Genome sequence of <i>Jatropha curcas</i> L., a non‐edible biodiesel plant, provides a resource to improve seed‐related traits

Ha, Jung Min; Shim, Sangrea; Lee, Taeyoung; Kang, Yang Jae; Hwang, Wooncheol; Jeong, Haneul; Laosatit, Kularb; Lee, Jayern; Kim, Sue K.; Satyawan, Dani; Lestari, Puji; Yoon, Min Young; Kim, Moon Y.; Chitikineni, Annapurna; Tanya, Patcharin; Somta, Prakit; Srinives, Peerasak; Varshney, Rajeev K.; Lee, Suk-Ha

doi:10.1111/pbi.12995

Cited by 62 publications

(46 citation statements)

References 123 publications

(164 reference statements)

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“…Breeding efforts of this biofuel crop will be accelerated by the in-depth knowledge of seed transcripts of J. curcas for obtaining functional genomics information to discover genes that encode enzymes involved in the biosynthesis of oil and toxin precursors and to describe their relevant metabolic pathways [14][15][16]. Therefore, it is necessary to establish a reliable method to characterize the temporal shifts in gene expression being in the background of the biochemical and metabolic processes which take place during seed maturation.…”

Section: Introductionmentioning

confidence: 99%

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

et al. 2020

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Background: Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray. Results: A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length. Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected. Conclusion: The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.

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Section: Introductionmentioning

confidence: 99%

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

et al. 2020

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“…However, its toxins and antinutritional compounds render the seed cake and oil unsuitable for use as animal feed and human consumption [13]. Therefore, efforts are required to increase oil yield and composition by improving the ability of the plant to produce favorable fruits/seeds with suitable compounds.Breeding efforts of this biofuel crop will be accelerated by the in-depth knowledge of seed transcripts of J. curcas for obtaining functional genomics information to discover genes that encode enzymes involved in the biosynthesis of oil and toxin precursors and to describe their relevant metabolic pathways [14][15][16]. Therefore, it is necessary to establish a reliable method to characterize the temporal shifts in gene expression being in the background of the biochemical and metabolic processes which take place during seed maturation.…”

mentioning

confidence: 99%

“…Furthermore, such data could help to identify, characterize and -if necessary -modify the possible transcripts of interest. In Jatropha, transcriptome studies generated data describing seed development and seed germination from manually pollinated plants, with the emphasis on differentially expressed genes related to lipid biosynthesis and toxic compounds [14][15][16][17][18]. In addition, whole genome sequencing was applied to identify protein-encoding genes, which could help in improving the traits of interest (e.g.…”

mentioning

confidence: 99%

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

Maghuly

Deák

Vierlinger

et al. 2020

Preprint

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Background: Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray. Results: A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9,111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length. Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected. Conclusion: The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.

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“…However, their expression was reported to be different in various plants. For instance, in sesame PDAT showed higher expression compared to DGAT, while in castor bean the DGAT showed a higher expression level compared to PDAT [14,[96][97]. In Jatropha, PDAT showed lower expression compare to DGAT1, as reported by Xu et al [89].…”

Section: Discussionmentioning

confidence: 51%

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

Maghuly

Deák

Vierlinger

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray. Results: A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9,111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length. Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected. Conclusion: The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.

show abstract

Genome sequence of Jatropha curcas L., a non‐edible biodiesel plant, provides a resource to improve seed‐related traits

Cited by 62 publications

References 123 publications

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

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