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Classification of PPRs in P sub-class (a) and PLS sub-class (b) in different legume species using PPR browser website. X axis represents number of proteins of a particular sub-class in different legume species represented on y axis. Numbers indicated on top of each bar in Figure 2 (a) represents number of P sub-class proteins in a particular species. PLS sub-class was further classified on the basis of C-terminal motifs i.e., DYW, E1, E2 and PLS as shown in Figure 2 (b) where, total height of each bar corresponds to total number of proteins in PLS sub-class of each species while different colours in each bar reflects proteins with different C-terminal motifs, their numbers represented in the table below y axis.
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PPR proteins comprises of several hundred members among land plants and govern a fascinating array of functions in organeller genomes that ranges from participation in stabilization of organeller transcripts, RNA editing to fertility restoration of CMS lines. Despite the availability of genome sequences of several legume species, comprehensive cata...
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Context 1
... proteins in legumes were classified into two sub-classes ( Figure 2) i.e., P and PLS, based on the presence and arrangement of different motifs. For 1 and 5 of predicted PPR protein sequences in Cajanus and Medicago, respectively no PPR domains were predicted and hence these could not be classified and were not included in further analysis. ...
Context 2
... all 6 species, small proportion of PPRs within P sub-class (2-6% of P sub- class) was observed to possess C-terminal motifs i.e., SMR, PRORP and LAGLIDADG. PLS sub-class was further sub categorized into PLS, E1, E2 and DYW and majority of the proteins were found to posess DYW editing motif ( Figure 2b) except in Cicer. None of the PPR was categorized into E + sub-group that is known to constitute proteins with a degenerate or truncated DYW domain [15]. ...
Similar publications
PPR proteins comprises of several hundred members among land plants and govern a fascinating array of functions in organeller genomes that ranges from participation in stabilization of organeller transcripts, RNA editing to fertility restoration of CMS lines. Despite the availability of genome sequences of several legume species, comprehensive cata...
Citations
... PPRs are involved in a wide range of events, including physiological and developmental processes and response to various biotic and abiotic stresses (Xing et al., 2018). There was also study suggested that PPR proteins govern a series of functions in organelles genomes, including the stabilization of organelles transcripts, RNA editing and the fertility restoration of CMS lines (Kaur & Verma, 2016 Temperature shows some dependency on altitude. Generally, higher altitude regions are colder than low altitude regions. ...
Allopolyploids are believed to inherit the genetic characteristics of its progenitors and exhibit stronger adaptability and vigor. The allotetraploid Isoetes sinensis was formed by the natural hybridization and polyploidization of two diploid progenitors, Isoetes taiwanensis and Isoetes yunguiensis, and was believed to have the potential to adapt to plateau environments. To explore the expression pattern of homoeologous genes and their contributions to altitude adaptation, we transplanted natural allotetraploid I. sinensis (TnTnYnYn) along the altitude gradient for a long-term, and harvested them in summer and winter, respectively. One year after transplanting, it still lived well, even in the extreme environment of the Qinghai-Tibet Plateau. Then, we performed high-throughput RNA sequencing to measure their gene expression level. A total of 7801 homoeologous genes were expressed, among which 5786 were identified as shared expression in different altitudes and seasons. We further found that altitude variations could change the subgenome bias trend of I. sinensis, but season could not. Moreover, the functions of uniquely expressed genes indicated that temperature might be an important restrictive factor during the adaptation process. Through the analysis of DEGs and uniquely expressed genes, we found that Y subgenome provided more contributions to high altitude adaptation than T subgenome. These adaptive traits to high altitude may be inherited from its plateau progenitor I. yunguiensis. Through weighted gene co-expression network analysis, pentatricopeptide repeats gene family and glycerophospholipid metabolism pathway were considered to play important roles in high-altitude adaptation. Totally, this study will enrich our understanding of allopolyploid in environmental adaptation.
... •The practice of organic farming gives the crop enough time to grow without the use of artificial growth injectors. But this practice won't be able to meet the world's demand for food as the organic food takes more time to grow when compared with the conventional practices of growing crops [65][66][67][68][69] . ...
In the ancient time, agriculture was practiced without the use of artificial chemicals. The use of artificial chemicals such as fertilizers and pesticides came into picture during the mid-19th century. This kind of agricultural practice was causing harm to the environment. With the rapid change in farming practices, organic farming came into existence in the 20th century. It made use of environment friendly practices by avoiding the use of artificial chemicals and making use of organic matter to raise crops. Organic food is beneficial to human health and the practice of organic farming keeps the environment clean.
... •The practice of organic farming gives the crop enough time to grow without the use of artificial growth injectors. But this practice won't be able to meet the world's demand for food as the organic food takes more time to grow when compared with the conventional practices of growing crops [65][66][67][68][69] . ...
In the ancient time, agriculture was practiced without the use of artificial chemicals. The use of artificial chemicals such as fertilizers and pesticides came into picture during the mid-19th century. This kind of agricultural practice was causing harm to the environment. With the rapid change in farming practices, organic farming came into existence in the 20th century. It made use of environment friendly practices by avoiding the use of artificial chemicals and making use of organic matter to raise crops. Organic food is beneficial to human health and the practice of organic farming keeps the environment clean.
... •The practice of organic farming gives the crop enough time to grow without the use of artificial growth injectors. But this practice won't be able to meet the world's demand for food as the organic food takes more time to grow when compared with the conventional practices of growing crops [65][66][67][68][69] . ...
In the ancient time, agriculture was practiced without the use of artificial chemicals. The use of artificial chemicals such as fertilizers and pesticides came into picture during the mid-19th century. This kind of agricultural practice was causing harm to the environment. With the rapid change in farming practices, organic farming came into existence in the 20th century. It made use of environment friendly practices by avoiding the use of artificial chemicals and making use of organic matter to raise crops. Organic food is beneficial to human health and the practice of organic farming keeps the environment clean.
... Unlike the numerous families of conservative PPR genes that regulate processing, as well as participate in the splicing, editing, stabilization and translation of organelle RNAs, RFL-PPR genes are organized into clusters and are characterized by an exceptionally high level of variability [27]. It is believed that allele-specific markers of RFL-PPR genes can be used for positional cloning of fertility restorer genes, as well as for efficient selection of the carriers of functional alleles of Rf loci [18,28]. In addition, an exceptionally high rate of evolution of the subfamily of RFL-PPR genes [29,30], as well as the important role of CMS and restoration of fertility in the formation of new species [31] allow us to consider them as a source of molecular markers for phylogenetic research. ...
The phenomenon of cytoplasmic male sterility (CMS), consisting in the inability to produce functional pollen due to mutations in mitochondrial genome, has been described in more than 150 plant species. With the discovery of nuclear fertility restorer (Rf) genes capable of suppressing the CMS phenotype, it became possible to use the CMS-Rf genetic systems as the basis for practical utilization of heterosis effect in various crops. Seed production of sunflower hybrids all over the world is based on the extensive use of the PET1 CMS combined with the Rf1 gene. At the same time, data on Rf1 localization, sequence, and molecular basis for the CMS PET1 type restoration of fertility remain unknown. Searching for candidate genes of the Rf1 gene has great fundamental and practical value. Therefore, in this study, association mapping of fertility restorer gene for CMS PET1 in sunflower was performed. The genome-wide association study (GWAS) results made it possible to isolate a segment 7.72 Mb in length on chromosome 13, in which 21 candidates for Rf1 fertility restorer gene were identified, including 20 pentatricopeptide repeat (PPR)family genes and one Probable aldehyde dehydrogenase gene. The results will serve as a basis for further study of the genetic nature and molecular mechanisms of pollen fertility restoration in sunflower, as well as for further intensification of sunflower breeding.
... The delineated genes encoding response regulator, arginine decarboxylase, Mediator transcription factor and PPR protein with synonymous and non-synonymous coding and intronic SNPs associated with SYP trait in chickpea are known to control gene expression dynamics and transcriptional regulatory pathways underlying growth, development and yield traits in multiple crop plants [50][51][52][53][54][55][56] . Essentially, the role of delineated most-promising SYP trait-associated PPR genes with synonymous SNPs in regulating fertility restoration, heterosis breeding and hybrid seed production is well-documented in crop plants including legumes 52,54,56,57 . ...
... The delineated genes encoding response regulator, arginine decarboxylase, Mediator transcription factor and PPR protein with synonymous and non-synonymous coding and intronic SNPs associated with SYP trait in chickpea are known to control gene expression dynamics and transcriptional regulatory pathways underlying growth, development and yield traits in multiple crop plants [50][51][52][53][54][55][56] . Essentially, the role of delineated most-promising SYP trait-associated PPR genes with synonymous SNPs in regulating fertility restoration, heterosis breeding and hybrid seed production is well-documented in crop plants including legumes 52,54,56,57 . Modulation of their gene expression can thereby enhance the overall seed yield. ...
We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.
... There are 19 polymorphic sites in the coding sequence and in the 5-or 3-end flanking regions of the dominant and recessive alleles of the candidate gene PPR13. Sorghum PPR13 gene differs significantly from other representatives of the PPR-RFL genes subfamily in the structure of PPR motifs [19][20][21]. Another candidate gene (Rf2) is located on 236,219 bp region of SDI02 chromosome. ...
Seven different types of cytoplasmic male sterility (CMS) are known for the grain sorghum (Sorghum bicolor L. Moench), however, only A1 (milo) is used in heterotic hybrid breeding. The genetic control of pollen fertility restoration of CMS A1 is complex and determined by two or three Rf (Restoration of Fertility) genes, and also by a number of modifiers. It is very little known about molecular mechanisms of CMS A1 and fertility restoration. Only one gene, Rf1, is identified at the molecular level (R.R. Klein et al., 2005). In the present paper we have demonstrated for the first time the nucleotide polymorphism in the coding regions of the recessive and dominant alleles of Rf2 gene and also of the candidate RFL-PPR gene homologous to the rice Rf1 gene. . Here, we studied polymorphism of the CMS-Rf genetic system related traits in sorghum accessions from the VIR collection, including the fertility restorers k-928 and k-929; a half-restorer k-1362, the sterile lines A- 10598 and A-83 (CMS A1) and their fertile analogs, the F8-F12 BC1-BC2 sister lines resistant to Schizaphis graminum Rond. which have been isolated among the hybrids derived from crosses between the sterile (CMS A1) line N-81 and lines k-929 and k-928, and also hybrids between the sister lines. For investigating variability of candidate genes associated with the CMS-Rf genetic system the reference sequences were selected from the bioinformatic database (http://www.ncbi.nlm.hih.gov), the eighth specific primers were designed, and the fragments amplified on the DNA of genotypes differing by the ability to suppression of the CMS phenotype were sequenced. In the CMS lines and fertility restorers a significant polymorphism (18 polymorphic sites) was revealed in the 825 bp fragment of the Rf2 coding region (reference fragment XM002459403.1, chromosome SDI02) and also in RFL-PPR candidate gene located in the chromosome 3 (reference fragment XM002458104.1). The sequenced regions of the structural nuclear gene ALDH2b encoding mitochondrial aldehyde dehydrogenase, the maize Rf2 gene homolog, and also of the mitochondrial F0F1 ATPase alpha subunit were identical in the CMS and fertility restorer lines. Variability of pollen fertility indices was studied using acetocarmine stained cytological preparations. The lines resistant to S. graminum, and their hybrids differed in the percentage of stained (fertile) pollen grains, the presence of anomalous large pollen grains (54-70 μm in diameter), giant pollen grains (up to 84 m in diameter) and deformed pollen grains. In the fertile F8-F12 BC1-BC2 lines which derived from the hybrids produced in crossings with fertility restorers, the frequency of stained pollen grains was relatively high and reached 72.2-83.8 % for k-929, and 57.4 and 63.4 % in two lines, respectively, for k-928; large pollen grains occurred at different frequency in five lines, and the giant ones were observed in two lines. The variability in pollen fertility could be due to the differences in the alleles derived from the recurrent parent.
... Though PPRs are encoded by nuclear genome, they are mostly targeted to either mitochondria or plastids for their functions [4] and thus play an important role in organeller gene regulation. By using classical genetic screens, number of PPR mutants have been characterized with varied phenotypes ranging from those showing photosynthetic defect [5] to restricted growth [6], defective seed and embryo development [7], aberrant leaf growth [8] and restoration of pollen fertility [9]; implying the role of PPRs as sequence specific RNA binding proteins in organelles. Other reports also suggest important role of PPR and these includes, abnormal splicing of chloroplast targeted PPR encoding Rpl2 gene in rice resulted in mutant with white stripe leaf (WSL mutant) characterized by enhanced sensitivity to abiotic stresses and chlorotic striations during its early development [10], Rf1A in rice functions in atp6 mRNA editing [11], RPF2 affects mitochondrial nad9 and cox3 mRNAs in arabidopsis [12] and so on. ...
... Volume 7 @BULLET Issue 3 @BULLET 1000203 J Data Mining Genomics Proteomics ISSN: 2153-0602 JDMGP, an open access journal Citation: Kaur P, Verma M, Chaduvula PK, Saxena S, Baliyan N, et al. (2016) Insights into PPR Gene Family in Cajanus cajan and Other Legume Species. J Data Mining Genomics Proteomics 7: 203. ...
... These include genes for respiratory pathway, photosynthesis, mRNA maturation etc. To possess an organelle localization feature, N Citation: Kaur P, Verma M, Chaduvula PK, Saxena S, Baliyan N, et al. (2016) Insights into PPR Gene Family in Cajanus cajan and Other Legume Species. J Data Mining Genomics Proteomics 7: 203. ...
PPR proteins comprises of several hundred members among land plants and govern a fascinating array of functions in organeller genomes that ranges from participation in stabilization of organeller transcripts, RNA editing to fertility restoration of CMS lines. Despite the availability of genome sequences of several legume species, comprehensive cataloguing of members of PPR gene family has not been carried out. In the current study, we identified 523, 830, 534,
816, 441 and 677 PPR proteins in Cajanus, Glycine, Phaseolus, Medicago, Vigna and Cicer genomes, respectively and their complete
in silico categorization was undertaken to classify them into various sub-classes and their localization prediction. Chromosomal coordinates of 271 Cajanus PPR genes were predicted and their homologues were identified in 5 other legumes revealing extensive genome conservation. PPR genes of all 6 legume species were further probed to identify restorer of fertility-like PPRs (RFLs) on the basis of protein clustering and followed by homology searches to already known Rf-PPR genes. Seventy RFL PPR genes (P sub-class) were identified and were scrutinized by phylogenetic analysis which revealed extended similarity and common features shared by these RFLs across the
species. Some of these RFL PPRs were present as small clusters in
Glycine, Phaseolus, Vigna and Cicer genomes. This study has generated a knowledge base about PPR gene family in legumes and opens several avenues for future investigations into their molecular functions, evolutionary relationships and their potential in identifying markers to enable cloning of Rf genes.
