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The complete chloroplast genome sequence of the biofuel plant Sacha Inchi, Plukenetia volubilis.

ABSTRACT: Sacha Inchi (Plukenetia volubilis) is a potential woody oil seed plant for producing healthy vegetable oil due to high content of α-linolenic acid in its seeds. In this study, we report the structure of the complete chloroplast genome of P. volubilis using high-throughput next-generation sequencing technology. The circular chloroplast genome is 161,733 bp in size, containing a pair of inverted repeat regions (IR) of 27,382 bp each, which were separated by a large single copy region (LSC) of 88,843 bp and a small single copy region (SSC) of 18,126 bp. The chloroplast genome harbors 135 genes, including 92 protein-coding genes, 35 tRNA genes and 8 rRNA genes. Based on the phylogenetic relationships between the chloroplast genome of P. volubilis and those of the other species, P. volubilis is most closely related to castor bean (Ricinus communis).

SUBMITTER: Hu XD

PROVIDER: S-EPMC7808370 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundSacha Inchi (Plukenetia volubilis L.), which belongs to the Euphorbiaceae, has been considered a new potential oil crop because of its high content of polyunsaturated fatty acids in its seed oil. The seed oil especially contains high amounts of α-linolenic acid (ALA), which is useful for the prevention of various diseases. However, little is known about the genetic information and genome sequence of Sacha Inchi, which has largely hindered functional genomics and molecular breeding studies.ResultsIn this study, a de novo transcriptome assembly based on transcripts sequenced in eight major organs, including roots, stems, shoot apexes, mature leaves, male flowers, female flowers, fruits, and seeds of Sacha Inchi was performed, resulting in a set of 124,750 non-redundant putative transcripts having an average length of 851 bp and an N50 value of 1909 bp. Organ-specific unigenes analysis revealed that the most organ-specific transcripts are found in female flowers (2244 unigenes), whereas a relatively small amount of unigenes are detected to be expressed specifically in other organs with the least in stems (24 unigenes). A total of 42,987 simple sequence repeats (SSRs) were detected, which will contribute to the marker assisted selection breeding of Sacha Inchi. We analyzed expression of genes related to the α-linolenic acid metabolism based on the de novo assembly and annotation transcriptome in Sacha Inchi. It appears that Sacha Inchi accumulates high level of ALA in seeds by strong expression of biosynthesis-related genes and weak expression of degradation-related genes. In particular, the up-regulation of FAD3 and FAD7 is consistent with high level of ALA in seeds of Sacha Inchi compared with in other organs. Meanwhile, several transcription factors (ABI3, LEC1 and FUS3) may regulate key genes involved in oil accumulation in seeds of Sacha Inchi.ConclusionsThe transcriptome of major organs of Sacha Inchi has been sequenced and de novo assembled, which will expand the genetic information for functional genomic studies of Sacha Inchi. In addition, the identification of candidate genes involved in ALA metabolism will provide useful resources for the genetic improvement of Sacha Inchi and the metabolic engineering of ALA biosynthesis in other plants.

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The complete chloroplast genome sequence of the biofuel plant Sacha Inchi, Plukenetia volubilis.

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