.txt
15.33 KB
-
SRR1946047_bwa_alt_3_pbj_5_rename_mx_all.bed
5.64 MB
-
SRR1946047_bwa_alt_3_pbj_5_rename.fasta
119.62 MB
-
SRR1946330_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.01 MB
-
SRR1946330_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.08 MB
-
SRR1946330_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.16 MB
-
SRR1946330_bwa_alt_3_pbj_6_rename_missing.txt
3.30 KB
-
SRR1946330_bwa_alt_3_pbj_6_rename_moved.txt
20.90 KB
-
SRR1946330_bwa_alt_3_pbj_6_rename_mx_all.bed
5.67 MB
-
SRR1946330_bwa_alt_3_pbj_6_rename.fasta
119.61 MB
-
SRR1946555_bwa_alt_3_pbj_6_rename_maker_tair10.aa
12.07 MB
-
SRR1946555_bwa_alt_3_pbj_6_rename_maker_tair10.bed
1.09 MB
-
SRR1946555_bwa_alt_3_pbj_6_rename_maker_tair10.cds
35.32 MB
-
SRR1946555_bwa_alt_3_pbj_6_rename_missing.txt
2.51 KB
-
SRR1946555_bwa_alt_3_pbj_6_rename_moved.txt
15.97 KB
-
SRR1946555_bwa_alt_3_pbj_6_rename_mx_all.bed
5.64 MB
-
SRR1946555_bwa_alt_3_pbj_6_rename.fasta
119.69 MB
Abstract
Recent pangenome studies have revealed that a large fraction (>20%) of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only evidence for PAV and Positional Variation (PosV) but that diversity in CNS is non-random, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting conserved and variable CNS roles in gene regulation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.