Figure S1. SAQR homologs are present in Arabidopsis lyrata, Arabidopsis halleri, Capsella rubella, Capsella grandiflora, and Bochera stricta.
Genome sequences and gene models of the six SAQR homologs downloaded from Phytozome 10.2 (http://phytozome.jgi.doe.gov/pz/portal.html)  SAQR homologs are conserved within their 5′ UTR and CDS regions and share a similar intron structure.  Genome sequences aligned using Kalign (http://www.ebi.ac.uk/Tools/msa/kalign/).

Gene alignments (Kalign)

Yellow highlight: Bases conserved among all homologs
Red text: Upstream Capsella gene sequence
Green Text: Arabidopsis thaliana 5’ UTR
Blue text: Arabidopsis thaliana CDS
Orange text: Arabidopsis thaliana 3’ UTR
Violet text: Arabidopsis thaliana intron sequence
Blue highlight: CDS start sites
Green highlight: Intron start sites

A. thaliana       1 CATCCACTTGAAATGAATCTAATTCATAAAATGATGTAACAGAAGCTTGAGGAATCCAAA
A. lyrata         1 CATCCACTTGAAATGAATCTAATTCATAAAATGATGTAACAAAAGCTTGAGGAATCCAAA
B. stricta        1 CATCCACTTGAAATGAATCTAATTCATAGTTTGATGTAACAAAAGTTTGAGAAATCCAAA
C. grandiflora    1 CATCCACTTGAAATGAATCTAATTCATAATTTGATGTAACAAAAGTTTGAGGAATC-AAA
C. rubella        1 CATCCACTTGAAATGAATCTAATTCATAATTTGATGTAACAAAAGTTTGAGGAATC-AAA
consensus         1 CATCCACTTGAAATGAATCTAATTCATAattTGATGTAACAaAAGtTTGAGgAATCcAAA

A. thaliana      61 CAATGTACATAC---------GTTAATACAACATGCAAGTTCATCTATAAATATGGAACC
A. lyrata        61 CAATGTGCAAACTTATGATAAGTTCATACAACATGCAACTTCATCTATAAATATGGAACC
B. stricta       61 CAATGTGCATAC---------GTACATACAACATACAAATTCATCTATAAATATAG----
C. grandiflora   60 CAATGTGCATAC---------GTACATTACA-----AATTTCATCTATAAATATTG----
C. rubella       60 CAATGTGCATAC---------GTACATTACA-----AATTTCATCTATAAATATTG----
consensus        61 CAATGTgCAtAC         GTacATacaAcatgcAA TTCATCTATAAATATgG    

A. thaliana     112 TTAACTCTCGGATAAGAATTCACCAAGGCAATACATTTT-----ACCTAAG-------AG
A. lyrata       121 TTAACTCTC------GAATTCACCAAGGCAATACATTTT-----AGCTAAACAAAAAAAT
B. stricta      108 -------------------TAACCTAGGCAATACATTTTCGAAACGATAAAGAAGAAGAA
C. grandiflora  102 -------------------TACCTAGGCAAATACATTTT-----AGATATGATAAAATAA
C. rubella      102 -------------------TACCTAGGCAAATACATTTT-----AGATATGATAAAATAA
consensus       121                    TaaCcaaGgcAATACATTTT     agaTAagg aaaa Aa

A. thaliana     160 AACAGAA-------AAAAGACACTTAGCAGGTGAAACAATGTCGTTTAGAAAAGTAGAGA
A. lyrata       170 AAGAGAA-------AAACAAAACTTTGTAGGTGAATCGATGTCGTTTAGAAAAGTAGAGA
B. stricta      149 AAAAAAA-------AAAAGACACTTGGCAGGGGAAATGATGTCGTTTAGAAACGTAGAGA
C. grandiflora  138 AGAAGAGGATAATCAAAAGACACATAGCGGGTGAAACGATGTCGTTTAGGAAAGTGGAGA
C. rubella      138 AGAAGAGGATAATCAAAAGACACATAGCGGGTGAAACGATGTCGTTTAGGAAAGTGGAGA
consensus       181 AaaAgAa       AAAagAcACtTaGcaGGtGAAacgATGTCGTTTAGaAAaGTaGAGA

A. thaliana     213 AGAAACCAACTGAAATGGGCCGAAACATGACCCACGAGAAGTCGGACTCTGATTCGGACA
A. lyrata       223 AGAAACCAACCGAAATGGGCCGTCAAATGACACACGAGAAGTCGGACTCTGACTCAGACA
B. stricta      202 AGAAATCAACCGAAATGAGCCGACACATGACCCACGAGAAGTCGGAATCTGATTCGGACA
C. grandiflora  198 AGAAACCAACCGAAATGGGCCGACACATGACCCACGAGAAGTCGAACTCTGATTCGTACA
C. rubella      198 AGAAACCAACCGAAATGGGCCGACACATGACCCACGAGAAGTCGAACTCTGATTCGTACA
consensus       241 AGAAAcCAACcGAAATGgGCCGacAcATGACcCACGAGAAGTCGgAcTCTGAtTCggACA

A. thaliana     273 ACGAAGGAGCCCCCATGACTGTTGGAGGTTACACTGAATTCGTTGCCCGCAGCGAC---T
A. lyrata       283 ACGAAGGAACCCCCATGACGGCTGGCGGTTACACTGAATTCGTTGCCCGCAGCGAC---T
B. stricta      262 ACGAAAGAACCCCCATGATGGCTCCAGGTTACAGTGAATATGTTACACGCAGCGAC---T
C. grandiflora  258 AAGAAGGAGCTCCCATGATGGCTCCAGGTTACACTGAAATGGTTAGCCGCAGCGACGAGT
C. rubella      258 AAGAAGGAGCTCCCATGATGGCTCCAGGTTACACTGAAATGGTTAGCCGCAGCGACGAGT
consensus       301 AcGAAgGAgCcCCCATGAtgGcTccaGGTTACAcTGAAtt GTTaccCGCAGCGAC   T

A. thaliana     330 CTGACTGGGACGAACCGGTTTATTCTGGCAAAGCCCGTTCTAATTATAACCTCACCGGCA
A. lyrata       340 CAGACTGGGACGAACCTTTTTATTCTGGCAAAGCCCGTTCTAA------------CCTCA
B. stricta      319 CTGACTGGGACGAACCGGTTGATTCTCGCAAACGCAGTCCTGA------------CCCCA
C. grandiflora  318 CTGACTGGGACGATCTTGTTGACTCTGGCAAAACCCGTGCTAG------------CCTCA
C. rubella      318 CTGACTGGGACGATCTTGTTGACTCTGGCAAAACCCGTGCTAG------------CCTCA
consensus       361 CtGACTGGGACGAaCctgTTgAtTCTgGCAAAgcCcGT CTaa            CctCA

A. thaliana     390 CCGCAAAAGGAACTGGTCCCATCAATAGCTTCAGCCGCAAACACTTCCCTAATTACTAAT
A. lyrata       388 CCACCAAGGAAACTGGTCCCACCAATAGCTACAGCCGCAAACATTTCTCTAATAACTGAT
B. stricta      367 TTGCCAAGGAAACTGGTCCTATCAATCGCTACAGCCGCAAATATTACTCTAATTACTAAG
C. grandiflora  366 CCGCCATGGAAACTGCTCCTATCAATCGTTTCAGCCGCAAGAATTTCTCTAATTACTAAG
C. rubella      366 CCGCCATGGAAACTGCTCCTATCAATCGTTTCAGCCGCAAGAATTTCTCTAATTACTAAG
consensus       421 ccgCcAagGaAACTGgTCCtAtCAATcGcTtCAGCCGCAAa AtTtCtCTAATtACTaAg

A. thaliana     450 CATGTA------AGCGGTTTGAACTCTATAATCAAGATTTAAAAGACGCTTTAAATTCGT
A. lyrata       448 CATGTA------AGAGGTTCGAATTCTATAATCAAGATT---AAGATTCTTGAAAATCAT
B. stricta      427 CATGTA------AGAGGTTCGAGTTCTAAAATCAAGATT---TAGATACTTGAAAATCAT
C. grandiflora  426 CATGCATGTAAGAGAGGTTCGAA-------------------------------------
C. rubella      426 CATGCATGTAAGAGAGGTTCGAA-------------------------------------
consensus       481 CATGtA      AGaGGTTcGAa tcta aatcaagatt    aga  ctt aaa tcgt

A. thaliana     504 AGAT-ATATCAATTATTGT-----------TAATTTTACATATTTTGCGTTATGTTTTT-
A. lyrata       499 GAATTACGTCATTTATTTT-----------------------TTTTCCGTTATGTTTTTT
B. stricta      478 GAAT-ATGTAACTAATTGTATGGTACCTTTTAATTTTATTTGTTTTGGGTTATGTTTT--
C. grandiflora  449 -----TTGTAGTTTATTGTATGGTTCCCTTTAATTTTATTTGTTTTGCGTTATGATTTT-
C. rubella      449 -----TTGTAGTTTATTGTATGGTTCCCTTTAATTTTATTTGTTTTGCGTTATGATTTT-
consensus       541 agat atgTaatTtATTgTatggt cc tttaattttatttgTTTTgcGTTATGtTTTt 

A. thaliana     551 CAGATGGGCAGTGCTACGTAAAAGTGAGAAA-CGAAGACATGCAGGCTCACTAGCTAGTT
A. lyrata       536 CAGATGGGCTTGGCAACGTAAAAGTGAGAAA-TGAAGATATGCAAGCTCATTA----GTT
B. stricta      535 CAGATGGGCTTGGCTACGTAAAAGGGAAAAAATGAAGACATGCTCATTAGTTA-------
C. grandiflora  503 CAGATG-GCTTGACAACGTAAAAGTGAAAAA-TGAAGACATGCTCATTAGGTG-------
C. rubella      503 CAGATG-GCTTGACAACGTAAAAGTGAAAAA-TGAAGACATGCTCATTAGGTG-------
consensus       601 CAGATGgGCttggCaACGTAAAAGtGAaAAA tGAAGAcATGCtcatTag Ta       

A. thaliana     610 GAATAATGCCCATATAAATT---ATGTACTATGTCTGAATGTAATAAATAAGAAT-----
A. lyrata       591 AAATAATGCCCATATAACTT---ATGTATTATGTCTGAATGTCATAAATAAGAAT-----
B. stricta      588 ----AAGACTCATATAAATT---ATGTATTATGTCTGAATGTAATAAATAAGAAT-----
C. grandiflora  554 ----AAGGCTCATATGAATTAGTATGTATTATGTCTGAATGTAATGAATAAGAATATAAG
C. rubella      554 ----AAGGCTCATATGAATTAGTATGTATTATGTCTGAATGTAATGAATAAGAATATAAG
consensus       661     AAggCtCATATaAaTT   ATGTAtTATGTCTGAATGTaATaAATAAGAAT     

A. thaliana     662 -------CCAAGGATGGATGATGACGCATGAAC----ATATCAATGATTATAGTCTCATT
A. lyrata       643 -------CCAAGGATGGATGATGCCGCATGAAC----ATATCAATGATTATAGTCTCATT
B. stricta      636 -------CCAAGGATGGAT---GCCTCATGAAA----ATATCAGTGATGATAATCTCATT
C. grandiflora  610 AATTAATCCAAGGATGATGGATGCCTCATGAACGAACATATCGGTGATGACAATCTCATT
C. rubella      610 AATTAATCCAAGGATGATGGATGCCTCATGAACGAACATATCGGTGATGACAATCTCATT
consensus       721        CCAAGGATGgatgatGcCtCATGAAc    ATATCagTGATgAtAaTCTCATT

A. thaliana     711 GTGCTTTCATGCAGTATTTATACAAAGCACTTATGGAAT-----------GAGTATGTTA
A. lyrata       692 GG--TTTCATGCGGT-TTTATACAAAGCAACTATGCAACTATGGAATGAGAAGAATGTTA
B. stricta      682 GG--TATCATGCGGTTTTTATGCAAAGCAACTATAGAAT-----------AAGAATGTTA
C. grandiflora  670 GG--TATTATGCGGTTTATATACAAAGTAACTATGGAAT-----------GATAATGTTA
C. rubella      670 GG--TATTATGCGGTTTATATACAAAGTAACTATGGAAT-----------GATAATGTTA
consensus       781 Gg  TaTcATGCgGTtTtTATaCAAAGcAacTATggAAt           gAgaATGTTA

A. thaliana     760 CATAACTCTACCTATACTTCTATTATTATGAACATATTAATTATAT--------------
A. lyrata       749 CATAACTCTAACTACTTCTATATTATTGTGAACAAATTAGTT---T--------------
B. stricta      729 TAT-ATAATATGGCTACTTCTAATATTATGAACAAGTAAATAGACC--------------
C. grandiflora  717 CTTAATTATAGCTACTTCTATTATATTATGAACAAGTAAATTATATCAATATGCCAAATT
C. rubella      717 CTTAATTATAGCTACTTCTATTATATTATGAACAAGTAAATTATATCAATATGCCAAATT
consensus       841 caTaAttaTAactacttcTaTaaTATTaTGAACAagTaAaTtatat              

A. thaliana     806 ---------ATA----------------AAAAAAAGCTTAATCTTTTACAATACTGTAAG
A. lyrata       792 ---------AAA----------------AATAAAAGCAGAATAATTTACAATACTATAAA
B. stricta      774 ---------AAATTAATTTCAAAACTTCAAATCTAGAATAATATTTTACAATACTTTAAA
C. grandiflora  777 CGTTTCGTCAAA--AAGTTTA-------AAATCTAGAATAATTTTTTACAAGACTATGTA
C. rubella      777 CGTTTCGTCAAA--AAGTTTA-------AAATCTAGAATGATTTTTTACAAGACTATGTA
consensus       901          AaA  aa tt a       AAatctAGaataAT tTTTACAAtACTaTaaa

A. thaliana     841 AGATGAGAACAATTGTAACAATTCCACACCACACCAAAACAAAAATAAAAAAATTGTAAC
A. lyrata       827 AGATGAGAACAGT------------------------------------------GTAAC
B. stricta      825 GGCC-------------------------------------------------TTGTAAT
C. grandiflora  828 ACAT------------------TCC------------------------------GTAAC
C. rubella      828 ACAT------------------TCC------------------------------GTAAC
consensus       961 agat                  tcc                              GTAAc

A. thaliana     901 AATTCCACATGTTATAGTCTTCTAGATTGCAATGA--TCAATATGAATCAAAGAATCTGA
A. lyrata       845 AATTCCACACGTTATAGTCTTCTAGATTGCAATGA--TCAATATGAATCAAAGAATCTGA
B. stricta      836 AATTCCCCCTA--------TTCTAGATCGCAATGAGATCAATATGAATC-----------
C. grandiflora  840 AATTCTCCTTT-------------------------------------------------
C. rubella      840 AATTCTCCTT--------------------------------------------------
consensus      1021 AATTCccC tg        ttctagat gcaatga  tcaatatgaatc           

A. thaliana     959 ATCTTGGACACCTATAATTGGGAACCAATTCTGTAATTGACATCCAAGTTAGGTAAAAAG
A. lyrata       903 ATCTTGGACACCTATAACTGAGAACCAATTCTGAGATTGACATCCAAA-TAGGTAAAAAG
B. stricta          ------------------------------------------------------------
C. grandiflora      ------------------------------------------------------------
C. rubella          ------------------------------------------------------------
consensus      1081                                                             
A. thaliana    1019 AAAATGCCATTCGAATTGATTCAATTTT-------------
A. lyrata       962 AAAATGCCATTCGAATTGATTCAATGTTAGCTAACTTTAGT
B. stricta          -----------------------------------------
C. grandiflora      -----------------------------------------
C. rubella          -----------------------------------------
consensus      1141                                          

Arabidopsis halleri
>A. halleri 
ATGTCGTTTAGAAAAGTAGAGAAGAAACCAACCGAAATGGGCCGACAGATGACCCACGAGAAGTCGGACTCTGACTCAGACAACGAAGGAACCCCCATGACGGCTGGCG

A. thaliana     1 ATGTCGTTTAGAAAAGTAGAGAAGAAACCAACTGAAATGGGCCGAAACATGACCCACGAG
A. halleri      1 ATGTCGTTTAGAAAAGTAGAGAAGAAACCAACCGAAATGGGCCGACAGATGACCCACGAG
A. lyrata       1 ATGTCGTTTAGAAAAGTAGAGAAGAAACCAACCGAAATGGGCCGTCAAATGACACACGAG
consensus       1 ATGTCGTTTAGAAAAGTAGAGAAGAAACCAACcGAAATGGGCCGacAgATGACcCACGAG

A. thaliana     61 AAGTCGGACTCTGATTCGGACAACGAAGGAGCCCCCATGACTGTTGGAG-
A. halleri      61 AAGTCGGACTCTGACTCAGACAACGAAGGAACCCCCATGACGGCTGGCGG
A. lyrata       61 AAGTCGGACTCTGACTCAGACAACGAAGGAACCCCCATGACGGCTGGCGG
consensus       61 AAGTCGGACTCTGAcTCaGACAACGAAGGAaCCCCCATGACgGcTGGcGg