The Complete Chloroplast Genome of Plukenetia volubilis Provides Insights Into the Organelle Inheritance

Abstract

Plukenetia volubilis L. (Malpighiales: Euphorbiaceae), also known as Sacha inchi, is considered a promising crop due to its high seed content of unsaturated fatty acids (UFAs), all of them highly valuable for food and cosmetic industries, but the genetic basis of oil biosynthesis of this non-model plant is still insufficient. Here, we sequenced the total DNA of Sacha inchi by using Illumina and Nanopore technologies and approached a de novo reconstruction of the whole nucleotide sequence and the organization of its 164,111 bp length of the chloroplast genome, displaying two copies of an inverted repeat sequence [inverted repeat A (IRA) and inverted repeat B (IRB)] of 28,209 bp, each one separating a small single copy (SSC) region of 17,860 bp and a large single copy (LSC) region of 89,833 bp. We detected two large inversions on the chloroplast genome that were not presented in the previously reported sequence and studied a promising cpDNA marker, useful in phylogenetic approaches. This chloroplast DNA (cpDNA) marker was used on a set of five distinct Colombian cultivars of P. volubilis from different geographical locations to reveal their phylogenetic relationships. Thus, we evaluated if it has enough resolution to genotype cultivars, intending to crossbreed parents and following marker’s trace down to the F1 generation. We finally elucidated, by using molecular and cytological methods on cut flower buds, that the inheritance mode of P. volubilis cpDNA is maternally transmitted and proposed that it occurs as long as it is physically excluded during pollen development. This de novo chloroplast genome will provide a valuable resource for studying this promising crop, allowing the determination of the organellar inheritance mechanism of some critical phenotypic traits and enabling the use of genetic engineering in breeding programs to develop new varieties.

Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants

“…Besides, our findings revealed that the total length, GC content, and gene composition of the cp genomes were almost identical in all species. Previous studies have shown that the cp genome of angiosperms is highly conserved at the genus level (Khan et al, 2020;Villanueva-Corrales et al, 2021;Feng et al, 2022). Moreover, previous research demonstrated that the rps19 gene existed in the IR region (Ahmed et al, 2012;Wang et al, 2022).…”

Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia, Boraginaceae) in China

“…Chloroplasts are key plant organelles that are involved in photosynthesis and important biological processes, such as fatty acid and amino acid synthesis ( Sugiura, 1992 ). The chloroplast genome of higher plants is a double-stranded and circular DNA molecule with a typical quadripartite structure ( Dong et al, 2013 , 2021a ; Villanueva-Corrales et al, 2021 ), including a pair of inverted repeats (IRs) as well as a large single copy (LSC) and a small single copy (SSC) region. The chloroplast genome encodes approximately 80 protein-coding, 30 transfer RNA (tRNA), and four ribosomal RNA (rRNA) genes, and the structure of the chloroplast genome, including the gene content and gene order, is conserved.…”

The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification

“…Overall, the structure and organization of the nine observed cp genomes in Thalictrum , including T. fargesii , follow the typical structure commonly found in angiosperms, except for a difference in tRNA content in T. viscosum , which contains 38 tRNAs instead of 37 ( Park et al., 2015 ; Daniell et al., 2016 ; He et al., 2019 ; Morales-Briones et al., 2019 ; He et al., 2021 ; Cai et al., 2022 ; Zhe et al., 2023 ). The total length, GC content, and gene composition were almost identical in the cp genomes of all studied species, and these highly conserved features might be due to a typical evolutionary passage in Thalictrum ( Khan et al., 2020 ; Villanueva-Corrales et al., 2021 ; Feng et al., 2022 ). Compared to the LSC and SSC regions, the IR region was more conserved among the cp genomes.…”