Chloroplast genome sequence of the wild tetraploid potato relative Solanum stoloniferum

Mitochondrial DNA Part B

2023

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Solanum iopetalum belongs to the Solanaceae family and is one of the tuber-bearing wild Solanum species. In this study, chloroplast genome sequencing of the species, completed with Illumina sequencing technology, is presented. The length of the chloroplast genome is 155,625 bp with a GC content of 37.86%. It comprises a large single copy (LSC) region of 86,057 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,593 bp. Additionally, 158 functional genes in the genome are identified, including 105 protein-coding genes, 8 ribosomal RNAs, and 45 transfer RNAs. Phylogenetic analysis revealed that S. iopetalum is grouped into a large clade with other Solanum species, including cultivated potatoes ( S. tuberosum ) and is closely related to Mexican Solanum species ( S. stoloniferum , S. verrucosum , S. hougasii , S. hjertingii , and S. demissum ). This study provides useful genomic information for future breeding and evolutionary studies of S. iopetalum and other Solanum species.

Section: Resultsmentioning

confidence: 99%

Complete chloroplast genome sequence of Solanum iopetalum, one of the tuber-bearing wild potato relatives

Mitochondrial DNA Part B

2023

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“…Overall GC content was 37.88%. The closest Solanum species were S. hougasii (MF471372) and S. stoloniferum (MF471373, Park 2018 ; Kim and Park 2020b ) each with a very high sequence identity of 99.97% and 99.96%, respectively. A total of 158 genes were annotated with an average length of 583.3 bp and gene features were typically identical to those of higher plants.…”

mentioning

confidence: 99%

Complete chloroplast genome sequence of Solanum hjertingii, one of the wild potato relatives

Mitochondrial DNA Part B

2022

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Solanum hjertingii is a wild tuber-bearing species classified in the Solanaceae family. The chloroplast genome of S. hjertingii was completed via de novo assembly using Illumina paired-end sequencing data. Total length of the chloroplast genome of S. hjertingii is 155,545 bp consisting of 85,976 bp in a large single copy, 18,383 bp in a small single copy, and 25,593 bp in a pair of inverted repeat regions. Its structure is circular and typically quadripartite. It contains 158 predicted genes in total, including 105 protein-coding, 45 tRNA, and eight rRNA genes. Maximum likelihood phylogenetic analysis of the sequence along with 33 species in the Solanaceae family revealed that S. hjertingii belongs to a large clade with other Solanum species including S. tuberosum and is most closely grouped in the clade with S. hougasii and S. stoloniferum in the clade.

Comparison of the complete chloroplast genome sequence ofSolanum stoloniferumwith other Solanum species generates PCR-based markers specific for Solanumstoloniferum

Kim

2020

J Plant Biotechnol

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Solanum stoloniferum, one of the wild tetraploid Solanum species belonging to the Solanaceae family, is an excellent resource for potato breeding owing to its resistance to several important pathogens. However, the sexual hybridization of S. stoloniferum with S. tuberosum (potato) is hampered due to the sexual incompatibility between the two species. To overcome this and introgress the various novel traits of S. stoloniferum in cultivated potatoes, cell fusion can be performed. The identification of the fusion products is crucial and can be achieved with the aid of molecular markers. In this study, the chloroplast genome sequence of S. stoloniferum was obtained by next-generation sequencing technology, and compared with that of six other Solanum species to identify S. stoloniferum-specific molecular markers. The length of the complete chloroplast genome of S. stoloniferum was found to be 155,567 bp. The structural organization of the chloroplast genome of S. stoloniferum was similar to that of the six other Solanum species studied. Phylogenetic analysis of S. stoloniferum with nine other Solanaceae family members revealed that S. stoloniferum was most closely related to S. berthaultii. Additional comparison of the complete chloroplast genome sequence of S. stoloniferum with that of five Solanum species revealed the presence of six InDels and 39 SNPs specific to S. stoloniferum. Based on these InDels and SNPs, four PCR-based markers were developed to differentiate S. stoloniferum from other Solanum species. These markers will facilitate the selection of fusion products and accelerate potato breeding using S. stoloniferum.