De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of <i>Scutellaria</i> L. Species
<i>Scutellaria</i> L. (family <i>Lamiaceae</i>) includes approximately 470 species found in most parts of the world and is commonly known as skullcaps. <i>Scutellaria</i> L. is a medicinal herb used as a folk remedy in Korea and East Asia, but it is difficult to i...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-12-01
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| Series: | Current Issues in Molecular Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1467-3045/43/3/152 |
| Summary: | <i>Scutellaria</i> L. (family <i>Lamiaceae</i>) includes approximately 470 species found in most parts of the world and is commonly known as skullcaps. <i>Scutellaria</i> L. is a medicinal herb used as a folk remedy in Korea and East Asia, but it is difficult to identify and classify various subspecies by morphological methods. Since <i>Scutellaria</i> L. has not been studied genetically, to expand the knowledge of species in the genus <i>Scutellaria</i> L., de novo whole-genome assembly was performed in <i>Scutellaria indica</i> var. <i>tsusimensis</i> (H. Hara) Ohwi using the Illumina sequencing platform. We aimed to develop a molecular method that could be used to classify <i>S.</i><i>indica</i> var. <i>tsusimensis</i> (H. Hara) Ohwi, <i>S. indica</i> L. and three other <i>Scutellaria</i> L. species. The assembly results for <i>S.</i><i>indica</i> var. <i>tsusimensis</i> (H. Hara) Ohwi revealed a genome size of 318,741,328 bp and a scaffold N50 of 78,430. The assembly contained 92.08% of the conserved BUSCO core gene set and was estimated to cover 94.65% of the genome. The obtained genes were compared with previously registered <i>Scutellaria</i> nucleotide sequences and similar regions using the NCBI BLAST service, and a total of 279 similar nucleotide sequences were detected. By selecting the 279 similar nucleotide sequences and nine chloroplast DNA barcode genes, primers were prepared so that the size of the PCR product was 100 to 1000 bp. As a result, a species-specific primer set capable of distinguishing five species of <i>Scutellaria</i> L. was developed. |
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| ISSN: | 1467-3037 1467-3045 |