Supporting Information Legends
Figure S1. Alignment of D1 and d1 CDS sequences.
A one nucleotide deletion (T) is found in the d1 mutant CDS, highlighted with red
box, the deletion results in premature stop codon as indicated by green box.
Figure S2. Gene structure and identification of d2.
(a) Gene structure of D2 and d2. d2 contains a truncated GmD2IN element insertion
that results in a duplication from +990 to +1520. Primers used for identification of d2
are shown under the gene structure. The pink box indicates the third exon and the
green box indicates the fourth exon. The dashed boxes indicate duplicated exons
generated from the GmD2IN insertion.
(b) Polymorphism of D2 fragments in the wild type, d1 and d1d2 mutants. The
fragments are amplified using primer set P1/P2. Because of the GmD2IN insertion,
the fragment cannot be amplified in d2 mutant.
(c) Polymorphism of D2 CDS in the wild type, d1 and d1d2 mutants. The
amplification product in the d2 is longer than the wild type and d1 mutant.
(d) Validation of the GmD2IN insertion in wild type, d1 and d1d2 mutants using
primers P1/P2/P3. In d2, a shorter band is amplified as compared with wild type and
the d1 mutant.
Figure S3. Alignment of D2 and d2 CDS sequences.
The GmD2IN causes duplication in d2 CDS. The duplication shared by D2 and d2 is
pointed out by green box; the duplicated sequences in d2 are indicated by a yellow
box. The duplication results in a premature stop codon in the coding sequence as
indicated by green box within the yellow box.
Figure S4. Expression of D1 and D2 in the wild type, d1, and d1d2 plants.
Transcription of D1 (a) and D2 (b) in leaves from wild type and mutants during
different developmental stages.
The bars indicate stand errors and the values are based on three technical replicates of
five independent plants.
Figure S5. Transcriptional level of D1 and D2 in the transgenic lines.
Transcription of D1 and D2 in different transgenic lines as determined by quantitative
PCR.
The bars indicate stand errors and the values are based on four technical replicates of
single plant.
Figure S6. Chls degradation and programmed cell death related
orthologous/homologous genes in Arabidopsis and soybean.
Figure S7. Transcription of Chl degradation and programmed cell death-related
genes in the wild type, d1, and d1d2 plants.
Chl degradation and programmed cell death related genes are examined in the wild
type and mutant leaves during different developmental stages.
(a) Glyma01g36620, (b) Glyma11g08730, (c) Glyma12g06310, (d) Glyma15g29900,
(e) Glyma07g09430, (f) Glyma09g32370, (g) Glyma11g19800, (h) Glyma12g08740,
(i) Glyma11g16070, (j) Glyma02g47120, (k) Glyma14g01620.
The bars indicate stand errors and the values are based on four technical replicates of
bulked samples.
Figure S8. Analysis of D1 and D2 flanking duplicated regions.
(a) Relationship of D1 and D2 duplicated regions as shown by Circos. The figure
shows the duplicated regions between Gm11 and other chromosomes.
(b) Correlation of D1 and D2 expression in different tissues.
(c) Transcriptional analysis of duplicated genes flanking D1 and D2. The up panel
indicates the transcriptional patterns of duplicated genes flanking D1 from Gm01. The
bottom panel indicates the transcriptional patterns of duplicated genes flanking D2
from Gm11. Each column in the panels indicates individual genes, and each gene in
Gm01 (up) is vs. its duplicated gene in Gm11 (bottom). Each line from up to the
bottom indicates individual samples, and the order of samples same as that of Figure
3a. The values are based on a single RNA-seq data experiment from bulked plants.
Figure S9. GmD2IN element distribution and expression in the soybean genome.
(a) Distribution of GmD2IN. The outermost circle indicates the pericentromeric
region of each chromosome, the second indicates the density of all TEs across the
genome, the third line indicates the distribution of genes (darker green indicates
higher gene density), and the inner circle indicates the distribution of GmD2IN
elements. The red lines indicate intact elements, the green lines indicate Solo elements,
and the blue lines indicate truncated elements.
(b) Transcription of GmD2IN elements in 28 various tissues. Each line from up to the
bottom indicates individual elements. The order of these elements is listed in Table S5.
The values are based on a single RNA-seq experiment from bulked plants.
Table S1. Genotype and sequencing of different accessions at the D1 and D2 loci
Table S2. Primer sequences used in this study
Table S3. Comparisons of senescence related and Chls degradation genes
between Arabidopsis and soybean
Table S4. Identification of GmD2IN (LTR insertion in the D2 gene) in soybean
genome
Table S5. Order of GmD2IN elements in Figure S9b