1 Research Article Genome-wide identification of PPR gene family and prediction analysis on restorer gene in Gossypium NAN ZHAO 1 , YUMEI WANG 1 † , and JINPING HUA ∗ Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education /Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China † Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China 1 These authors contributed equally to this work. Email: Nan Zhao: [email protected]Yumei Wang: [email protected]Jinping Hua: [email protected]∗ For correspondence E-mail: [email protected]Running title PPR gene evolution in Gossypium species. Keywords. Gossypium; PPR gene family; phylogenetic analysis; cytoplasmic male sterility; restorer gene.
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Research Article
Genome-wide identification of PPR gene family and prediction analysis on
restorer gene in Gossypium
NAN ZHAO 1, YUMEI WANG 1 †, and JINPING HUA ∗
Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and
Utilization of Ministry of Education /Beijing Key Laboratory of Crop Genetic Improvement, College of
Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
† Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei,
(dS) and the dN/dS value (Jore et al. 2011). As we observed, most PPR genes were under
purifying selection (figure 3A, Additional file 3: table S3). Interestingly, average dN and dS
values of RFLs (36 D5-RFLs and 19 A2-RFLs) genes were higher than other PPR genes, as
also reported in Fujii et al. (2011). The D5-RFLs evolved faster than other PPR genes, on the
contrary, A2-RFLs had a lower evolutionary rate than other PPR genes (figure 3C, Additional
file 3: table S3). It’s likely that the restorer gene might derived from D sub-genome (Wu et al.
2014), especially for those cotton lines with D genome sterile cytoplasm, such as 2074A
containing G. hirsutum nuclear and G. harknessii sterile cytoplasm in our study, resulting in a
specific nuclear-cytoplasmic interaction combination. Maybe it is a much more complex
question than the difference in polyploid or diploid cotton, because most cotton CMS lines
were created by hybridizing between different species.
In addition, in order to clarify the relationship between the evolution pattern of PPR
genes and biological functions involved in cotton, we conducted GO annotation to A2-D5
homologous PPR genes (Additional file 4: figure S3), and categorized by dN, dS and dN/dS
value. We detected that PPR genes related to localization contain the lowest dN/dS value
(figure 3B, Additional file 3: table S3), which suggested that this kind of PPR genes suffered
evolutionary constraint during the divergence process of G. raimondii (D5) and G. arboreum
(A2). Most PPR genes were targeted in mitochondria and a few in chloroplasts, which
correspond to the organelles-targeting peptide sequence in the N end of most of PPR genes
(Lurin et al. 2004).
Subcellular localization and Subfamily analysis of PPR candidate genes
For the 36 D5-RFLs, 19 A2-RFLs, 15 AD1 PPR genes in cotton and 6 Rf genes in other species,
most of them were targeted in mitochondria, a few in chloroplasts.These results were verified
by subcellular localization from three softwares (TargetP, Predotar and ProtComp). That is,
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72% of PPR genes were in mitochondria, 10% in chloroplasts, and 16% overlapped (figure 4),
as observed that most Rf-PPR genes were targeted to mitochondria (Bentolila et al. 2002;
Komori et al. 2004; Lurin et al. 2004).
PPR gene family was divided into PLS subfamily and P subfamily, while PLS subfamily
was further subdivided into four groups: PLS group, E group, E+ group and DYW group
(Lurin et al. 2004). In our research, we analyzed PPR motif arrangement of 36 D5-RFLs, 19
A2-RFLs, 15 G. hirsutum (AD1) PPR genes in cotton and 6 Rf genes in other species using
HMMER matrix (defined by 7 conservative domains: P, L, L2, S, E, E+ and DYW) of PPR
gene family in Arabidopsis thaliana. 6 Rf -PPR genes belonged to the P subfamily (Bentolila
et al. 2002), 36 D5-RFLs and 19 A2-RFLs genes were also attached to P subfamily. However,
15 G. hirsutum (AD1) PPR genes covered all kinds of PPR gene family groups, in which a
variety of classical PPR domains were lined up in a particular order (Lurin et al. 2004)
(Additional file 5: table S4).
RNA-seq and qRT-PCR analyses of PPR candidate gene expressions
In order to verify whether these PPR candidate genes are associated with fertility restoration
in cotton, we performed expression analysis of 36 D5-RFLs, 19 A2-RFLs, 15 AD1 PPR genes
based on RNA-seq data of young buds in CMS line 2074A, maintainer line 2074B and fertile
material FA (unpublished). Compared with the maintainer line 2074B containing normal
fertile cytoplasm from G. hirsutum, the CMS line 2074A and the fertile material FA have the
same male sterile cytoplasm from G. harknessii. However, when hybridizing with the restorer
line E5903 that has normal fertile nuclear and cytoplasm from G. harknessii, the sterile line
2074A produced the fertile FA due to the recombination of a dominant gene Rf with original
recessive non-functional allele rf. All three cotton lines almost have the isogenic nuclear
genomes comprised of A sub-genome and D sub-genome, i.e. they may have different alleles
and/or differential expression of the same restorer gene. In our study, we found that most of
these PPR candidate genes were highly expressed in FA, while lowly expressed in maintainer
line and sterile line (figure 5). Furthermore, 8 of these PPR candidate genes were up-regulated
in FA than in sterile line, which confirmed that these candidate genes are likely related to
fertility restoration in cotton (table 2). Some restorer genes could reduce the abundance of
CMS-related transcripts at transcriptional or post-transcriptional levels, such as Rf-PPR592 in
CMS-RM petunia (Bentolila et al. 2002). In addition, there are also some restorer genes that
function at the genetic or protein levels, such as Fr in CMS-Sprite bean (Mackenzie and
Chase 1990; Janska et al. 1998) and Rf3 in CMS-WA rice (Luo et al. 2013), thus further
experiments are still needed to reveal the molecular mechanism of fertility restoration.
Furthermore, to validate the RNA-seq expression data by experiments, we then
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carried on qRT-PCR to analyze the differential expression of PPR candidate genes in CMS
lines 2074A and 2074S, their maintainer line 2074B, restorer line E5903 and fertile hybrid
material F1s (FA, 2074A×E5903; FS, 2074S×E5903). Taking cotton housekeeping genes
UBQ7 as internal control, we analyzed the relative expression of 8 PPR candidate genes in
young buds of 6 cottons through real-time fluorescent quantitative PCR technology. As a
result, we found that the expression of two PPR candidate genes, Gorai.005g0470 (D5) and
Cotton_A_08373 (A2), were higher in FA than in sterile line 2074A, while were similar in
expression pattern in 6 cottons (figure 6). At the same time, the up-regulated times of these
two genes in FA than in sterile lines 2074A were 3.45 and 12.59 by RNA-seq, respectively. In
addition, these two PPR genes share high homology, which indicates that their common
ancestor gene appeared before the divergence of D5 and A2 genomes. During the process of
subsequent evolution, they were under purifying selection (Additional file 3: table S3).
Through the phylogenetic analyses, we found that they had a close evolution relationship to
the restorer gene Rf_PPR592 in petunia (Bentolila et al. 2002). In this study, we turned the
progeny of the sterile line 2074A into the fertile FA by the possible Rf gene from D2 nuclear
genome. Therefore, Gorai.005g0470 derived from D5 is more likely to be the candidate Rf
gene of G. harknessii CMS lines 2074A than Cotton_A_08373 in A2. We hope that our results
might provide some helps for studying the restorer genes in cotton.
Conclusion
Totally 482 and 433 PPR genes in two diploid cotton species, G. raimondii (D5) and G.
arboreum (A2) were identified in this study. They were evenly distributed over chromosomes
with few clustered. Phylogenetic analyses produced 36 D5-RFLs and 19 A2-RFLs, thereinto,
D5-RFLs evolved faster than other PPR genes. These RFLs accompanied by 15 AD1-PPR
genes were further brought into a comprehensive phylogenetic analysis, which resulted in 8
cotton PPR candidate genes clustering together with 6 Rf genes in other plant species. 2 of
PPR candidate genes, Gorai.005g0470 (D5) and Cotton_A_08373 (A2) were confirmed to be
up-regulated in fertile lines than in sterile line in cotton by RNA-seq and qRT-PCR analyses.
Our study provided preliminary insights into PPR genes evolution and the RFL genes in
cotton.
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Figure legends
Figure 1. Distribution of PPR genes number over chromosomes in G. raimondii (D5) and G.
arboreum (A2) genomes. The number of PPR genes on 13 chromosomes in G. raimondii (D5)
was denoted in the sign of ”●”, while that in G. arboreum (A2) was marked in the sign
of ”+”. Except for PPR genes on 13 chromosomes, there were also few PPR genes whose
chromosome location had not been identified, namely, “others”.
Figure 2. Comprehensive phylogenetic analyses of PPR genes from G. raimondii, G.
arboreum and G. hirsutum L. by Maximum Likelihood method. According to the species, the
genes were illustrated in different shapes, box: G. raimondii, dot: G. arboreum, diamond: G.
hirsutum, Outgroups are six restorer genes from five different species, Petunia x hybrid,
Oryza sativa ssp. indica, B. napus, R. sativus and A. thaliana. They were marked by triangle
and the corresponding branches are in bold. These genes keeping a close evolution
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relationship with other restorer genes are marked in solid shapes.
Figure 3. Nucleotide substitution rates of homologous PPR genes in G. raimondii (D5) and G.
arboreum (A2) genomes. (a) Density distribution of dN/dS values of PPR homologous genes
between G. raimondii (D5) and G. arboreum (A2) genomes. (b) Average nucleotide
substitution rates of RFLs and other PPR genes in G. raimondii (D5) and G. arboreum (A2)
genomes. (c) Box plot for the distribution of dN/dS values of D5-A2 PPR homologies on
secondary level GO terms.
Figure 4. Sub-cellular localization of PPR genes in G. raimondii (D5), G. arboreum (A2) and
G. hirsutum (AD1) genomes. TP, PD and PC represented three softwares, TargetP, Predotar
and ProtComp, separately. The dark blue denoted mitochondria, the light blue chloroplasts,
the white unsure.
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Figure 5. Expression analysis of PPR candidate genes in G. raimondii (D5), G. arboreum (A2)
and G. hirsutum (AD1) genomes. Based on RNA-seq data of sterile line 2074A, maintainer
line 2074B and fertile material AE1 (F1 [2074A × E5903]), the expression of PPR candidate
genes was calculated by the method of RPKM. The gene expression was denoted by different
colors, green represented relatively down-regulated, and red meant relatively up-regulated.
Two PPR candidate genes in G. arboreum (A2) genome and four PPR candidate genes in G.
raimondii (D5) genome were marked by red arrows on the right and were relatively
up-regulated in AE1 [PPR-21 (Gorai.010G053600.1) and PPR-22 (Gorai.010G053600.2)
were two different transcripts of the same gene (Gorai.010G0536), so there were seven red
arrows]). Two green arrows marked down-regulated genes in AE1.
Figure 6. Relative expression analysis of 8 PPR candidate gene s in buds of 6 different
fertility cotton species. The expression in bud of 2074A was considered as the control, and
UBQ7 was used as reference gene, and the control. The value is calculated with the method of
2-ΔΔCt.
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Additional files
Additional file 1: Figure S1. Single-chromosome phylogenetic analyses of PPR genes in G.
raimondii (D5) genome and G. arboreum (A2) genome by Maximum Likelihood method.
Figure S2. Phylogenetic analysis on PPR genes on chromosome D05 in G. hirsutum (AD1)
genome. Box: G. raimondii; dot: G. arboretum; triangle: outgroups (Petunia x hybrid, Oryza
sativa ssp. indica, B. napus, R. sativus and A. thaliana); solid: candidate PPR genes.
Additional file 2: Table S1. Information of PPR candidate genes derived from 13
chromosomes of G. raimondii (D5) genome. Table S2. Information of PPR candidate genes
derived from 13 chromosomes of G. arboreum (A2) genome.
Table S1 Information of PPR candidate genes derived from 13 chromosomes of G. raimondii (D5) genome
Chromosome No. of gene Gene No. of sequence Sequence
chr01 1 Gorai.001G1316 1 Gorai.001G131600.1
chr02 2 Gorai.002G0718 3 Gorai.002G071800.1,
Gorai.002G071800.2
Gorai.002G1010 Gorai.002G101000.1
chr03 1 Gorai.003G1716 1 Gorai.003G171600.1
chr04 3 Gorai.004G2907 3 Gorai.004G290700.1
Gorai.004G2406 Gorai.004G240600.1
Gorai.004G2438 Gorai.004G243800.1
chr05 1 Gorai.005G0470 1 Gorai.005G047000.1
chr06 2 Gorai.006G2252 2 Gorai.006G225200.1
16
Gorai.006G2471 Gorai.006G247100.1
chr07 1 Gorai.007G1431 1 Gorai.007G143100.1
chr08 1 Gorai.008G0443 1 Gorai.008G044300.1
chr09 4 Gorai.009G3762 4 Gorai.009G376200.1
Gorai.009G2580 Gorai.009G258000.1
Gorai.009G0058 Gorai.009G005800.1
Gorai.009G1519 Gorai.009G151900.1
chr10 4 Gorai.010G2281 9 Gorai.010G228100.1,
Gorai.010G228100.2
Gorai.010G0536
Gorai.010G053600.1,
Gorai.010G053600.2
Gorai.010G0325
Gorai.010G032500.1,
Gorai.010G032500.2,
Gorai.010G032500.3
Gorai.010G0722
Gorai.010G072200.1,
Gorai.010G072200.2
chr11 10 Gorai.011G1557 11 Gorai.011G155700.1
Gorai.011G1515 Gorai.011G151500.1
Gorai.011G1514 Gorai.011G151400.1
Gorai.011G1511 Gorai.011G151100.1
Gorai.011G1512 Gorai.011G151200.1
Gorai.011G1451 Gorai.011G145100.1
Gorai.011G1464
Gorai.011G146400.1,
Gorai.011G146400.2
Gorai.011G1466 Gorai.011G146600.1
Gorai.011G1450 Gorai.011G145000.1
Gorai.011G1465 Gorai.011G146500.1
chr12 4 Gorai.012G1593 9 Gorai.012G159300.1,
Gorai.012G159300.2,
Gorai.012G159300.3
Gorai.012G1205
Gorai.012G120500.1,
Gorai.012G120500.2
Gorai.012G0303
Gorai.012G030300.1,
Gorai.012G030300.2
Gorai.012G1494
Gorai.012G149400.1,
Gorai.012G149400.2
chr13 2 Gorai.013G0606 4 Gorai.013G060600.1,
Gorai.013G060600.2
Gorai.013G0109
Gorai.013G010900.1,
Gorai.013G010900.2
Total No. 36 50
Table S2 Information of PPR candidate genes derived from 13 chromosomes of G. arboreum (A2) genome
Chromosome No. of gene Gene No. of sequence Sequence
chr01 1 Cotton_A_32157 1 Cotton_A_32157
chr02 3
Cotton_A_37656
3
Cotton_A_37656
Cotton_A_28832 Cotton_A_28832
Cotton_A_00514 Cotton_A_00514
chr03 2 Cotton_A_16847
2 Cotton_A_16847
Cotton_A_18522 Cotton_A_18522
chr04 2 Cotton_A_26557 2 Cotton_A_26557
17
Cotton_A_03817 Cotton_A_03817
chr05 1 Cotton_A_08373 1 Cotton_A_08373
chr06 1 Cotton_A_27681 1 Cotton_A_27681
chr07 1 Cotton_A_06850 1 Cotton_A_06850
chr08 0 -- 0 --
chr09 1 Cotton_A_02931 1 Cotton_A_02931
chr10 2 Cotton_A_04606
2 Cotton_A_04606
Cotton_A_29300 Cotton_A_29300
chr11 3
Cotton_A_13069
3
Cotton_A_13069
Cotton_A_17619 Cotton_A_17619
Cotton_A_14743 Cotton_A_14743
chr12 0 -- 0 --
chr13 1 Cotton_A_26837 1 Cotton_A_26837
others 1 Cotton_A_37173 1 Cotton_A_37173
Total No. 19 19
Additional file 3: Table S3. Nucleotide substitution rates of PPR homologous genes between
G. raimondii (D5) and G. arboreum (A2) genomes.
Table S3. Nucleotide substitution rates of PPR homologous genes between G. raimondii (D5) and G. arboreum (A2)
genomes
Numbe
r gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
1c 2 (Cotton_A_11317) vs. 1 (Gorai.009G1666) 0.017 0.009 1.980c
2 2 (Cotton_A_28224) vs. 1 (Gorai.013G0655) 0.016 0.014 1.140
3 2 (Cotton_A_09575) vs. 1 (Gorai.001G1210) 0.014 0.014 1.051
4 2 (Cotton_A_34843) vs. 1 (Gorai.012G1341) 0.015 0.014 1.042
5 2 (Cotton_A_31264) vs. 1 (Gorai.004G1601) 0.042 0.042 1.015
6 2 (Cotton_A_11768) vs. 1 (Gorai.012G1877) 0.022 0.022 1.013
7b 2 (Cotton_A_06304) vs. 1 (Gorai.002G0718) 0.014 0.014 0.999
8b 2 (Cotton_A_19072) vs. 1 (Gorai.012G0303) 0.035 0.037 0.957
9 2 (Cotton_A_01860) vs. 1 (Gorai.006G1315) 0.023 0.025 0.939
10 2 (Cotton_A_32325) vs. 1 (Gorai.001G2487) 0.019 0.021 0.935
11 2 (Cotton_A_27929) vs. 1 (Gorai.013G1240) 0.018 0.020 0.928
12 2 (Cotton_A_18719) vs. 1 (Gorai.001G2147) 0.046 0.050 0.917
18
13b 2 (Cotton_A_23084) vs. 1 (Gorai.011G1451) 0.015 0.018 0.851
14 2 (Cotton_A_02450) vs. 1 (Gorai.006G1772) 0.015 0.017 0.848
15 2 (Cotton_A_39828) vs. 1 (Gorai.001G2016) 0.016 0.019 0.832
16 2 (Cotton_A_20263) vs. 1 (Gorai.012G0213) 0.062 0.075 0.831
17 2 (Cotton_A_17523) vs. 1 (Gorai.011G0381) 0.013 0.015 0.825
18 2 (Cotton_A_35996) vs. 1 (Gorai.004G0976) 0.046 0.058 0.802
19 2 (Cotton_A_10814) vs. 1 (Gorai.008G0282) 0.120 0.152 0.792
20 2 (Cotton_A_11187) vs. 1 (Gorai.003G0412) 0.025 0.032 0.769
21 2 (Cotton_A_27680) vs. 1 (Gorai.008G1927) 0.018 0.024 0.763
22b 2 (Cotton_A_24724) vs. 1 (Gorai.006G2471) 0.027 0.036 0.748
23 2 (Cotton_A_24061) vs. 1 (Gorai.006G1651) 0.016 0.021 0.747
24 2 (Cotton_A_22811) vs. 1 (Gorai.005G1522) 0.019 0.026 0.745
25 2 (Cotton_A_40801) vs. 1 (Gorai.010G1366) 0.021 0.029 0.725
26 2 (Cotton_A_05635) vs. 1 (Gorai.001G0212) 0.018 0.025 0.718
27b 2 (Cotton_A_30591) vs. 1 (Gorai.003G1716) 0.032 0.046 0.710
28 2 (Cotton_A_03316) vs. 1 (Gorai.004G0658) 0.023 0.032 0.708
29 2 (Cotton_A_01798) vs. 1 (Gorai.006G1265) 0.013 0.019 0.699
30 2 (Cotton_A_26211) vs. 1 (Gorai.003G0971) 0.073 0.105 0.691
31 2 (Cotton_A_26989) vs. 1 (Gorai.004G0714) 0.012 0.017 0.684
32 2 (Cotton_A_33958) vs. 1 (Gorai.003G0875) 0.011 0.017 0.683
33 2 (Cotton_A_32710) vs. 1 (Gorai.008G2494) 0.015 0.022 0.674
34a 2 (Cotton_A_04606) vs. 1 (Gorai.009G1866) 0.016 0.023 0.672
35 2 (Cotton_A_22116) vs. 1 (Gorai.002G2139) 0.021 0.032 0.667
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
36 2 (Cotton_A_17776) vs. 1 (Gorai.008G2735) 0.019 0.029 0.666
37 2 (Cotton_A_17484) vs. 1 (Gorai.011G0686) 0.015 0.023 0.663
38 2 (Cotton_A_36527) vs. 1 (Gorai.013G1385) 0.019 0.029 0.660
39 2 (Cotton_A_02090) vs. 1 (Gorai.008G0415) 0.021 0.031 0.659
40 2 (Cotton_A_13788) vs. 1 (Gorai.010G1922) 0.014 0.021 0.656
41 2 (Cotton_A_10685) vs. 1 (Gorai.007G3051) 0.013 0.020 0.630
42 2 (Cotton_A_37988) vs. 1 (Gorai.001G2469) 0.014 0.022 0.629
43 2 (Cotton_A_33828) vs. 1 (Gorai.013G0985) 0.014 0.022 0.625
44 2 (Cotton_A_22551) vs. 1 (Gorai.004G0846) 0.015 0.024 0.614
45 2 (Cotton_A_06956) vs. 1 (Gorai.009G0970) 0.052 0.085 0.613
46 2 (Cotton_A_34686) vs. 1 (Gorai.001G1887) 0.016 0.026 0.611
47 2 (Cotton_A_23085) vs. 1 (Gorai.011G1450) 0.064 0.105 0.607
19
48 2 (Cotton_A_06080) vs. 1 (Gorai.012G0077) 0.077 0.127 0.607
49 2 (Cotton_A_23145) vs. 1 (Gorai.013G1741) 0.021 0.034 0.601
50 2 (Cotton_A_32339) vs. 1 (Gorai.007G0962) 0.016 0.027 0.598
51ab 2 (Cotton_A_26557) vs. 1 (Gorai.007G1431) 0.064 0.107 0.597
52 2 (Cotton_A_20633) vs. 1 (Gorai.007G0758) 0.032 0.055 0.590
53 2 (Cotton_A_18215) vs. 1 (Gorai.005G1471) 0.014 0.024 0.588
54 2 (Cotton_A_07425) vs. 1 (Gorai.009G4553) 0.017 0.029 0.588
55 2 (Cotton_A_16281) vs. 1 (Gorai.010G0532) 0.014 0.023 0.586
56 2 (Cotton_A_36956) vs. 1 (Gorai.012G0712) 0.012 0.021 0.585
57 2 (Cotton_A_16549) vs. 1 (Gorai.006G0786) 0.019 0.033 0.582
58 2 (Cotton_A_28680) vs. 1 (Gorai.002G1322) 0.016 0.027 0.579
59 2 (Cotton_A_30727) vs. 1 (Gorai.011G1778) 0.018 0.031 0.578
60 2 (Cotton_A_26765) vs. 1 (Gorai.001G1106) 0.011 0.020 0.575
61 2 (Cotton_A_24224) vs. 1 (Gorai.013G1917) 0.017 0.030 0.574
62 2 (Cotton_A_28020) vs. 1 (Gorai.001G0406) 0.015 0.025 0.572
63 2 (Cotton_A_04063) vs. 1 (Gorai.009G2942) 0.016 0.029 0.567
64 2 (Cotton_A_07524) vs. 1 (Gorai.011G0889) 0.012 0.021 0.565
65 2 (Cotton_A_10449) vs. 1 (Gorai.011G2299) 0.082 0.148 0.555
66 2 (Cotton_A_36721) vs. 1 (Gorai.002G0574) 0.079 0.144 0.553
67 2 (Cotton_A_30330) vs. 1 (Gorai.010G2078) 0.015 0.028 0.553
68 2 (Cotton_A_06176) vs. 1 (Gorai.008G1784) 0.012 0.022 0.551
69 2 (Cotton_A_20922) vs. 1 (Gorai.008G1195) 0.015 0.027 0.549
70 2 (Cotton_A_01973) vs. 1 (Gorai.007G0468) 0.015 0.028 0.549
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
71 2 (Cotton_A_33269) vs. 1 (Gorai.003G1164) 0.024 0.043 0.549
72 2 (Cotton_A_24707) vs. 1 (Gorai.011G2260) 0.016 0.029 0.543
73 2 (Cotton_A_07464) vs. 1 (Gorai.009G4512) 0.015 0.028 0.542
74 2 (Cotton_A_13263) vs. 1 (Gorai.001G1344) 0.015 0.028 0.539
75 2 (Cotton_A_25685) vs. 1 (Gorai.005G1720) 0.016 0.029 0.538
76 2 (Cotton_A_09296) vs. 1 (Gorai.007G2760) 0.020 0.038 0.536
77 2 (Cotton_A_40007) vs. 1 (Gorai.013G0825) 0.013 0.024 0.533
78 2 (Cotton_A_20041) vs. 1 (Gorai.013G2630) 0.019 0.036 0.532
79 2 (Cotton_A_13147) vs. 1 (Gorai.004G1887) 0.019 0.035 0.528
80 2 (Cotton_A_29248) vs. 1 (Gorai.010G2243) 0.015 0.029 0.526
81 2 (Cotton_A_34976) vs. 1 (Gorai.011G1657) 0.027 0.051 0.523
82 2 (Cotton_A_35366) vs. 1 (Gorai.002G1719) 0.016 0.030 0.521
20
83 2 (Cotton_A_14076) vs. 1 (Gorai.001G1484) 0.016 0.031 0.521
84 2 (Cotton_A_33069) vs. 1 (Gorai.006G0742) 0.066 0.127 0.520
85 2 (Cotton_A_13386) vs. 1 (Gorai.008G1951) 0.026 0.050 0.516
86 2 (Cotton_A_37189) vs. 1 (Gorai.005G1479) 0.017 0.032 0.515
87 2 (Cotton_A_25515) vs. 1 (Gorai.010G1802) 0.016 0.032 0.511
88 2 (Cotton_A_16155) vs. 1 (Gorai.011G0974) 0.012 0.023 0.511
89 2 (Cotton_A_15955) vs. 1 (Gorai.008G1022) 0.016 0.031 0.509
90ab 2 (Cotton_A_18522) vs. 1 (Gorai.013G0606) 0.075 0.148 0.509
91 2 (Cotton_A_27424) vs. 1 (Gorai.009G1101) 0.014 0.027 0.508
92 2 (Cotton_A_22374) vs. 1 (Gorai.013G1986) 0.012 0.023 0.506
93 2 (Cotton_A_04268) vs. 1 (Gorai.003G1421) 0.025 0.049 0.505
94 2 (Cotton_A_00752) vs. 1 (Gorai.005G2425) 0.019 0.038 0.503
95 2 (Cotton_A_40015) vs. 1 (Gorai.010G1439) 0.012 0.023 0.501
96 2 (Cotton_A_03759) vs. 1 (Gorai.007G1608) 0.010 0.020 0.501
97a 2 (Cotton_A_14743) vs. 1 (Gorai.006G0084) 0.018 0.037 0.498
98 2 (Cotton_A_23993) vs. 1 (Gorai.004G0731) 0.015 0.030 0.498
99 2 (Cotton_A_09794) vs. 1 (Gorai.003G0326) 0.016 0.032 0.491
100 2 (Cotton_A_21717) vs. 1 (Gorai.005G2322) 0.010 0.021 0.490
101 2 (Cotton_A_41153) vs. 1 (Gorai.013G1059) 0.017 0.035 0.490
102 2 (Cotton_A_09162) vs. 1 (Gorai.007G0312) 0.016 0.033 0.489
103 2 (Cotton_A_25415) vs. 1 (Gorai.009G4142) 0.016 0.032 0.488
104b 2 (Cotton_A_06370) vs. 1 (Gorai.012G1494) 0.012 0.024 0.486
105 2 (Cotton_A_37545) vs. 1 (Gorai.003G1355) 0.013 0.027 0.485
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
106 2 (Cotton_A_25609) vs. 1 (Gorai.005G1943) 0.024 0.049 0.483
107 2 (Cotton_A_01539) vs. 1 (Gorai.003G0072) 0.014 0.029 0.480
108 2 (Cotton_A_04493) vs. 1 (Gorai.008G1563) 0.014 0.030 0.479
109 2 (Cotton_A_33520) vs. 1 (Gorai.009G3754) 0.029 0.060 0.478
110 2 (Cotton_A_01088) vs. 1 (Gorai.009G0711) 0.019 0.039 0.477
111 2 (Cotton_A_08027) vs. 1 (Gorai.008G2080) 0.016 0.035 0.476
112 2 (Cotton_A_20227) vs. 1 (Gorai.008G1687) 0.011 0.023 0.476
113 2 (Cotton_A_07222) vs. 1 (Gorai.001G0292) 0.059 0.125 0.473
114 2 (Cotton_A_32576) vs. 1 (Gorai.008G0862) 0.016 0.033 0.472
115 2 (Cotton_A_13722) vs. 1 (Gorai.009G2054) 0.022 0.047 0.471
116 2 (Cotton_A_23893) vs. 1 (Gorai.003G1142) 0.038 0.080 0.471
117 2 (Cotton_A_12931) vs. 1 (Gorai.009G0926) 0.012 0.025 0.470
21
118 2 (Cotton_A_28094) vs. 1 (Gorai.005G1628) 0.017 0.035 0.469
119 2 (Cotton_A_39104) vs. 1 (Gorai.009G4026) 0.014 0.030 0.468
120 2 (Cotton_A_01590) vs. 1 (Gorai.003G0127) 0.047 0.101 0.468
121 2 (Cotton_A_14708) vs. 1 (Gorai.006G0114) 0.020 0.043 0.466
122 2 (Cotton_A_29057) vs. 1 (Gorai.012G0843) 0.013 0.028 0.465
123 2 (Cotton_A_00282) vs. 1 (Gorai.002G2674) 0.015 0.033 0.458
124 2 (Cotton_A_24369) vs. 1 (Gorai.007G2126) 0.013 0.028 0.455
125 2 (Cotton_A_36268) vs. 1 (Gorai.006G0702) 0.017 0.038 0.453
126 2 (Cotton_A_32770) vs. 1 (Gorai.007G1442) 0.011 0.023 0.452
127 2 (Cotton_A_28557) vs. 1 (Gorai.002G1203) 0.012 0.026 0.452
128 2 (Cotton_A_19260) vs. 1 (Gorai.008G2669) 0.014 0.032 0.451
129 2 (Cotton_A_26614) vs. 1 (Gorai.004G0254) 0.014 0.031 0.447
130 2 (Cotton_A_37026) vs. 1 (Gorai.008G0731) 0.045 0.100 0.445
131b 2 (Cotton_A_30160) vs. 1 (Gorai.011G1557) 0.078 0.175 0.444
132 2 (Cotton_A_28368) vs. 1 (Gorai.007G2806) 0.013 0.029 0.443
133 2 (Cotton_A_12602) vs. 1 (Gorai.004G0487) 0.018 0.041 0.441
134 2 (Cotton_A_17392) vs. 1 (Gorai.008G2642) 0.016 0.037 0.439
135 2 (Cotton_A_29863) vs. 1 (Gorai.012G0397) 0.011 0.024 0.438
136b 2 (Cotton_A_13296) vs. 1 (Gorai.001G1316) 0.135 0.311 0.433
137 2 (Cotton_A_26223) vs. 1 (Gorai.003G0959) 0.014 0.033 0.433
138 2 (Cotton_A_13509) vs. 1 (Gorai.010G1420) 0.013 0.031 0.426
139b 2 (Cotton_A_16278) vs. 1 (Gorai.010G0536) 0.018 0.041 0.426
140 2 (Cotton_A_10671) vs. 1 (Gorai.007G3063) 0.038 0.090 0.425
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
141 2 (Cotton_A_13298) vs. 1 (Gorai.001G1314) 0.010 0.024 0.423
142 2 (Cotton_A_38722) vs. 1 (Gorai.011G1213) 0.011 0.027 0.423
143 2 (Cotton_A_25573) vs. 1 (Gorai.009G1720) 0.017 0.040 0.422
144 2 (Cotton_A_21594) vs. 1 (Gorai.006G1964) 0.012 0.028 0.421
145 2 (Cotton_A_04706) vs. 1 (Gorai.009G1765) 0.014 0.032 0.420
146 2 (Cotton_A_17973) vs. 1 (Gorai.005G2043) 0.009 0.021 0.420
147b 2 (Cotton_A_34636) vs. 1 (Gorai.010G0722) 0.011 0.026 0.419
148 2 (Cotton_A_19585) vs. 1 (Gorai.005G0851) 0.016 0.038 0.419
149 2 (Cotton_A_28977) vs. 1 (Gorai.006G0322) 0.016 0.040 0.415
150 2 (Cotton_A_27278) vs. 1 (Gorai.010G2089) 0.020 0.049 0.415
151 2 (Cotton_A_16896) vs. 1 (Gorai.009G0068) 0.021 0.049 0.415
152 2 (Cotton_A_28444) vs. 1 (Gorai.005G1433) 0.013 0.033 0.413
22
153 2 (Cotton_A_03342) vs. 1 (Gorai.013G1342) 0.014 0.034 0.413
154 2 (Cotton_A_00872) vs. 1 (Gorai.013G0288) 0.012 0.028 0.413
155 2 (Cotton_A_10869) vs. 1 (Gorai.007G0604) 0.016 0.040 0.413
156 2 (Cotton_A_16777) vs. 1 (Gorai.013G1692) 0.023 0.056 0.411
157 2 (Cotton_A_35842) vs. 1 (Gorai.005G0550) 0.017 0.041 0.405
158 2 (Cotton_A_10841) vs. 1 (Gorai.009G0215) 0.011 0.028 0.405
159 2 (Cotton_A_26278) vs. 1 (Gorai.006G1122) 0.008 0.019 0.404
160 2 (Cotton_A_01069) vs. 1 (Gorai.009G0728) 0.011 0.028 0.403
161 2 (Cotton_A_09130) vs. 1 (Gorai.007G0282) 0.014 0.036 0.402
162 2 (Cotton_A_12265) vs. 1 (Gorai.007G1696) 0.017 0.043 0.401
163 2 (Cotton_A_18227) vs. 1 (Gorai.010G0016) 0.010 0.025 0.401
164 2 (Cotton_A_18697) vs. 1 (Gorai.001G2161) 0.017 0.043 0.400
165 2 (Cotton_A_11292) vs. 1 (Gorai.009G1643) 0.026 0.065 0.399
166 2 (Cotton_A_02403) vs. 1 (Gorai.007G0141) 0.010 0.025 0.399
167 2 (Cotton_A_30825) vs. 1 (Gorai.012G0828) 0.010 0.026 0.398
168 2 (Cotton_A_34712) vs. 1 (Gorai.009G3026) 0.016 0.040 0.397
169 2 (Cotton_A_16289) vs. 1 (Gorai.010G0526) 0.025 0.063 0.397
170a 2 (Cotton_A_37656) vs. 1 (Gorai.003G0508) 0.010 0.025 0.396
171a 2 (Cotton_A_03817) vs. 1 (Gorai.007G1554) 0.009 0.022 0.395
172 2 (Cotton_A_13567) vs. 1 (Gorai.008G2191) 0.019 0.049 0.392
173 2 (Cotton_A_36306) vs. 1 (Gorai.006G0750) 0.034 0.087 0.391
174 2 (Cotton_A_15492) vs. 1 (Gorai.007G0816) 0.017 0.043 0.390
175 2 (Cotton_A_26419) vs. 1 (Gorai.008G1310) 0.017 0.044 0.389
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
176 2 (Cotton_A_41044) vs. 1 (Gorai.005G1192) 0.014 0.035 0.388
177 2 (Cotton_A_32294) vs. 1 (Gorai.001G1527) 0.009 0.022 0.387
178 2 (Cotton_A_31588) vs. 1 (Gorai.012G1018) 0.008 0.021 0.386
179 2 (Cotton_A_27659) vs. 1 (Gorai.013G0860) 0.044 0.115 0.386
180 2 (Cotton_A_15598) vs. 1 (Gorai.010G2189) 0.014 0.036 0.383
181b 2 (Cotton_A_30368) vs. 1 (Gorai.009G2580) 0.010 0.026 0.380
182b 2 (Cotton_A_24432) vs. 1 (Gorai.011G1512) 0.017 0.046 0.378
183 2 (Cotton_A_05741) vs. 1 (Gorai.004G2583) 0.009 0.025 0.378
184 2 (Cotton_A_30003) vs. 1 (Gorai.001G1384) 0.013 0.034 0.377
185 2 (Cotton_A_04299) vs. 1 (Gorai.005G0022) 0.009 0.024 0.376
186 2 (Cotton_A_02560) vs. 1 (Gorai.013G2504) 0.016 0.043 0.372
187 2 (Cotton_A_35950) vs. 1 (Gorai.002G2403) 0.019 0.052 0.371
23
188ab 2 (Cotton_A_08373) vs. 1 (Gorai.005G0470) 0.013 0.035 0.370
189 2 (Cotton_A_26200) vs. 1 (Gorai.003G0982) 0.015 0.042 0.370
190 2 (Cotton_A_17963) vs. 1 (Gorai.005G2054) 0.007 0.018 0.370
191 2 (Cotton_A_17735) vs. 1 (Gorai.008G2697) 0.017 0.047 0.369
192b 2 (Cotton_A_02057) vs. 1 (Gorai.008G0443) 0.018 0.048 0.368
193 2 (Cotton_A_30072) vs. 1 (Gorai.006G0901) 0.013 0.034 0.364
194 2 (Cotton_A_31804) vs. 1 (Gorai.004G1641) 0.018 0.051 0.363
195 2 (Cotton_A_26302) vs. 1 (Gorai.004G1943) 0.009 0.024 0.362
196 2 (Cotton_A_39558) vs. 1 (Gorai.009G0359) 0.010 0.027 0.362
197 2 (Cotton_A_40005) vs. 1 (Gorai.001G1983) 0.011 0.031 0.361
198 2 (Cotton_A_10110) vs. 1 (Gorai.011G2952) 0.021 0.058 0.360
199 2 (Cotton_A_38063) vs. 1 (Gorai.006G0458) 0.011 0.031 0.359
200 2 (Cotton_A_34312) vs. 1 (Gorai.001G1555) 0.054 0.150 0.357
201 2 (Cotton_A_31539) vs. 1 (Gorai.012G0855) 0.016 0.045 0.355
202 2 (Cotton_A_35528) vs. 1 (Gorai.009G0027) 0.012 0.034 0.355
203 2 (Cotton_A_35532) vs. 1 (Gorai.009G0032) 0.009 0.026 0.354
204 2 (Cotton_A_20411) vs. 1 (Gorai.009G3837) 0.010 0.028 0.353
205 2 (Cotton_A_23909) vs. 1 (Gorai.005G0195) 0.103 0.296 0.349
206 2 (Cotton_A_38340) vs. 1 (Gorai.010G1312) 0.016 0.047 0.348
207 2 (Cotton_A_07872) vs. 1 (Gorai.008G2292) 0.017 0.049 0.347
208 2 (Cotton_A_19584) vs. 1 (Gorai.005G0852) 0.012 0.036 0.346
209 2 (Cotton_A_23809) vs. 1 (Gorai.005G1813) 0.012 0.035 0.346
210 2 (Cotton_A_00454) vs. 1 (Gorai.002G2491) 0.014 0.041 0.343
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
211 2 (Cotton_A_10325) vs. 1 (Gorai.001G0085) 0.008 0.023 0.342
212 2 (Cotton_A_34264) vs. 1 (Gorai.004G1072) 0.011 0.033 0.341
213 2 (Cotton_A_37646) vs. 1 (Gorai.008G0725) 0.011 0.031 0.340
214 2 (Cotton_A_00653) vs. 1 (Gorai.005G2529) 0.016 0.048 0.340
215 2 (Cotton_A_24627) vs. 1 (Gorai.011G1119) 0.017 0.050 0.340
216 2 (Cotton_A_16144) vs. 1 (Gorai.009G2412) 0.010 0.029 0.339
217a 2 (Cotton_A_02931) vs. 1 (Gorai.011G0480) 0.013 0.039 0.337
218 2 (Cotton_A_35522) vs. 1 (Gorai.009G1913) 0.006 0.018 0.336
219 2 (Cotton_A_25881) vs. 1 (Gorai.008G1273) 0.013 0.038 0.336
220 2 (Cotton_A_10533) vs. 1 (Gorai.013G2656) 0.018 0.054 0.334
221 2 (Cotton_A_09637) vs. 1 (Gorai.006G2666) 0.012 0.035 0.333
222 2 (Cotton_A_01123) vs. 1 (Gorai.009G0676) 0.011 0.034 0.333
24
223 2 (Cotton_A_24301) vs. 1 (Gorai.004G2353) 0.013 0.039 0.330
224 2 (Cotton_A_05860) vs. 1 (Gorai.001G2321) 0.023 0.071 0.329
225 2 (Cotton_A_26945) vs. 1 (Gorai.009G3291) 0.009 0.027 0.329
226 2 (Cotton_A_12830) vs. 1 (Gorai.013G1878) 0.012 0.037 0.328
227 2 (Cotton_A_15541) vs. 1 (Gorai.013G1581) 0.014 0.042 0.328
228 2 (Cotton_A_06044) vs. 1 (Gorai.012G0114) 0.010 0.031 0.328
229 2 (Cotton_A_07988) vs. 1 (Gorai.008G2109) 0.015 0.045 0.327
230 2 (Cotton_A_17092) vs. 1 (Gorai.009G1232) 0.012 0.037 0.327
231 2 (Cotton_A_31527) vs. 1 (Gorai.012G0866) 0.010 0.032 0.325
232 2 (Cotton_A_15473) vs. 1 (Gorai.007G0798) 0.009 0.028 0.321
233 2 (Cotton_A_09139) vs. 1 (Gorai.007G0293) 0.036 0.112 0.320
234 2 (Cotton_A_32227) vs. 1 (Gorai.010G2146) 0.010 0.031 0.320
235 2 (Cotton_A_09931) vs. 1 (Gorai.004G2035) 0.013 0.042 0.318
236 2 (Cotton_A_23072) vs. 1 (Gorai.011G1462) 0.010 0.030 0.317
237 2 (Cotton_A_32556) vs. 1 (Gorai.006G2453) 0.013 0.042 0.317
238 2 (Cotton_A_27318) vs. 1 (Gorai.013G2436) 0.013 0.041 0.316
239 2 (Cotton_A_33638) vs. 1 (Gorai.010G1884) 0.009 0.029 0.315
240 2 (Cotton_A_21338) vs. 1 (Gorai.008G0551) 0.008 0.025 0.314
241 2 (Cotton_A_25940) vs. 1 (Gorai.006G0534) 0.011 0.036 0.312
242 2 (Cotton_A_21752) vs. 1 (Gorai.002G2007) 0.010 0.033 0.307
243 2 (Cotton_A_01226) vs. 1 (Gorai.009G0573) 0.011 0.036 0.306
244 2 (Cotton_A_30013) vs. 1 (Gorai.001G1393) 0.017 0.057 0.304
245 2 (Cotton_A_28264) vs. 1 (Gorai.012G1386) 0.011 0.037 0.303
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
246 2 (Cotton_A_09578) vs. 1 (Gorai.001G1213) 0.010 0.032 0.302
247 2 (Cotton_A_18311) vs. 1 (Gorai.012G0512) 0.008 0.025 0.302
248 2 (Cotton_A_32575) vs. 1 (Gorai.008G0863) 0.010 0.034 0.301
249 2 (Cotton_A_17786) vs. 1 (Gorai.002G0314) 0.018 0.059 0.300
250 2 (Cotton_A_27064) vs. 1 (Gorai.006G0233) 0.016 0.054 0.300
251 2 (Cotton_A_01162) vs. 1 (Gorai.009G0634) 0.007 0.022 0.299
252b 2 (Cotton_A_03417) vs. 1 (Gorai.012G1205) 0.010 0.032 0.297
253 2 (Cotton_A_08971) vs. 1 (Gorai.005G2117) 0.011 0.036 0.295
254 2 (Cotton_A_13392) vs. 1 (Gorai.008G1947) 0.011 0.037 0.289
255 2 (Cotton_A_18561) vs. 1 (Gorai.003G1318) 0.015 0.051 0.287
256 2 (Cotton_A_18120) vs. 1 (Gorai.007G2674) 0.009 0.031 0.286
257 2 (Cotton_A_04319) vs. 1 (Gorai.005G0042) 0.018 0.064 0.284
25
258 2 (Cotton_A_14721) vs. 1 (Gorai.006G0103) 0.013 0.044 0.284
259 2 (Cotton_A_30439) vs. 1 (Gorai.013G1427) 0.009 0.033 0.281
260 2 (Cotton_A_14702) vs. 1 (Gorai.006G0119) 0.009 0.031 0.280
261 2 (Cotton_A_13590) vs. 1 (Gorai.008G2169) 0.018 0.067 0.277
262 2 (Cotton_A_22790) vs. 1 (Gorai.009G3664) 0.019 0.071 0.274
263 2 (Cotton_A_38720) vs. 1 (Gorai.008G0933) 0.011 0.039 0.273
264 2 (Cotton_A_27473) vs. 1 (Gorai.004G0668) 0.023 0.085 0.273
265 2 (Cotton_A_36351) vs. 1 (Gorai.007G2493) 0.012 0.043 0.273
266b 2 (Cotton_A_23070) vs. 1 (Gorai.011G1464) 0.008 0.028 0.273
267 2 (Cotton_A_10904) vs. 1 (Gorai.013G1892) 0.007 0.027 0.269
268 2 (Cotton_A_22715) vs. 1 (Gorai.001G2759) 0.013 0.047 0.269
269 2 (Cotton_A_19225) vs. 1 (Gorai.001G0393) 0.010 0.038 0.268
270 2 (Cotton_A_37812) vs. 1 (Gorai.005G1369) 0.011 0.040 0.266
271b 2 (Cotton_A_23068) vs. 1 (Gorai.011G1466) 0.011 0.042 0.266
272 2 (Cotton_A_14943) vs. 1 (Gorai.012G1311) 0.014 0.052 0.266
273 2 (Cotton_A_34606) vs. 1 (Gorai.005G0815) 0.013 0.050 0.264
274 2 (Cotton_A_37555) vs. 1 (Gorai.007G3444) 0.016 0.062 0.264
275 2 (Cotton_A_18626) vs. 1 (Gorai.001G0621) 0.011 0.041 0.262
276 2 (Cotton_A_36364) vs. 1 (Gorai.013G1093) 0.009 0.033 0.261
277 2 (Cotton_A_00058) vs. 1 (Gorai.002G0209) 0.013 0.051 0.260
278 2 (Cotton_A_15782) vs. 1 (Gorai.008G0143) 0.010 0.038 0.260
279 2 (Cotton_A_07841) vs. 1 (Gorai.009G1982) 0.008 0.029 0.259
280 2 (Cotton_A_23711) vs. 1 (Gorai.006G0946) 0.009 0.035 0.258
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
281 2 (Cotton_A_07488) vs. 1 (Gorai.011G0852) 0.011 0.042 0.256
282 2 (Cotton_A_14663) vs. 1 (Gorai.007G2016) 0.007 0.029 0.256
283 2 (Cotton_A_31974) vs. 1 (Gorai.008G1999) 0.013 0.051 0.256
284b 2 (Cotton_A_16907) vs. 1 (Gorai.009G0058) 0.004 0.017 0.255
285 2 (Cotton_A_15028) vs. 1 (Gorai.007G2884) 0.012 0.046 0.255
286 2 (Cotton_A_23793) vs. 1 (Gorai.005G1802) 0.012 0.048 0.255
287 2 (Cotton_A_28198) vs. 1 (Gorai.006G0256) 0.029 0.114 0.255
288 2 (Cotton_A_16255) vs. 1 (Gorai.009G0096) 0.009 0.037 0.253
289 2 (Cotton_A_04367) vs. 1 (Gorai.005G0092) 0.014 0.055 0.253
290 2 (Cotton_A_41137) vs. 1 (Gorai.012G0916) 0.008 0.031 0.252
291 2 (Cotton_A_30639) vs. 1 (Gorai.002G2377) 0.013 0.051 0.252
292 2 (Cotton_A_22070) vs. 1 (Gorai.006G0131) 0.009 0.035 0.250
26
293 2 (Cotton_A_07731) vs. 1 (Gorai.007G0907) 0.011 0.042 0.249
294 2 (Cotton_A_32048) vs. 1 (Gorai.009G1272) 0.009 0.037 0.244
295 2 (Cotton_A_18858) vs. 1 (Gorai.010G0754) 0.010 0.043 0.244
296 2 (Cotton_A_39875) vs. 1 (Gorai.004G1105) 0.011 0.045 0.241
297 2 (Cotton_A_02968) vs. 1 (Gorai.007G1523) 0.008 0.034 0.241
298 2 (Cotton_A_15244) vs. 1 (Gorai.008G0378) 0.011 0.046 0.239
299a 2 (Cotton_A_06850) vs. 1 (Gorai.010G0097) 0.012 0.050 0.238
300 2 (Cotton_A_34461) vs. 1 (Gorai.013G1092) 0.011 0.047 0.237
301b 2 (Cotton_A_28288) vs. 1 (Gorai.010G2281) 0.012 0.050 0.236
302 2 (Cotton_A_00777) vs. 1 (Gorai.005G2405) 0.010 0.043 0.235
303 2 (Cotton_A_00501) vs. 1 (Gorai.002G2447) 0.011 0.048 0.234
304a 2 (Cotton_A_27681) vs. 1 (Gorai.008G1926) 0.011 0.046 0.232
305 2 (Cotton_A_01429) vs. 1 (Gorai.008G2890) 0.009 0.041 0.230
306 2 (Cotton_A_36910) vs. 1 (Gorai.008G0795) 0.007 0.032 0.230
307 2 (Cotton_A_13066) vs. 1 (Gorai.006G1904) 0.015 0.064 0.228
308 2 (Cotton_A_22059) vs. 1 (Gorai.008G1383) 0.009 0.040 0.228
309a 2 (Cotton_A_17619) vs. 1 (Gorai.006G0833) 0.014 0.062 0.228
310 2 (Cotton_A_11411) vs. 1 (Gorai.008G0595) 0.006 0.027 0.226
311 2 (Cotton_A_10175) vs. 1 (Gorai.002G2387) 0.009 0.040 0.225
312 2 (Cotton_A_30897) vs. 1 (Gorai.005G1925) 0.009 0.040 0.224
313 2 (Cotton_A_25648) vs. 1 (Gorai.011G0157) 0.013 0.059 0.223
314 2 (Cotton_A_17704) vs. 1 (Gorai.008G0480) 0.007 0.031 0.221
315 2 (Cotton_A_39243) vs. 1 (Gorai.001G1919) 0.010 0.045 0.220
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
316 2 (Cotton_A_20788) vs. 1 (Gorai.011G0198) 0.006 0.029 0.220
317 2 (Cotton_A_09744) vs. 1 (Gorai.004G1816) 0.008 0.036 0.217
318 2 (Cotton_A_16921) vs. 1 (Gorai.009G0043) 0.009 0.042 0.216
319 2 (Cotton_A_11129) vs. 1 (Gorai.009G0222) 0.008 0.038 0.216
320 2 (Cotton_A_02867) vs. 1 (Gorai.009G4208) 0.008 0.038 0.214
321a 2 (Cotton_A_00514) vs. 1 (Gorai.002G2433) 0.012 0.057 0.211
322 2 (Cotton_A_10654) vs. 1 (Gorai.007G3077) 0.007 0.034 0.210
323 2 (Cotton_A_06403) vs. 1 (Gorai.012G1462) 0.010 0.048 0.209
324 2 (Cotton_A_06599) vs. 1 (Gorai.007G3630) 0.008 0.040 0.209
325b 2 (Cotton_A_06512) vs. 1 (Gorai.002G1010) 0.009 0.046 0.204
326 2 (Cotton_A_13417) vs. 1 (Gorai.006G1548) 0.007 0.033 0.201
327 2 (Cotton_A_14089) vs. 1 (Gorai.001G1496) 0.009 0.044 0.200
27
328 2 (Cotton_A_06029) vs. 1 (Gorai.012G0133) 0.009 0.044 0.199
329d 2 (Cotton_A_09201) vs. 1 (Gorai.007G0350) 0.844d 4.238d 0.199
330 2 (Cotton_A_00336) vs. 1 (Gorai.002G2612) 0.007 0.034 0.198
331 2 (Cotton_A_00413) vs. 1 (Gorai.002G2536) 0.010 0.049 0.198
332 2 (Cotton_A_11971) vs. 1 (Gorai.004G0145) 0.017 0.087 0.196
333 2 (Cotton_A_23841) vs. 1 (Gorai.011G2097) 0.007 0.036 0.196
334 2 (Cotton_A_32763) vs. 1 (Gorai.001G1035) 0.008 0.040 0.195
335b 2 (Cotton_A_15714) vs. 1 (Gorai.013G0109) 0.009 0.044 0.194
336 2 (Cotton_A_10104) vs. 1 (Gorai.011G2958) 0.011 0.057 0.191
337 2 (Cotton_A_03168) vs. 1 (Gorai.013G2242) 0.012 0.063 0.190
338 2 (Cotton_A_30406) vs. 1 (Gorai.002G0333) 0.008 0.045 0.187
339 2 (Cotton_A_26582) vs. 1 (Gorai.008G2983) 0.006 0.034 0.186
340 2 (Cotton_A_34750) vs. 1 (Gorai.010G1466) 0.009 0.048 0.184
341 2 (Cotton_A_01310) vs. 1 (Gorai.008G2774) 0.008 0.042 0.182
342 2 (Cotton_A_28304) vs. 1 (Gorai.010G2266) 0.012 0.064 0.179
343 2 (Cotton_A_17970) vs. 1 (Gorai.005G2046) 0.006 0.032 0.177
344 2 (Cotton_A_19296) vs. 1 (Gorai.005G1892) 0.010 0.057 0.176
345b 2 (Cotton_A_11911) vs. 1 (Gorai.004G2907) 0.006 0.035 0.174
346 2 (Cotton_A_14952) vs. 1 (Gorai.012G1318) 0.010 0.061 0.171
347 2 (Cotton_A_05786) vs. 1 (Gorai.004G2627) 0.007 0.041 0.170
348 2 (Cotton_A_21706) vs. 1 (Gorai.005G2333) 0.008 0.050 0.170
349 2 (Cotton_A_34969) vs. 1 (Gorai.007G3347) 0.010 0.062 0.168
350 2 (Cotton_A_23465) vs. 1 (Gorai.009G2221) 0.008 0.049 0.168
Table S3. Nucleotide substitution rates of PPR homologous genes between D5 and A2 genomes (continued)
Number gene 2 (A2) vs. gene.1 (D5) dN dS dN/dS
351 2 (Cotton_A_23222) vs. 1 (Gorai.007G1207) 0.011 0.063 0.167
352 2 (Cotton_A_22065) vs. 1 (Gorai.008G1377) 0.011 0.068 0.163
353 2 (Cotton_A_11026) vs. 1 (Gorai.009G0768) 0.007 0.044 0.159
354 2 (Cotton_A_08048) vs. 1 (Gorai.008G2059) 0.006 0.041 0.153
355 2 (Cotton_A_00793) vs. 1 (Gorai.005G2375) 0.010 0.069 0.152
356b 2 (Cotton_A_26149) vs. 1 (Gorai.009G1519) 0.008 0.050 0.151
357 2 (Cotton_A_07893) vs. 1 (Gorai.008G2279) 0.006 0.039 0.150
358 2 (Cotton_A_01507) vs. 1 (Gorai.003G0040) 0.006 0.037 0.147
359 2 (Cotton_A_30269) vs. 1 (Gorai.006G1151) 0.006 0.042 0.137
360 2 (Cotton_A_09295) vs. 1 (Gorai.007G2759) 0.006 0.042 0.133
361 2 (Cotton_A_00464) vs. 1 (Gorai.002G2481) 0.008 0.058 0.132
362 2 (Cotton_A_12077) vs. 1 (Gorai.006G1689) 0.004 0.034 0.131
28
363 2 (Cotton_A_16188) vs. 1 (Gorai.011G0940) 0.005 0.035 0.130
364 2 (Cotton_A_16572) vs. 1 (Gorai.006G0758) 0.007 0.058 0.127
365b 2 (Cotton_A_08850) vs. 1 (Gorai.012G1593) 0.004 0.033 0.124
366 2 (Cotton_A_04919) vs. 1 (Gorai.010G2491) 0.004 0.040 0.111
367 2 (Cotton_A_34884) vs. 1 (Gorai.010G0323) 0.005 0.049 0.104
368 2 (Cotton_A_21237) vs. 1 (Gorai.011G2051) 0.002 0.020 0.100
369 2 (Cotton_A_27764) vs. 1 (Gorai.003G1285) 0.004 0.040 0.097
370 2 (Cotton_A_02937) vs. 1 (Gorai.011G0486) 0.004 0.041 0.096
371 2 (Cotton_A_29102) vs. 1 (Gorai.008G0687) 0.004 0.038 0.091
372 2 (Cotton_A_19432) vs. 1 (Gorai.001G2565) 0.004 0.050 0.084
373a 2 (Cotton_A_13069) vs. 1 (Gorai.006G1901) 0.003 0.043 0.063
374 2 (Cotton_A_11956) vs. 1 (Gorai.004G0129) 0.002 0.035 0.048
375a 2 (Cotton_A_28832) vs. 1 (Gorai.002G1171) 0.002 0.047 0.040
376b 2 (Cotton_A_34882) vs. 1 (Gorai.010G0325) 0.002 0.045 0.034
377 2 (Cotton_A_36582) vs. 1 (Gorai.009G3548) 0.000 0.021 0.000
Note:
a A PPR candidate sequence derived from A2 genome existed in this pair of homologous sequences;
b A PPR candidate sequence derived from D5 genome existed in this pair of homologous sequences;
c This pair of homologous sequences owned the maximum value of dN/dS(shown in bold and underline fonts);
d This pair of homologous sequences owned the maximum value of dN and dS(shown in bold and underline fonts)
Additional file 4: Figure S3. GO annotation of PPR homologous genes between G.
raimondii (D5) and G. arboreum (A2) genomes. (a) GO bar chart of D5-A2 PPR homologies in
secondary level GO terms of 3 main GO categories (biological process, cellular component
and molecular function). Input list, D5-A2 PPR homologous sequences. Background/reference,
cotton genome locus (phytozome). (b) GO hieratical graph of D5-A2 PPR homologies for
biological process. The more significant statistically, the darker the note color was. (c) GO
hieratical graph of D5-A2 PPR homologies for cellular component. The more significant
statistically, the darker the note color was.
29
Additional file 5: Table S4. Sub-family analysis of 70 PPR candidate genes in G. raimondii
(D5), G. arboreum (A2) and G. hirsutum (AD1) genomes. Table S5. Sub-family analysis of 8
PPR candidate genes in G. raimondii (D5), G. arboreum (A2) and G. hirsutum (AD1) genomes. Table S4 Sub-family analysis of 70 PPR candidate genes in G. raimondii (D5), G. arboreum (A2) and G. hirsutum
(AD1) genomes
Chromos
ome Genea
Subfam
ily
No. of
amino acids
No. of
Motif Motif arrangementb
Gossypium raimondii
Chr01 Gorai.001G1
316 P 419 12 8-P-P-P-P-P-P-P-P-P-P-P-P-6
Chr02 Gorai.002G0
718(1) P 787 18
63-P-22-P-32-P-35-P-P-P-P-P-P-P-P-P-P-P-4-P-P-P-
P-13
Chr02 Gorai.002G0
718(2) P 787 18
63-P-22-P-32-P-35-P-P-P-P-P-P-P-P-P-P-P-4-P-P-P-
P-13
Chr02 Gorai.002G1
010 P 1063 25
84-P-P-P-P-P-P-P-P-3-P-P-P-P-P-P-6-P-P-1-P-3-P-P-
P-P-39-P-5-P-P-P-68
Chr03 Gorai.003G1
716 P 598 13 115-P-P-P-P-P-P-S-5-P-P-P-1-P-P-P-28
Chr04 Gorai.004G2
406 P 509 12 69-P-P-P-P-3-P-P-P-P-P-P-P-P-21
Chr04 Gorai.004G2
438 P 647 15 101-P-P-P-P-P-P-P-P-P-P-P-P-P-P-P-21
Chr04 Gorai.004G2
907 P 584 11 19-P-35-P-P-3-P-P-P-P-P-P-P-P-144
Chr06 Gorai.006G2
252 P 508 4 144-P-P-1-P-P-227
Chr06 Gorai.006G2
471 P 638 14 106-P-P-P-P-P-P-P-S-4-P-P-3-P-3-P-P-P-41
Chr07 Gorai.007G1
431 P 366 9 30-P-P-P-P-P-P-2-P-P-P-35
Chr08 Gorai.008G0 P 631 13 152-P-1-P-P-P-P-P-P-P-P-P-P-P-P-25
30
443
Chr09 Gorai.009G0
058 P 716 15 167-P-P-P-P-P-2-P-P-P-P-P-P-P-P-P-P-27
Chr09 Gorai.009G1
519 P 692 14 141-P-P-P-P-P-P-3-P-P-P-3-P-P-P-P-33-P-35
Chr09 Gorai.009G2
580 P 632 12 86-P-43-P-P-P-P-P-P-P-P-P-P-5-P-87
Chr09 Gorai.009G3
762 P 435 6 166-P-P-8-P-P-P-P
Chr10 Gorai.010G0
325(1) P 595 14 105-P-P-P-2-P-P-P-P-P-P-P-P-P-P-P-11
Chr10 Gorai.010G0
325(2) P 554 14 64-P-P-P-2-P-P-P-P-P-P-P-P-P-P-P-11
Chr10 Gorai.010G0
325(3) P 595 14 105-P-P-P-2-P-P-P-P-P-P-P-P-P-P-P-11
Chr10 Gorai.010G0
536(1) P 722 14 117-P-36-S-4-P-P-P-P-P-1-P-P-41-P-P-P-P-P-46
Table S4 Sub-family analysis of 70 PPR candidate genes in G. raimondii (D5), G. arboreum (A2) and G.
hirsutum (AD1) genomes (continued)
Chromos
ome Genea
Subfam
ily
No. of
amino acids
No. of
Motif Motif arrangementb
Chr10 Gorai.010G0
536(2) P 646 14 41-P-37-S-4-P-P-P-P-P-1-P-P-41-P-P-P-P-P-46
Chr10 Gorai.010G0
722(1) P 632 10 110-P-P-P-4-P-P-P-5-P-P-P-P-136
Chr10 Gorai.010G0
722(2) P 632 10 110-P-P-P-4-P-P-P-5-P-P-P-P-136
Chr10 Gorai.010G2
281(1) P 638 14 122-P-5-P-P-1-P-P-P-S-4-P-P-1-P-2-P-P-P-P-24
Chr10 Gorai.010G2
281(2) P 638 14 122-P-5-P-P-1-P-P-P-S-4-P-P-1-P-2-P-P-P-P-24
Chr11 Gorai.011G1
450(1) P 586 15 68-P-P-P-P-P-P-P-P-P-P-P-P-P-P-2-P
Chr11 Gorai.011G1
451(1) P 558 14 47-P-P-P-P-P-P-P-P-P-P-P-P-P-P-21
Chr11 Gorai.011G1
464(1) P 519 13 43-P-P-P-P-P-P-P-P-1-P-P-P-P-P-21
Chr11 Gorai.011G1
464(2) P 367 10 9-P-P-P-P-P-1-P-P-P-P-P-8
Chr11 Gorai.011G1
465 P 93 3 8-P-P-P
31
Chr11 Gorai.011G1
466 P 371 8 99-P-P-P-P-P-P-P-P-2
Chr11 Gorai.011G1
511 P 73 1 25-P-13
Chr11 Gorai.011G1
512 P 626 15 54-P-35-P-P-P-P-P-P-P-P-P-P-P-P-P-P-21
Chr11 Gorai.011G1
514 P 442 10 113-P-P-P-P-P-P-P-P-P-P
Chr11 Gorai.011G1
515 P 824 20
65-P-P-P-P-P-P-P-P-2-P-P-P-P-2-P-1-P-63-P-P-P-P-
P-P-1
Chr11 Gorai.011G1
557 P 536 13 67-P-1-P-P-P-P-P-P-P-19-P-P-P-2-P-P-17
Chr12 Gorai.012G0
303(1) P 524 10 136-P-P-P-1-P-P-P-P-P-17-P-P-20
Chr12 Gorai.012G0
303(2) P 431 9 44-P-62-P-P-P-P-P-P-P-P-14
Chr12 Gorai.012G1
205(1) P 763 14 193-P-P-P-P-P-P-P-P-P-P-P-P-P-P-84
Chr12 Gorai.012G1
205(2) P 763 14 193-P-P-P-P-P-P-P-P-P-P-P-P-P-P-84
Chr12 Gorai.012G1
494(1) P 536 9 168-P-P-P-P-P-P-P-P-1-P-55
Chr12 Gorai.012G1
494(2) P 384 9 16-P-P-P-P-P-P-P-P-1-P-55
Table S4 Sub-family analysis of 70 PPR candidate genes in G. raimondii (D5), G. arboreum (A2) and G.
hirsutum (AD1) genomes (continued)
Chromos
ome Genea
Subfam
ily
No. of
amino acids
No. of
Motif Motif arrangementb
Chr12 Gorai.012G1
593(1) P 868 18
72-S-6-P-P-P-P-P-P-P-P-P-P-P-25-P-P-P-P-P-45-P-1
06
Chr12 Gorai.012G1
593(2) P 868 18
72-S-6-P-P-P-P-P-P-P-P-P-P-P-25-P-P-P-P-P-45-P-1
06
Chr12 Gorai.012G1
593(3) P 868 18
72-S-6-P-P-P-P-P-P-P-P-P-P-P-25-P-P-P-P-P-45-P-1
06
Chr13 Gorai.013G0
109(1) P 960 15 316-P-P-P-2-P-1-P-P-P-P-P-P-P-P-P-P-P-123
Chr13 Gorai.013G0
109(2) P 755 12 316-P-P-P-2-P-1-P-P-P-P-P-P-P-P-23
Chr13 Gorai.013G0
606(1) P 555 13 43-P-P-35-P-P-P-P-P-P-P-P-2-P-P-P-22
Chr13 Gorai.013G0 P 416 11 9-P-P-P-P-P-P-P-P-2-P-P-P-22
32
606(2)
Gossypium arboreum
Chr01 Cotton_A_32
157 P 195 5 9-P-P-P-P-P-13
Chr03 Cotton_A_26
557 P 440 11 8-P-4-P-P-P-P-P-P-P-2-P-P-P-45
Chr03 Cotton_A_03
817 P 523 9 153-S-4-P-3-P-P-4-P-P-2-P-35-P-P-24
Chr04 Cotton_A_06
850 P 704 7 368-P-S-5-P-35-P-P-P-P-21
Chr05 Cotton_A_26
837 P 415 11 8-P-P-P-P-P-P-P-P-P-P-P-22
Chr06 Cotton_A_04
606 P 566 8 169-P-P-34-P-P-P-P-35-P-P-48
Chr06 Cotton_A_29
300 P 587 14 54-P-35-P-P-1-P-P-P-P-P-P-P-P-P-P-P-21
Chr07 Cotton_A_16
847 P 573 13 103-P-P-P-P-P-3-P-P-P-P-P-P-P-P-12
Chr07 Cotton_A_18
522 P 622 14 111-P-P-P-P-P-P-P-P-P-P-P-P-P-P-21
Chr08 Cotton_A_02
931 P 734 14 173-P-P-P-P-3-P-P-P-P-P-3-P-P-P-P-36-P-39
Chr09 Cotton_A_27
681 P 759 19 38-P-9-P-P-P-P-P-P-P-P-P-P-P-P-P-P-P-4-P-P-P-54
Chr10 Cotton_A_13
069 P 466 8 130-S-3-P-P-5-P-P-P-P-P-54
Chr10 Cotton_A_17
619 P 398 6 175-P-P-P-P-P-P-16
Table S4 Sub-family analysis of 70 PPR candidate genes in G. raimondii (D5), G. arboreum (A2) and G.
hirsutum (AD1) genomes (continued)
Chromos
ome Genea
Subfam
ily
No. of
amino acids No. of Motif Motif arrangementb
Chr10 Cotton_A_14
743 P 544 14 8-P-35-P-P-P-P-P-P-P-P-P-P-P-P-P-21
Chr12 Cotton_A_37
656 P 1525 18
239-P-37-P-P-P-P-P-P-P-72-P-36-P-1-S-41-P-41-
P-P-35-P-1-P-P-35-P-376
Chr12 Cotton_A_28
832 P 706 14 165-P-3-P-41-P-1-P-1-P-P-P-P-P-P-P-P-P-P-21
Chr12 Cotton_A_00
514 P 817 20
108-P-P-P-P-P-P-P-P-P-P-P-P-P-P-P-P-P-P-1-P-1
-P-12
Gossypium hirsutum
33
GhBah0036h0
9 P 480 8 104-S-42-P-41-P-P-P-P-P-1-P-24
GhDeg5330 P 471 9 90-S-5-S-4-P-P-4-P-P-P-P-P-66
GhI12 P 458 7 118-P-36-P-P-P-P-P-4-P-59
GhK14 P 846 16 273-P-P-P-P-P-P-3-P-P-P-P-P-3-P-P-P-P-P-13
GhPPR3 P 547 10 155-P-2-P-1-P-P-P-P-1-P-P-5-P-1-P-42
GhPPR4 P 337 4 175-P-P-P-P-22
GhPPR5 P 288 7 11-P-P-2-P-P-2-P-P-5-P-29
GhPPRH1 P 638 17 P-P-P-P-P-P-P-P-P-P-P-P-P-P-P-P-1-P-47
GhPPRH2 P 851 16 237-P-P-P-P-P-P-P-P-P-P-P-35-P-P-P-P-P-21
GhMX55E05 E 522 12 87-L-7-S-3-P-L-S-P-L-S-P-L2-S-9-E