Genome-wide analysis of drought induced gene expression changes in flax (<i>Linum usitatissimum</i>)

Dash, Prasanta K.; Cao, Yongguo; Jailani, A. Abdul Kader; Gupta, Payal; Venglat, Prakash; Xiang, Daoquan; Rai, Rhitu; Sharma, R.C.; Thirunavukkarasu, Nepolean; Abdin, M. Z.; Yadava, Devendra K.; Singh, Nagendra; Singh, Jas; Selvaraj, Gopalan; Deyholos, Mike; Kumar, Polumetla Ananda; Datla, Raju

doi:10.4161/gmcr.29742

Cited by 69 publications

(53 citation statements)

References 78 publications

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“…It was noticeable that the number of DEGs in phloem and root was one order of magnitude lower than in flower or leaf, however, when both tissues were grouped and compared against the other organs, a total of 3287 genes were found to be down‐regulated and 3346 overexpressed, suggesting that root and phloem share many DEGs that are quenched when one organ is compared against the other. Our data support a correlation of gene expression in shoot and root that has been previously reported (Dash et al ., ; Kelly et al ., ; Sarkar et al ., ).…”

Section: Resultsmentioning

confidence: 98%

An RNA‐Seq‐based reference transcriptome for Citrus

Terol

Tadeo

Ventimilla

et al. 2015

Plant Biotechnology Journal

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Summary Previous RNA‐Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA‐Seq analysis, obtained from 12 Citrus species: C. medica, C. aurantifolia, C. limon, C. bergamia, C. clementina, C. deliciosa, C. reshni, C. maxima, C. paradisi, C. aurantium, C. sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C. clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19 739, and a total of 73 797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail.

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Section: Resultsmentioning

confidence: 98%

An RNA‐Seq‐based reference transcriptome for Citrus

Terol

Tadeo

Ventimilla

et al. 2015

Plant Biotechnology Journal

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“…It has been a challenge for banana breeders to produce disease resistant polyploid hybrids through genetic recombination. Like other crops (Dash et al, 2014), availability of structural genome information has opened up vistas to saturate the genome with molecular markers which would enable banana researchers to select good plant type at an early stage in commercial plantation. Structural genomics of banana has further delineated molecular mechanisms of dwarfing, imparting disease resistance, role of phyto-hormones in parthenocarpy and pivotal role of transcription factors in formation of this iconic fruit.…”

Section: Conclusion and Future Perspectivementioning

confidence: 99%

Translating the “Banana Genome” to Delineate Stress Resistance, Dwarfing, Parthenocarpy and Mechanisms of Fruit Ripening

Dash

Rai

2016

Front. Plant Sci.

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Evolutionary frozen, genetically sterile and globally iconic fruit “Banana” remained untouched by the green revolution and, as of today, researchers face intrinsic impediments for its varietal improvement. Recently, this wonder crop entered the genomics era with decoding of structural genome of double haploid Pahang (AA genome constitution) genotype of Musa acuminata. Its complex genome decoded by hybrid sequencing strategies revealed panoply of genes and transcription factors involved in the process of sucrose conversion that imparts sweetness to its fruit. Historically, banana has faced the wrath of pandemic bacterial, fungal, and viral diseases and multitude of abiotic stresses that has ruined the livelihood of small/marginal farmers’ and destroyed commercial plantations. Decoding structural genome of this climacteric fruit has given impetus to a deeper understanding of the repertoire of genes involved in disease resistance, understanding the mechanism of dwarfing to develop an ideal plant type, unraveling the process of parthenocarpy, and fruit ripening for better fruit quality. Further, injunction of comparative genomics will usher in integration of information from its decoded genome and other monocots into field applications in banana related but not limited to yield enhancement, food security, livelihood assurance, and energy sustainability. In this mini review, we discuss pre- and post-genomic discoveries and highlight accomplishments in structural genomics, genetic engineering and forward genetic accomplishments with an aim to target genes and transcription factors for translational research in banana.

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“…Therefore, it is widely grown in the western and northwestern provinces in China, such as Gansu and Inner Mongolia, which experience the highest drought frequency and longest drought in East Asia [11]. Nonetheless, DS still represents a major limit to linseed production [12]. Since 1995, when long-term traditional breeding programmes to enhance linseed stress tolerance and improve crop yield under periodic drought, transgenic linseed plants have been obtained for enhancing tolerance to DS [13,14].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencing

Wang

Tan

et al. 2020

Preprint

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Background: Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known about how linseed coordinates the expression of drought resistance gene in response to different level of drought stress (DS) on the genome-wide level.Results: To explore the linseed transcriptional response of DS and repeated drought (RD) stress, we determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) and reduce and visualize GO (REVIGO) enrichment analysis showed that upregulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance than those of NY-17 were under DS. In addition, 4436 linseed transcription factors were identified, and 1190 were responsive to stress treatments. Moreover, protein-protein interaction (PPI) network analysis showed that the proline biosynthesis pathway interacts with stress response genes through RAD50 (DNA repair protein 50) interacting protein 1 (RIN-1). Finally, proline biosynthesis and DNA repair structural gene expression patterns were verified by RT- PCR.Conclusions: The drought tolerance of Z141 may be related to its upregulation of drought tolerance genes under DS. Proline may play an important role in linseed drought tolerance by maintaining cell osmotic and protecting DNA from ROS damage.. In summary, this study provides a new perspective to understand the drought adaptability of linseed.

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Genome-wide analysis of drought induced gene expression changes in flax (Linum usitatissimum)

Abstract: These authors contributed equally to this work.

Cited by 69 publications

References 78 publications

An RNA‐Seq‐based reference transcriptome for Citrus

An RNA‐Seq‐based reference transcriptome for Citrus

Translating the “Banana Genome” to Delineate Stress Resistance, Dwarfing, Parthenocarpy and Mechanisms of Fruit Ripening

Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencing

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