The first Illumina-based de novo transcriptome analysis and molecular marker development in Napier grass (Pennisetum purpureum)

Zhou, Sifan; Wang, Chengran; Frazier, Taylor P.; Yan, Haidong; Chen, Peilin; Chen, Zhihong; Huang, Linkai; Zhang, Xinquan; Yan, Peng; Ma, Xiao; Yan, Yanhong

doi:10.1007/s11032-018-0852-8

Cited by 28 publications

(20 citation statements)

References 97 publications

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“…Moreover, a total of 178, 330 of the 196,124 unigenes (90.93%) in the RT sample and 129,746 of the 140,766 unigenes (92.17%) in the CT sample were annotated to public databases (Nr, Nt, Swis-sProt, GO, KOG and KEGG) for comprehensive analysis Table S3). Compared with previous studies in plants of the genus Pennisetum, which reported 103,454 annotated unigenes from 197,466 unigenes [27], the present study obtained more complete annotation information.…”

Section: Discussioncontrasting

confidence: 56%

SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum

Xiang

et al. 2020

BMC Genomics

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Background: Pennisetum giganteum, an abundant, fast-growing perennial C 4 grass that belongs to the genus Pennisetum, family Poaceae, has been developed as a source of biomass for mushroom cultivation and production, as a source of forage for cattle and sheep, and as a tool to remedy soil erosion. However, having a chilling-sensitive nature, P. giganteum seedlings need to be protected while overwintering in most temperate climate regions. Results:To elucidate the cold stress responses of P. giganteum, we carried out comprehensive full-length transcriptomes from leaf and root tissues under room temperature (RT) and chilling temperature (CT) using PacBio Iso-Seq long reads. We identified 196,124 and 140,766 full-length consensus transcripts in the RT and CT samples, respectively. We then systematically performed functional annotation, transcription factor identification, long noncoding RNAs (lncRNAs) prediction, and simple sequence repeat (SSR) analysis of those full-length transcriptomes. Isoform analysis revealed that alternative splicing events may be induced by cold stress in P. giganteum, and transcript variants may be involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in P. giganteum. Furthermore, the fatty acid composition determination and gene expression level analysis supported that C18 unsaturated fatty acid biosynthesis and metabolism pathways may play roles during cold stress in P. giganteum. Conclusions:We provide the first comprehensive full-length transcriptomic resource for the abundant and fastgrowing perennial grass Pennisetum giganteum. Our results provide a useful transcriptomic resource for exploring the biological pathways involved in the cold stress responses of P. giganteum.

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Section: Discussioncontrasting

confidence: 56%

SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum

Xiang

et al. 2020

BMC Genomics

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show abstract

“…Moreover, a total of 178,330 of the 196,124 unigenes (90.93%) in the RT sample and 129,746 of the 140,766 unigenes (92.17%) in the CT sample were annotated to public databases (Nr, Nt, SwissProt, GO, KOG and KEGG) for comprehensive analysis (Supplementary Table 3). Compared with previous studies in plants of the genus Pennisetum, which reported 103,454 annotated unigenes from 197,466 unigenes [27], the present study obtained more complete annotation information.…”

Section: Giganteumcontrasting

confidence: 56%

SMRT Sequencing of a Full-length Transcriptome Reveals Transcript Variants Involved in C18 Unsaturated Fatty Acid Biosynthesis and Metabolism Pathways at Chilling Temperature in Pennisetum giganteum

Xiang²,

et al. 2019

Preprint

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Background Pennisetum giganteum, an abundant, fast-growing perennial C4 grass that belongs to the genus Pennisetum, family Poaceae, has been developed as a source of biomass for mushroom cultivation and production, as a source of forage for cattle and sheep, and as a tool to remedy soil erosion. However, having a chilling-sensitive nature, P. giganteum seedlings need to be protected while overwintering in most temperate climate regions. Results To elucidate the cold stress responses of P. giganteum, we carried out comprehensive full-length transcriptomes from leaf and root tissues under room temperature (RT) and chilling temperature (CT) using PacBio Iso-Seq long reads. We identified 196,124 and 140,766 full-length consensus transcripts in the RT and CT samples, respectively. We then systematically performed functional annotation, transcription factor identification, long non-coding RNAs (lncRNAs) prediction, and simple sequence repeat (SSR) analysis of those full-length transcriptomes. Isoform analysis revealed that alternative splicing events may be induced by cold stress in P. giganteum, and transcript variants may be involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in P. giganteum. Furthermore, the fatty acid composition determination and gene expression level analysis supported that C18 unsaturated fatty acid biosynthesis and metabolism pathways may play roles during cold stress in P. giganteum. Conclusions We provide the first comprehensive full-length transcriptomic resource for the abundant and fast-growing perennial grass Pennisetum giganteum. Our results provide a useful transcriptomic resource for exploring the biological pathways involved in the cold stress responses of P. giganteum.

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“…The DArTseq sequence reads corresponding to the SNP and SilicoDArT markers were aligned to Napier grass genomic [30] and transcriptome [31] sequences using the bwa mem sequence alignment method [32], and the sequences were annotated using the GeneBank NCBI blastx tool (https://blast. ncbi.nlm.nih.gov/Blast.cgi).…”

Section: Marker-trait Association Analysismentioning

confidence: 99%

“…Nucleotide sequences of the associated markers were retrieved from the available Napier grass genomic [30] and transcriptomic [31] sequence data by aligning the DArTseq short sequence reads (approximately 55 nucleotides (nt)) corresponding to each SilicoDArT marker ( Supplementary Table S1). Seven of the SilicoDArT markers were aligned with the assembled genomic sequences [30].…”

Section: Analysis Of Nucleotide Sequences Corresponding To the Associmentioning

confidence: 99%

“…The DArTseq genotyping platform [52] produces short sequence reads, averaging about 55 nt in length, corresponding to each of the SilicoDArT and SNP markers [12]. In this study, the short sequence reads corresponding to the associated markers were compared with previously reported Napier grass genomic [30] and transcriptome [31] sequences. Very few of the DArTseq sequence reads aligned with the assembled genomic sequences, as only assembled sequences longer than 200 nt were used in the comparison.…”

Section: Markers Associated With Dry Weight Yields and Metabolizable mentioning

confidence: 99%

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Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus purpureus) Improvement

Habte¹,

Muktar²,

Abdena³

et al. 2020

Agronomy

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The evaluation of forage crops for adaptability and performance across production systems and environments is one of the main strategies used to improve forage production. To enhance the genetic resource base and identify traits responsible for increased feed potential of Napier grass, forty-five genotypes from Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Brazil, were evaluated for forage biomass yield and feed nutritional quality in a replicated trial under wet and dry season conditions in Ethiopia. The results revealed significant variation in forage yield and feed nutritional qualities among the genotypes and between the wet and dry seasons. Feed fiber components were lower in the dry season, while crude protein, in vitro organic matter digestibility, and metabolizable energy were higher. Based on the cumulative biomass and metabolizable energy yield, top performing genotypes were identified that are candidates for future forage improvement studies. Furthermore, the marker-trait association study identified diagnostic single nucleotide polymorphisms (SNP) and SilicoDArT markers and potential candidate genes that could differentiate high biomass yielding and high metabolizable energy genotypes in the collection.

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The first Illumina-based de novo transcriptome analysis and molecular marker development in Napier grass (Pennisetum purpureum)

Cited by 28 publications

References 97 publications

SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum

SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum

SMRT Sequencing of a Full-length Transcriptome Reveals Transcript Variants Involved in C18 Unsaturated Fatty Acid Biosynthesis and Metabolism Pathways at Chilling Temperature in Pennisetum giganteum

Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus purpureus) Improvement

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