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Jisen Zhang - One of the best experts on this subject based on the ideXlab platform.

  • Evolutionary expansion and functional divergence of sugar transporters in Saccharum (S. spontaneum and S. officinarum).
    The Plant journal : for cell and molecular biology, 2020
    Co-Authors: Qing Zhang, Xiuting Hua, Ray Ming, Zhengchao Wang, Muqing Zhang, Hong Liu, Yuan Yuan, Yan Shi, Jisen Zhang
    Abstract:

    The sugar transporter (ST) family is considered to be the most important gene family for sugar accumulation, but limited information about the ST family in the important sugar-yielding crop Saccharum is available due to its complex genetic background. Here, 105 ST genes were identified and clustered into eight subfamilies in Saccharum spontaneum. Comparative genomics revealed that tandem duplication events contributed to ST gene expansions of two subfamilies, PLT and STP, in S. spontaneum, indicating an early evolutionary step towards high sugar content in Saccharum. The analyses of expression patterns were based on four large datasets with a total of 226 RNA sequencing samples from S. spontaneum and Saccharum officinarum. The results clearly demonstrated 50 ST genes had different spatiotemporal expression patterns in leaf tissues, 10 STs were specifically expressed in the stem, and 10 STs responded to the diurnal rhythm. Heterologous expression experiments in the defective yeast strain EBY.VW4000 indicated STP13, pGlcT2, VGT3, and TMT4 are the STs with most affinity for glucose/fructose and SUT1_T1 has the highest affinity to sucrose. Furthermore, metabolomics analysis suggested STP7 is a sugar starvation-induced gene and STP13 has a function in retrieving sugar in senescent tissues. PLT11, PLT11_T1, TMT3, and TMT4 contributed to breaking the limitations of the storage sink. SUT1, SUT1_T1, PLT11, TMT4, pGlcT2, and VGT3 responded for different functions in these two Saccharum species. This study demonstrated the evolutionary expansion and functional divergence of the ST gene family and will enable the further investigation of the molecular mechanism of sugar metabolism in Saccharum.

  • comparative analysis of sucrose phosphate synthase sps gene family between Saccharum officinarum and Saccharum spontaneum
    BMC Plant Biology, 2020
    Co-Authors: Xingtan Zhang, Qing Zhang, Xiuting Hua, Ray Ming, Lanping Chen, Qian Zhao, Zhengchao Wang, Haibao Tang, Muqing Zhang, Jisen Zhang
    Abstract:

    Background Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum, generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. Results In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum, respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum species as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem (SPSA) and leaf (SPSB) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. Conclusions SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum.

  • Identification and Characterization of microRNAs from Saccharum officinarum L by Deep Sequencing
    Tropical Plant Biology, 2017
    Co-Authors: Aijuan Xue, Qing Zhang, Xingtan Zhang, Ray Ming, Muchen Cai, Jisen Zhang
    Abstract:

    In modern sugarcane cultivars, around 70–80% of the genetic information originates from Saccharum officinarum, which contributed important sugar content traits. Although several studies have identified microRNAs in Saccharum hybrids, they have not yet been studied in S. officinarum. In this study, by deep sequencing and in silico approaches, 268 miRNA candidates were predicted in S. officinarum, and 52 were found to likely be real miRNAs based on our analysis with stringent criteria. Among these 52 miRNAs, 43 miRNAs from 26 miRNA families were found to have homologous miRNAs in public miRBase Release 21, and 9 miRNAs were identified to be novel in S. officinarum. Out of the 52 miRNAs, 6 were randomly chosen and verified by stem-loop RT-PCR. The 52 miRNAs were predicted to have 237 and 76 targets in sugarcane and sorghum, respectively, including auxin response factor, MADS-box transcription factor, zinc finger-like protein. MicroRNAs were found to be involved in critical sugarcane pathways, such as sucrose metabolism and cellulose metabolism. In addition, the first miRNA (sof-novel1) derived from the Saccharum chloroplast genome was identified. These results provide the foundation for future studies to distinguish the miRNAs from S. spontaneum and S. officinarum in Saccharum hybrid, and valuable information to further study the miRNA functions in Saccharum species.

  • Evolution and expression of the fructokinase gene family in Saccharum.
    BMC genomics, 2017
    Co-Authors: Yihong Chen, Qing Zhang, Xingtan Zhang, Liming Wang, Xiuting Hua, Ray Ming, Jisen Zhang
    Abstract:

    Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity. In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S. spontaneum. Phylogenetic analysis based on representative monocotyledon and dicotyledon plant species suggested that the FRK gene family is ancient and its evolutionary history can be traced in duplicated descending order: SsFRK4, SsFRK6/SsFRK7,SsFRK5, SsFRK3 and SsFRK1/SsFRK2. Among the close orthologs, the number and position of exons in FRKs were conserved; in contrast, the size of introns varied among the paralogous FRKs in Saccharum. Genomic constraints were analyzed within the gene alleles and between S. spontaneum and Sorghum bicolor, and gene expression analysis was performed under drought stress and with exogenous applications of plant hormones. FRK1, which was under strong functional constraint selection, was conserved among the gene allelic haplotypes, and displayed dominant expression levels among the gene families in the control conditions, suggesting that FRK1 plays a major role in the phosphorylation of fructose. FRK3 and FRK5 were dramatically induced under drought stress, and FRK5 was also found to increase its expression levels in the mature stage of Saccharum. Similarly, FRK3 and FRK5 were induced in response to drought stress in Saccharum. FRK2 and FRK7 displayed lower expression levels than the other FRK family members; FRK2 was under strong genomic selection constraints whereas FRK7 was under neutral selection. FRK7 may have become functionally redundant in Saccharum through pseudogenization. FRK4 and FRK6 shared the most similar expression pattern: FRK4 was revealed to have higher expression levels in mature tissues than in premature tissues of Saccharum, and FRK6 presented a slight increase under drought stress. Our study presents a comprehensive genomic study of the entire FRK gene family in Saccharum, providing the foundations for approaches to characterize the molecular mechanism regulated by the SsFRK family in sugarcane.

  • Additional file 5: of Evolution and expression of the fructokinase gene family in Saccharum
    2017
    Co-Authors: Yihong Chen, Qing Zhang, Xingtan Zhang, Liming Wang, Xiuting Hua, Ray Ming, Jisen Zhang
    Abstract:

    Heatmap of the expression levels of SsFRK gene family members under ABA treatment. SR: S. robustum Molokai6081; SS: S. spontaneum SES208; SO: S. officinarum LA Purple; SH: hybrid cultivar ROC-22; IN: internode; LR: leaf roll; LF: leaf. Internnodes 3,9,15, internnodes 3,9,15, internodes 3,8,13 and internodes 3, 6, 9 were from Saccharum officinarum (LA Purple), ROC-22, Saccharum robustum (Molokai6081) and Saccharum spontaneum (SES208), respectively. (PPTX 205 kb

Angélique D'hont - One of the best experts on this subject based on the ideXlab platform.

  • Molecular insights into the origin of the brown rust resistance gene Bru1 among Saccharum species.
    TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2017
    Co-Authors: Heng-bo Wang, Chen Pinghua, Yan-qing Yang, Angélique D'hont
    Abstract:

    Key message Analysis of 387 sugarcane clones using Bru 1 diagnostic markers revealed two possible sources of Bru 1 in Chinese cultivars: one from Saccharum spontaneum and another from Saccharum robustum of New Guinea.

  • Inter-Alu-like species-specific sequences in the Saccharum complex
    Theoretical and Applied Genetics, 1999
    Co-Authors: Karine Alix, Jean-christophe Glaszmann, Florence Paulet, Angélique D'hont
    Abstract:

    Alu sequences constitute the most abundant family of short interspersed nuclear elements, SINEs, in the primate genome. The Alu-PCR method, which consists of amplification between Alu sequences, is usually applied in human genetics to provide polymorphic markers. Here we report the presence of Alu-like sequences in sugarcane and related species by applying the Alu-PCR-like method. Amplifications using a PCR primer defined in conserved regions of Alu human sequences lead to specific complex multiband profiles in all the Saccharum and related genera clones surveyed. The isolation and characterisation of the amplified genus-specific inter-Alu-like fragments allowed us to isolate repeated sequences that are specific for different genera of the Saccharum complex: MsCIR2 from Miscanthus, EaCIR6 and EaCIR7 from Erianthus, and SrCIR2 from Saccharum. Two PCR diagnostic tests were developed from the inter-Alu-like sequences MsCIR2 and EaCIR6, and proved efficient in identifying intergeneric hybrids Saccharum×Miscanthus or Saccharum×Erianthus, respectively. The present study illustrates how the Alu-PCR-like method could help investigating the origin of amphiploid species and monitoring introgression in plants.

  • Isolation and characterization of a satellite DNA family in the Saccharum complex
    Genome, 1998
    Co-Authors: Karine Alix, Franc-christophe Baurens, Jean-christophe Glaszmann, Florence Paulet, Angélique D'hont
    Abstract:

    EaCIR1, a 371-bp Erianthus-specific satellite DNA sequence, was cloned from TaqI restricted genomic DNA after agarose-gel electrophoresis. This sequence has 77% homology with a 365-bp satellite of Helictotrichon convolutum and 72% homology with a 353-bp tandem repeat sequence from Oryza sativa. PCR primers defined in the conserved regions of these repetitive sequences were used to isolate other satellite DNAs in different representatives of the Saccharum complex: SoCIR1 in Saccharum officinarum, SrCIR1 in Saccharum robustum, SsCIR1 and SsCIR2 in Saccharum spontaneum, and MsCIR1 in Miscanthus sinensis. EaCIR1 and SoCIR1 were localized to subtelomeric regions of the chromosomes by fluorescence in situ hybridization. Southern hybridization experiments, using two representatives of this repeat sequence family as probes, illustrated contrasting species-specificity and demonstrated the existence of similar repetitive elements in sorghum and maize.Key words: satellite DNA, sugarcane, Saccharum complex, Gramineae...

  • Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes
    Genome, 1998
    Co-Authors: Angélique D'hont, Karine Alix, David Ison, Catherine Roux, Jean-christophe Glaszmann
    Abstract:

    18S-5.6S-25S and 5S ribosomal DNA (rDNA) sites were located by in situ hybridization to the three main species of the Saccharum genus. For each species and each rDNA family, the position and number of sites in the various cytotypes suggested the presence of one locus and basic chromosome numbers of 10 for Saccharum officinarum and Saccharum robustum and\i 8 forSaccharum spontaneum. The implications of these results for the genetic maps of modern cultivars derived from crosses between the species S. officinarum and S. spontaneum are discussed.Key words: sugarcane, Saccharum, 18S-5.6S-25S rRNA, 5S rRNA, basic chromosome number, in situ hybridization.

  • A satellite DNA family in the Saccharum complex
    1998
    Co-Authors: Karine Alix, Franc-christophe Baurens, Jean-christophe Glaszmann, Angélique D'hont
    Abstract:

    The search for species-specific repeat sequences was initiated to provide a new molecular tool to investigate the phylogenetic relationships within the #Saccharum# complex, and to monitor introgression programs carried out in sugarcane breeding. Taq1 digested genomic DNA, separated by electrophoresis, facilitated identification of a 371 bp #Erianthus#-specific satellite DNA, EACIR1, which shows high sequence homology to other #Gramineae# satellite DNAs. PCR primers defined in the conserved regions of these various sequences were used to isolate another repetitive sequence, SOCIR1, a 361 bp #Saccharum#-specific satellite DNA. EACIR1 and SOCIR1 were localized to subtelomeric regions of chromosomes by #in situ# hybridization. The occurence of this satellite family in the #Saccharum# complex and in #Gramineae# species, was investigated by PCR and Southern hybridization experiments. The results were in accordance with previous phylogenetic schemes of the #Saccharum# complex, and demonstrated the existence of similar repetitive sequences in sorghum and maize. These satellite sequences could provide useful PCR markers to determine the pedigree of putative hybrids implicated in sugarcane introgression programs. (Texte integral)

Jianping Wang - One of the best experts on this subject based on the ideXlab platform.

  • Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane
    BMC Evolutionary Biology, 2019
    Co-Authors: Dyfed Lloyd Evans, Shailesh Joshi, Jianping Wang
    Abstract:

    For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ‘Saccharum Complex’, an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are 8 million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the ‘Saccharum complex’ to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.

  • Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane
    BMC, 2019
    Co-Authors: Dyfed Lloyd Evans, Shailesh V. Joshi, Jianping Wang
    Abstract:

    Abstract Background For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ‘Saccharum Complex’, an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. Results Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. Conclusion For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are 8 million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the ‘Saccharum complex’ to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae

  • Natural Allelic Variations in Highly Polyploidy Saccharum Complex.
    Frontiers in plant science, 2016
    Co-Authors: Jian Song, Jack C. Comstock, Jisen Zhang, Xiping Yang, Marcio F. R. Resende, Leandro G. Neves, James Todd, Jianping Wang
    Abstract:

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90 %. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.

Karine Alix - One of the best experts on this subject based on the ideXlab platform.

  • Inter-Alu-like species-specific sequences in the Saccharum complex
    Theoretical and Applied Genetics, 1999
    Co-Authors: Karine Alix, Jean-christophe Glaszmann, Florence Paulet, Angélique D'hont
    Abstract:

    Alu sequences constitute the most abundant family of short interspersed nuclear elements, SINEs, in the primate genome. The Alu-PCR method, which consists of amplification between Alu sequences, is usually applied in human genetics to provide polymorphic markers. Here we report the presence of Alu-like sequences in sugarcane and related species by applying the Alu-PCR-like method. Amplifications using a PCR primer defined in conserved regions of Alu human sequences lead to specific complex multiband profiles in all the Saccharum and related genera clones surveyed. The isolation and characterisation of the amplified genus-specific inter-Alu-like fragments allowed us to isolate repeated sequences that are specific for different genera of the Saccharum complex: MsCIR2 from Miscanthus, EaCIR6 and EaCIR7 from Erianthus, and SrCIR2 from Saccharum. Two PCR diagnostic tests were developed from the inter-Alu-like sequences MsCIR2 and EaCIR6, and proved efficient in identifying intergeneric hybrids Saccharum×Miscanthus or Saccharum×Erianthus, respectively. The present study illustrates how the Alu-PCR-like method could help investigating the origin of amphiploid species and monitoring introgression in plants.

  • Isolation and characterization of a satellite DNA family in the Saccharum complex
    Genome, 1998
    Co-Authors: Karine Alix, Franc-christophe Baurens, Jean-christophe Glaszmann, Florence Paulet, Angélique D'hont
    Abstract:

    EaCIR1, a 371-bp Erianthus-specific satellite DNA sequence, was cloned from TaqI restricted genomic DNA after agarose-gel electrophoresis. This sequence has 77% homology with a 365-bp satellite of Helictotrichon convolutum and 72% homology with a 353-bp tandem repeat sequence from Oryza sativa. PCR primers defined in the conserved regions of these repetitive sequences were used to isolate other satellite DNAs in different representatives of the Saccharum complex: SoCIR1 in Saccharum officinarum, SrCIR1 in Saccharum robustum, SsCIR1 and SsCIR2 in Saccharum spontaneum, and MsCIR1 in Miscanthus sinensis. EaCIR1 and SoCIR1 were localized to subtelomeric regions of the chromosomes by fluorescence in situ hybridization. Southern hybridization experiments, using two representatives of this repeat sequence family as probes, illustrated contrasting species-specificity and demonstrated the existence of similar repetitive elements in sorghum and maize.Key words: satellite DNA, sugarcane, Saccharum complex, Gramineae...

  • Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes
    Genome, 1998
    Co-Authors: Angélique D'hont, Karine Alix, David Ison, Catherine Roux, Jean-christophe Glaszmann
    Abstract:

    18S-5.6S-25S and 5S ribosomal DNA (rDNA) sites were located by in situ hybridization to the three main species of the Saccharum genus. For each species and each rDNA family, the position and number of sites in the various cytotypes suggested the presence of one locus and basic chromosome numbers of 10 for Saccharum officinarum and Saccharum robustum and\i 8 forSaccharum spontaneum. The implications of these results for the genetic maps of modern cultivars derived from crosses between the species S. officinarum and S. spontaneum are discussed.Key words: sugarcane, Saccharum, 18S-5.6S-25S rRNA, 5S rRNA, basic chromosome number, in situ hybridization.

  • A satellite DNA family in the Saccharum complex
    1998
    Co-Authors: Karine Alix, Franc-christophe Baurens, Jean-christophe Glaszmann, Angélique D'hont
    Abstract:

    The search for species-specific repeat sequences was initiated to provide a new molecular tool to investigate the phylogenetic relationships within the #Saccharum# complex, and to monitor introgression programs carried out in sugarcane breeding. Taq1 digested genomic DNA, separated by electrophoresis, facilitated identification of a 371 bp #Erianthus#-specific satellite DNA, EACIR1, which shows high sequence homology to other #Gramineae# satellite DNAs. PCR primers defined in the conserved regions of these various sequences were used to isolate another repetitive sequence, SOCIR1, a 361 bp #Saccharum#-specific satellite DNA. EACIR1 and SOCIR1 were localized to subtelomeric regions of chromosomes by #in situ# hybridization. The occurence of this satellite family in the #Saccharum# complex and in #Gramineae# species, was investigated by PCR and Southern hybridization experiments. The results were in accordance with previous phylogenetic schemes of the #Saccharum# complex, and demonstrated the existence of similar repetitive sequences in sorghum and maize. These satellite sequences could provide useful PCR markers to determine the pedigree of putative hybrids implicated in sugarcane introgression programs. (Texte integral)

Ray Ming - One of the best experts on this subject based on the ideXlab platform.

  • Evolutionary expansion and functional divergence of sugar transporters in Saccharum (S. spontaneum and S. officinarum).
    The Plant journal : for cell and molecular biology, 2020
    Co-Authors: Qing Zhang, Xiuting Hua, Ray Ming, Zhengchao Wang, Muqing Zhang, Hong Liu, Yuan Yuan, Yan Shi, Jisen Zhang
    Abstract:

    The sugar transporter (ST) family is considered to be the most important gene family for sugar accumulation, but limited information about the ST family in the important sugar-yielding crop Saccharum is available due to its complex genetic background. Here, 105 ST genes were identified and clustered into eight subfamilies in Saccharum spontaneum. Comparative genomics revealed that tandem duplication events contributed to ST gene expansions of two subfamilies, PLT and STP, in S. spontaneum, indicating an early evolutionary step towards high sugar content in Saccharum. The analyses of expression patterns were based on four large datasets with a total of 226 RNA sequencing samples from S. spontaneum and Saccharum officinarum. The results clearly demonstrated 50 ST genes had different spatiotemporal expression patterns in leaf tissues, 10 STs were specifically expressed in the stem, and 10 STs responded to the diurnal rhythm. Heterologous expression experiments in the defective yeast strain EBY.VW4000 indicated STP13, pGlcT2, VGT3, and TMT4 are the STs with most affinity for glucose/fructose and SUT1_T1 has the highest affinity to sucrose. Furthermore, metabolomics analysis suggested STP7 is a sugar starvation-induced gene and STP13 has a function in retrieving sugar in senescent tissues. PLT11, PLT11_T1, TMT3, and TMT4 contributed to breaking the limitations of the storage sink. SUT1, SUT1_T1, PLT11, TMT4, pGlcT2, and VGT3 responded for different functions in these two Saccharum species. This study demonstrated the evolutionary expansion and functional divergence of the ST gene family and will enable the further investigation of the molecular mechanism of sugar metabolism in Saccharum.

  • comparative analysis of sucrose phosphate synthase sps gene family between Saccharum officinarum and Saccharum spontaneum
    BMC Plant Biology, 2020
    Co-Authors: Xingtan Zhang, Qing Zhang, Xiuting Hua, Ray Ming, Lanping Chen, Qian Zhao, Zhengchao Wang, Haibao Tang, Muqing Zhang, Jisen Zhang
    Abstract:

    Background Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum, generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. Results In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum, respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum species as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem (SPSA) and leaf (SPSB) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. Conclusions SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum.

  • Identification and Characterization of microRNAs from Saccharum officinarum L by Deep Sequencing
    Tropical Plant Biology, 2017
    Co-Authors: Aijuan Xue, Qing Zhang, Xingtan Zhang, Ray Ming, Muchen Cai, Jisen Zhang
    Abstract:

    In modern sugarcane cultivars, around 70–80% of the genetic information originates from Saccharum officinarum, which contributed important sugar content traits. Although several studies have identified microRNAs in Saccharum hybrids, they have not yet been studied in S. officinarum. In this study, by deep sequencing and in silico approaches, 268 miRNA candidates were predicted in S. officinarum, and 52 were found to likely be real miRNAs based on our analysis with stringent criteria. Among these 52 miRNAs, 43 miRNAs from 26 miRNA families were found to have homologous miRNAs in public miRBase Release 21, and 9 miRNAs were identified to be novel in S. officinarum. Out of the 52 miRNAs, 6 were randomly chosen and verified by stem-loop RT-PCR. The 52 miRNAs were predicted to have 237 and 76 targets in sugarcane and sorghum, respectively, including auxin response factor, MADS-box transcription factor, zinc finger-like protein. MicroRNAs were found to be involved in critical sugarcane pathways, such as sucrose metabolism and cellulose metabolism. In addition, the first miRNA (sof-novel1) derived from the Saccharum chloroplast genome was identified. These results provide the foundation for future studies to distinguish the miRNAs from S. spontaneum and S. officinarum in Saccharum hybrid, and valuable information to further study the miRNA functions in Saccharum species.

  • Evolution and expression of the fructokinase gene family in Saccharum.
    BMC genomics, 2017
    Co-Authors: Yihong Chen, Qing Zhang, Xingtan Zhang, Liming Wang, Xiuting Hua, Ray Ming, Jisen Zhang
    Abstract:

    Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity. In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S. spontaneum. Phylogenetic analysis based on representative monocotyledon and dicotyledon plant species suggested that the FRK gene family is ancient and its evolutionary history can be traced in duplicated descending order: SsFRK4, SsFRK6/SsFRK7,SsFRK5, SsFRK3 and SsFRK1/SsFRK2. Among the close orthologs, the number and position of exons in FRKs were conserved; in contrast, the size of introns varied among the paralogous FRKs in Saccharum. Genomic constraints were analyzed within the gene alleles and between S. spontaneum and Sorghum bicolor, and gene expression analysis was performed under drought stress and with exogenous applications of plant hormones. FRK1, which was under strong functional constraint selection, was conserved among the gene allelic haplotypes, and displayed dominant expression levels among the gene families in the control conditions, suggesting that FRK1 plays a major role in the phosphorylation of fructose. FRK3 and FRK5 were dramatically induced under drought stress, and FRK5 was also found to increase its expression levels in the mature stage of Saccharum. Similarly, FRK3 and FRK5 were induced in response to drought stress in Saccharum. FRK2 and FRK7 displayed lower expression levels than the other FRK family members; FRK2 was under strong genomic selection constraints whereas FRK7 was under neutral selection. FRK7 may have become functionally redundant in Saccharum through pseudogenization. FRK4 and FRK6 shared the most similar expression pattern: FRK4 was revealed to have higher expression levels in mature tissues than in premature tissues of Saccharum, and FRK6 presented a slight increase under drought stress. Our study presents a comprehensive genomic study of the entire FRK gene family in Saccharum, providing the foundations for approaches to characterize the molecular mechanism regulated by the SsFRK family in sugarcane.

  • Additional file 5: of Evolution and expression of the fructokinase gene family in Saccharum
    2017
    Co-Authors: Yihong Chen, Qing Zhang, Xingtan Zhang, Liming Wang, Xiuting Hua, Ray Ming, Jisen Zhang
    Abstract:

    Heatmap of the expression levels of SsFRK gene family members under ABA treatment. SR: S. robustum Molokai6081; SS: S. spontaneum SES208; SO: S. officinarum LA Purple; SH: hybrid cultivar ROC-22; IN: internode; LR: leaf roll; LF: leaf. Internnodes 3,9,15, internnodes 3,9,15, internodes 3,8,13 and internodes 3, 6, 9 were from Saccharum officinarum (LA Purple), ROC-22, Saccharum robustum (Molokai6081) and Saccharum spontaneum (SES208), respectively. (PPTX 205 kb