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Frequency of SNPs and INDELs in the highly variable genic regions of chloroplast genome sequences in the alloplasmic CMS lines relative to the fertile line. The grey bars indicate the frequencies of highly variable protein-coding genes. The black bars indicate the average frequency of SNPs or INDELs in the genic regions, in total
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The complete chloroplast genomes of sunflower fertile line HA89 and isonuclear CMS lines with four different cytoplasmic backgrounds (PET1, PET2, ANN2 and MAX) were sequenced. A total of 451 polymorphic sites, with including 58 SSRs, 317 SNPs and 76 microindels were revealed between the fertile and CMS cytotypes. Among the alloplasmic male-sterile...
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... (A)9 (A)9 rpl2-rps19 IRB Table 3: Nonsynonymous substitution in the chloroplast genomes of the sunflower alloplasmic CMS lines Position Ref PET1 PET2 ANN2 MAX1 Gene Region 2984 A G matk Phe195Ser LSC 14496 A G rpoB Gln481Arg Table 4: Number of SNPs and INDELs identified between the complete chloroplast genome sequences of the reference sequences (NC_007977.1) and HA89-alloplasmic CMS lines Type of sequence ------------------------------------------------------------------------------------------------------------------------------------- Genic Intronic Intergenic Total -------------------------- --------------------------- ---------------------------- ------------------------- Type of cytoplasm SNP Indel SNP Indel SNP Indel SNP Indel Fertile line 0 2 0 0 1 4 1 6 CMS-PET1 9 2 4 0 10 8 23 10 CMS-PET2 54 3 13 5 87 33 154 41 CMS-ANN2 52 3 10 4 80 32 142 39 CMS-MAX 71 3 11 2 114 38 196 43 Meantime, the average frequency of SNPs and INDELs in the genic regions was 0.0046. Some chloroplast genes such as rpoC2, atpA, rbcL, ndhF and ycf1 were distinguished by a higher level of polymorphism. Interestingly, the highest increase in frequency was characterized for the ycf1 gene, with a 4.3-fold increases in frequency observed in the CMS- ANN2 line (Fig. 2). In a study devoted to a comparative analysis of the complete chloroplast genome sequences of the male-fertile line and two CMS lines of onions, it was reported that the average frequency of SNPs and INDELs in the non-genic regions was 0.0057, while the mean frequency in the genic regions was 0.0016 ( Kim et al., 2015). Among intergenic regions, the most polymorphic was the regions between the ndhF-rpl32, petN-psbM and trnS-trnG genes. Meanwhile, as in our study, an increase in frequency of SNPs and INDELs in the genic regions was observed in the ndhF (3.5-fold) and ycf1 (4.2-fold times) genes (Kim et al., 2015). It was shown that the rpo genes are highly variable and reliable phylogenetic markers, effective in the reconstruction of interrelations of species belonging to the same genus ( Krawczyk and Sawicki 2013). A high level of polymorphism of ndh, rpoC2, rbcL and ycf1 genes is also demonstrated in other studies ( Wei et al., 2017;Joseph et al., 2013;Benkeblia, ...
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... (A)9 (A)9 rpl2-rps19 IRB Table 3: Nonsynonymous substitution in the chloroplast genomes of the sunflower alloplasmic CMS lines Position Ref PET1 PET2 ANN2 MAX1 Gene Region 2984 A G matk Phe195Ser LSC 14496 A G rpoB Gln481Arg Table 4: Number of SNPs and INDELs identified between the complete chloroplast genome sequences of the reference sequences (NC_007977.1) and HA89-alloplasmic CMS lines Type of sequence ------------------------------------------------------------------------------------------------------------------------------------- Genic Intronic Intergenic Total -------------------------- --------------------------- ---------------------------- ------------------------- Type of cytoplasm SNP Indel SNP Indel SNP Indel SNP Indel Fertile line 0 2 0 0 1 4 1 6 CMS-PET1 9 2 4 0 10 8 23 10 CMS-PET2 54 3 13 5 87 33 154 41 CMS-ANN2 52 3 10 4 80 32 142 39 CMS-MAX 71 3 11 2 114 38 196 43 Meantime, the average frequency of SNPs and INDELs in the genic regions was 0.0046. Some chloroplast genes such as rpoC2, atpA, rbcL, ndhF and ycf1 were distinguished by a higher level of polymorphism. Interestingly, the highest increase in frequency was characterized for the ycf1 gene, with a 4.3-fold increases in frequency observed in the CMS- ANN2 line (Fig. 2). In a study devoted to a comparative analysis of the complete chloroplast genome sequences of the male-fertile line and two CMS lines of onions, it was reported that the average frequency of SNPs and INDELs in the non-genic regions was 0.0057, while the mean frequency in the genic regions was 0.0016 ( Kim et al., 2015). Among intergenic regions, the most polymorphic was the regions between the ndhF-rpl32, petN-psbM and trnS-trnG genes. Meanwhile, as in our study, an increase in frequency of SNPs and INDELs in the genic regions was observed in the ndhF (3.5-fold) and ycf1 (4.2-fold times) genes (Kim et al., 2015). It was shown that the rpo genes are highly variable and reliable phylogenetic markers, effective in the reconstruction of interrelations of species belonging to the same genus ( Krawczyk and Sawicki 2013). A high level of polymorphism of ndh, rpoC2, rbcL and ycf1 genes is also demonstrated in other studies ( Wei et al., 2017;Joseph et al., 2013;Benkeblia, ...
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Rf candidate genes were related to the super D05_PPR-cluster and verified to be individually nonfunctional.
Abstract
Restorer of fertility (Rf) genes of cytoplasmic male sterility (CMS) is commonly found to be PPR (pentatricopeptide repeat) genes, which are mostly located in a cluster of PPR genes with high similarity. Here, Homocap-se...
Citations
... 21 of the cpSSR loci in Helianthus contain polyadenine (polyA) and 12 of cpSSRs contain polythymine (polyT), while multiple C and G nucleotides were only represented in 2 and 1 loci, respectively. These results are similar to the data from other studies that cpSSRs are mainly composed of polyT and polyA repeats (Kuang et al., 2011;Ni et al., 2016;Azarin et al., 2018). Probably, due to the energetically more advantageous separation of chains consisting of homopolymers A and T in comparison with poly GC, the slipped-strand mispairing in poly A and poly T repeats occurs more often (Cocco et al., 2004). ...
Sequencing and a comparative analysis of the complete chloroplast genomes of seven perennial Helianthus species were carried out. The chloroplast genomes have a typical quadripartite structure, including large and small single regions and a pair of inverted repeats. Genome sizes were between 151,152 bp and 151,289 bp. The genome of H. grosseserratus was the smallest, while that of H. microcephalus was the largest. The size variation of the chloroplast genomes is substantially due to the change in the length of simple sequence repeats (SSRs) in non-coding regions. An analysis of these SSRs revealed 35 polymorphic loci (average PIC value > 0.5) that can be used to examine ecological and evolutionary processes in wild Helianthus species. Eight divergence hotspots, including five intergenic regions (petN-psbM, clpP intron, rps3-rpl16, ndhD-ccsA, and ndhF-rpl32) and three gene regions (rbcL, ycf1, and ndhF) were also identified in Helianthus chloroplast genomes. The evolutionary selection pressure analysis revealed a strong purifying selection. Only the rbcL gene experienced efficiency of positive selection at the annual/perennial transitions. The inverted repeat (IR)/single copy (SC) boundaries were identical in all of these (Helianthus) species. In general, the comparison of the genomes revealed low levels of sequence variability (Pi = 0.00051). This indicates that the chloroplast genomes of the studied perennial species of Helianthus, in addition to purifying selection, are closely related and have a recent divergence time.
The vast majority of commercial sunflower hybrids worldwide are produced using cytoplasmic male sterility (CMS) of the PET1 type, resulting from the interspecific hybridization of Helianthus petiolaris with Helianthus annuus. In this study, the open reading frame, orfH522, associated with the CMS-PET1 phenotype, was revealed for the first time in the 3’-flanking region of the mitochondrial atpA gene in wild H. annuus. An analysis of whole genome data from 1089 accessions showed that the frequency of occurrence of CMS-orfH522 in wild H. annuus populations is 3.58%, while in wild H. petiolaris populations, it is 1.26%. The presence of additional genomic data with insufficient coverage of the orfH522 sequence indicates that the potential frequency of occurrence of CMS-orfH522 in natural sunflower populations may be two times higher. Based on these results and previous studies, PET1-CMS was suggested to be a natural cytotype of H. annuus, and the appearance of the CMS phenotype in cultivated sunflowers is associated with the loss of stabilizing nuclear genes of fertility restorers, which occurred during interspecific hybridization. These data may explain the patterns of differential cytoplasmic and nuclear introgression occurring in wild sunflower and are useful for further evolutionary studies.
