The Experts below are selected from a list of 1647 Experts worldwide ranked by ideXlab platform

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

  • single molecule real time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research
    BMC Genomics, 2015
    Co-Authors: Lingli Dong, Hongfang Liu, Juncheng Zhang, Shuangjuan Yang, Guanyi Kong, Jeffrey Shihchieh Chu, Nansheng Chen, Daowen Wang
    Abstract:

    The large and complex hexaploid genome has greatly hindered genomics studies of common wheat (Triticum aestivum, AABBDD). Here, we investigated transcripts in common wheat developing caryopses using the emerging single-molecule real-time (SMRT) sequencing technology PacBio RSII, and assessed the resultant data for improving common wheat genome annotation and grain transcriptome research. We obtained 197,709 full-length non-chimeric (FLNC) reads, 74.6 % of which were estimated to carry complete open reading frame. A total of 91,881 high-quality FLNC reads were identified and mapped to 16,188 chromosomal loci, corresponding to 13,162 known genes and 3026 new genes not annotated previously. Although some FLNC reads could not be unambiguously mapped to the current draft genome sequence, many of them are likely useful for studying highly similar homoeologous or paralogous loci or for improving chromosomal contig assembly in further research. The 91,881 high-quality FLNC reads represented 22,768 unique transcripts, 9591 of which were newly discovered. We found 180 transcripts each spanning two or three previously annotated adjacent loci, suggesting that they should be merged to form correct gene models. Finally, our data facilitated the identification of 6030 genes differentially regulated during Caryopsis development, and full-length transcripts for 72 transcribed gluten gene members that are important for the end-use quality control of common wheat. Our work demonstrated the value of PacBio transcript sequencing for improving common wheat genome annotation through uncovering the loci and full-length transcripts not discovered previously. The resource obtained may aid further structural genomics and grain transcriptome studies of common wheat.

  • Additional file 9: of Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research
    2015
    Co-Authors: Lingli Dong, Hongfang Liu, Juncheng Zhang, Shuangjuan Yang, Guanyi Kong, Nansheng Chen, Jeffrey Chu, Daowen Wang
    Abstract:

    List of 6030 genes with differentially expressed transcripts during Caryopsis development. (XLSX 546 kb

Maree Brennan - One of the best experts on this subject based on the ideXlab platform.

  • the quality of barley husk Caryopsis adhesion is not correlated with Caryopsis cuticle permeability
    Journal of Plant Physiology, 2019
    Co-Authors: Maree Brennan, Linda Paterson, Anis Amalin Assaadah Baharudin, Maria Staniszmigal, Peter N Hoebe
    Abstract:

    Abstract Adhesion of the barley husk to the underlying Caryopsis requires the development of a cuticular cementing layer on the Caryopsis surface. Differences in adhesion quality among genotypes have previously been correlated with cementing layer composition, which is thought to influence Caryopsis cuticle permeability, the hypothesised mechanism of adhesion mediation. It is not yet known whether differences in adhesion quality among genotypes are determined by changes in Caryopsis cuticle permeability. We examined changes in candidate cementing layer biosynthetic and regulatory genes to investigate the genetic mechanisms behind husk adhesion quality. We used both commercially relevant UK malting cultivars and older European lines to ensure phenotypic diversity in adhesion quality. An ethylene responsive transcription factor (NUD) is required for the development of the cementing layer. To examine correlations between gene expression, cementing layer permeability and husk adhesion quality we also treated cultivars with ethephon (2-chloroethylphosphonic acid) which breaks down to ethylene, and silver thiosulphate which inhibits ethylene reception, and measured Caryopsis cuticle permeability. Differential adhesion qualities among genotypes are not determined by NUD expression during development of the cementing material alone, but could result from differences in biosynthetic gene expression during cementing layer development in response to longer-term NUD expression patterns. Altered Caryopsis cuticle permeability does result in altered adhesion quality, but the correlation is not consistently positive or negative. Cuticle permeability is therefore not the mechanism that determines husk adhesion quality, but is likely a consequence of the required cuticular compositional changes that determine adhesion.

  • use of raman microspectroscopy to predict malting barley husk adhesion quality
    Plant Physiology and Biochemistry, 2019
    Co-Authors: Maree Brennan, Alison Mcdonald, Cairistiona F E Topp
    Abstract:

    Abstract Good quality husk-Caryopsis adhesion is essential for malting barley, but that quality is influenced by Caryopsis surface lipid composition. Raman spectroscopy was applied to lipid extracts from barley caryopses of cultivars with differential adhesion qualities. Principal component regression indicated that Raman spectroscopy can distinguish among cultivars with good and poor quality adhesion due to differences in compounds associated with adhesion quality.

  • Table_3_Development and Quality of Barley Husk Adhesion Correlates With Changes in Caryopsis Cuticle Biosynthesis and Composition.XLSX
    2019
    Co-Authors: Maree Brennan, Cairistiona F E Topp, Pete E. Hedley, Jenny Morris, Luke Ramsay, Steve Mitchell, Tom Shepherd, William T. B. Thomas, Stephen P. Hoad
    Abstract:

    The caryopses of barley become firmly adhered to the husk during grain development through a cuticular cementing layer on the Caryopsis surface. The degree of this attachment varies among cultivars, with poor quality adhesion causing “skinning”, an economically significant grain quality defect for the malting industry. Malting cultivars encompassing a range of husk adhesion qualities were grown under a misting treatment known to induce skinning. Development of the cementing layer was examined by electron microscopy and compositional changes of the cementing layer were investigated with gas-chromatography followed by mass spectroscopy. Changes in gene expression during adhesion development were examined with a custom barley microarray. The abundance of transcripts involved early in cuticular lipid biosynthesis, including those encoding acetyl-CoA carboxylase, and all four members of the fatty acid elongase complex of enzymes, was significantly higher earlier in Caryopsis development than later. Genes associated with subsequent cuticular lipid biosynthetic pathways were also expressed higher early in development, including the decarbonylation and reductive pathways, and sterol biosynthesis. Changes in cuticular composition indicate that lowered proportions of alkanes and higher proportions of fatty acids are associated with development of good quality husk adhesion, in addition to higher proportions of sterols.

  • Development and Quality of Barley Husk Adhesion Correlates With Changes in Caryopsis Cuticle Biosynthesis and Composition
    Frontiers Media S.A., 2019
    Co-Authors: Maree Brennan, Cairistiona F E Topp, Pete E. Hedley, Jenny Morris, Luke Ramsay, Steve Mitchell, Tom Shepherd, William T. B. Thomas, Stephen P. Hoad
    Abstract:

    The caryopses of barley become firmly adhered to the husk during grain development through a cuticular cementing layer on the Caryopsis surface. The degree of this attachment varies among cultivars, with poor quality adhesion causing “skinning”, an economically significant grain quality defect for the malting industry. Malting cultivars encompassing a range of husk adhesion qualities were grown under a misting treatment known to induce skinning. Development of the cementing layer was examined by electron microscopy and compositional changes of the cementing layer were investigated with gas-chromatography followed by mass spectroscopy. Changes in gene expression during adhesion development were examined with a custom barley microarray. The abundance of transcripts involved early in cuticular lipid biosynthesis, including those encoding acetyl-CoA carboxylase, and all four members of the fatty acid elongase complex of enzymes, was significantly higher earlier in Caryopsis development than later. Genes associated with subsequent cuticular lipid biosynthetic pathways were also expressed higher early in development, including the decarbonylation and reductive pathways, and sterol biosynthesis. Changes in cuticular composition indicate that lowered proportions of alkanes and higher proportions of fatty acids are associated with development of good quality husk adhesion, in addition to higher proportions of sterols

Nansheng Chen - One of the best experts on this subject based on the ideXlab platform.

  • single molecule real time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research
    BMC Genomics, 2015
    Co-Authors: Lingli Dong, Hongfang Liu, Juncheng Zhang, Shuangjuan Yang, Guanyi Kong, Jeffrey Shihchieh Chu, Nansheng Chen, Daowen Wang
    Abstract:

    The large and complex hexaploid genome has greatly hindered genomics studies of common wheat (Triticum aestivum, AABBDD). Here, we investigated transcripts in common wheat developing caryopses using the emerging single-molecule real-time (SMRT) sequencing technology PacBio RSII, and assessed the resultant data for improving common wheat genome annotation and grain transcriptome research. We obtained 197,709 full-length non-chimeric (FLNC) reads, 74.6 % of which were estimated to carry complete open reading frame. A total of 91,881 high-quality FLNC reads were identified and mapped to 16,188 chromosomal loci, corresponding to 13,162 known genes and 3026 new genes not annotated previously. Although some FLNC reads could not be unambiguously mapped to the current draft genome sequence, many of them are likely useful for studying highly similar homoeologous or paralogous loci or for improving chromosomal contig assembly in further research. The 91,881 high-quality FLNC reads represented 22,768 unique transcripts, 9591 of which were newly discovered. We found 180 transcripts each spanning two or three previously annotated adjacent loci, suggesting that they should be merged to form correct gene models. Finally, our data facilitated the identification of 6030 genes differentially regulated during Caryopsis development, and full-length transcripts for 72 transcribed gluten gene members that are important for the end-use quality control of common wheat. Our work demonstrated the value of PacBio transcript sequencing for improving common wheat genome annotation through uncovering the loci and full-length transcripts not discovered previously. The resource obtained may aid further structural genomics and grain transcriptome studies of common wheat.

  • Additional file 9: of Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research
    2015
    Co-Authors: Lingli Dong, Hongfang Liu, Juncheng Zhang, Shuangjuan Yang, Guanyi Kong, Nansheng Chen, Jeffrey Chu, Daowen Wang
    Abstract:

    List of 6030 genes with differentially expressed transcripts during Caryopsis development. (XLSX 546 kb

Cairistiona F E Topp - One of the best experts on this subject based on the ideXlab platform.

  • use of raman microspectroscopy to predict malting barley husk adhesion quality
    Plant Physiology and Biochemistry, 2019
    Co-Authors: Maree Brennan, Alison Mcdonald, Cairistiona F E Topp
    Abstract:

    Abstract Good quality husk-Caryopsis adhesion is essential for malting barley, but that quality is influenced by Caryopsis surface lipid composition. Raman spectroscopy was applied to lipid extracts from barley caryopses of cultivars with differential adhesion qualities. Principal component regression indicated that Raman spectroscopy can distinguish among cultivars with good and poor quality adhesion due to differences in compounds associated with adhesion quality.

  • Table_3_Development and Quality of Barley Husk Adhesion Correlates With Changes in Caryopsis Cuticle Biosynthesis and Composition.XLSX
    2019
    Co-Authors: Maree Brennan, Cairistiona F E Topp, Pete E. Hedley, Jenny Morris, Luke Ramsay, Steve Mitchell, Tom Shepherd, William T. B. Thomas, Stephen P. Hoad
    Abstract:

    The caryopses of barley become firmly adhered to the husk during grain development through a cuticular cementing layer on the Caryopsis surface. The degree of this attachment varies among cultivars, with poor quality adhesion causing “skinning”, an economically significant grain quality defect for the malting industry. Malting cultivars encompassing a range of husk adhesion qualities were grown under a misting treatment known to induce skinning. Development of the cementing layer was examined by electron microscopy and compositional changes of the cementing layer were investigated with gas-chromatography followed by mass spectroscopy. Changes in gene expression during adhesion development were examined with a custom barley microarray. The abundance of transcripts involved early in cuticular lipid biosynthesis, including those encoding acetyl-CoA carboxylase, and all four members of the fatty acid elongase complex of enzymes, was significantly higher earlier in Caryopsis development than later. Genes associated with subsequent cuticular lipid biosynthetic pathways were also expressed higher early in development, including the decarbonylation and reductive pathways, and sterol biosynthesis. Changes in cuticular composition indicate that lowered proportions of alkanes and higher proportions of fatty acids are associated with development of good quality husk adhesion, in addition to higher proportions of sterols.

  • Development and Quality of Barley Husk Adhesion Correlates With Changes in Caryopsis Cuticle Biosynthesis and Composition
    Frontiers Media S.A., 2019
    Co-Authors: Maree Brennan, Cairistiona F E Topp, Pete E. Hedley, Jenny Morris, Luke Ramsay, Steve Mitchell, Tom Shepherd, William T. B. Thomas, Stephen P. Hoad
    Abstract:

    The caryopses of barley become firmly adhered to the husk during grain development through a cuticular cementing layer on the Caryopsis surface. The degree of this attachment varies among cultivars, with poor quality adhesion causing “skinning”, an economically significant grain quality defect for the malting industry. Malting cultivars encompassing a range of husk adhesion qualities were grown under a misting treatment known to induce skinning. Development of the cementing layer was examined by electron microscopy and compositional changes of the cementing layer were investigated with gas-chromatography followed by mass spectroscopy. Changes in gene expression during adhesion development were examined with a custom barley microarray. The abundance of transcripts involved early in cuticular lipid biosynthesis, including those encoding acetyl-CoA carboxylase, and all four members of the fatty acid elongase complex of enzymes, was significantly higher earlier in Caryopsis development than later. Genes associated with subsequent cuticular lipid biosynthetic pathways were also expressed higher early in development, including the decarbonylation and reductive pathways, and sterol biosynthesis. Changes in cuticular composition indicate that lowered proportions of alkanes and higher proportions of fatty acids are associated with development of good quality husk adhesion, in addition to higher proportions of sterols

Lingli Dong - One of the best experts on this subject based on the ideXlab platform.

  • single molecule real time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research
    BMC Genomics, 2015
    Co-Authors: Lingli Dong, Hongfang Liu, Juncheng Zhang, Shuangjuan Yang, Guanyi Kong, Jeffrey Shihchieh Chu, Nansheng Chen, Daowen Wang
    Abstract:

    The large and complex hexaploid genome has greatly hindered genomics studies of common wheat (Triticum aestivum, AABBDD). Here, we investigated transcripts in common wheat developing caryopses using the emerging single-molecule real-time (SMRT) sequencing technology PacBio RSII, and assessed the resultant data for improving common wheat genome annotation and grain transcriptome research. We obtained 197,709 full-length non-chimeric (FLNC) reads, 74.6 % of which were estimated to carry complete open reading frame. A total of 91,881 high-quality FLNC reads were identified and mapped to 16,188 chromosomal loci, corresponding to 13,162 known genes and 3026 new genes not annotated previously. Although some FLNC reads could not be unambiguously mapped to the current draft genome sequence, many of them are likely useful for studying highly similar homoeologous or paralogous loci or for improving chromosomal contig assembly in further research. The 91,881 high-quality FLNC reads represented 22,768 unique transcripts, 9591 of which were newly discovered. We found 180 transcripts each spanning two or three previously annotated adjacent loci, suggesting that they should be merged to form correct gene models. Finally, our data facilitated the identification of 6030 genes differentially regulated during Caryopsis development, and full-length transcripts for 72 transcribed gluten gene members that are important for the end-use quality control of common wheat. Our work demonstrated the value of PacBio transcript sequencing for improving common wheat genome annotation through uncovering the loci and full-length transcripts not discovered previously. The resource obtained may aid further structural genomics and grain transcriptome studies of common wheat.

  • Additional file 9: of Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research
    2015
    Co-Authors: Lingli Dong, Hongfang Liu, Juncheng Zhang, Shuangjuan Yang, Guanyi Kong, Nansheng Chen, Jeffrey Chu, Daowen Wang
    Abstract:

    List of 6030 genes with differentially expressed transcripts during Caryopsis development. (XLSX 546 kb