Molecular Discrimination and Phylogenetic Relationships of <i>Physalis</i> Species Based on ITS2 and <i>rbcL</i> DNA Barcode Sequence
Plants of the genus <i>Physalis</i> are of economic interest because of their fleshy edible fruits with high nutritional value. Some species have high medicinal value with a long history of ethno-medicinal use to treat diverse diseases. There is therefore a need to correctly discriminate...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-11-01
|
| Series: | Crops |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2673-7655/3/4/27 |
| _version_ | 1797381537032830976 |
|---|---|
| author | Katherine Pere Kenneth Mburu Edward K. Muge John Maina Wagacha Evans N. Nyaboga |
| author_facet | Katherine Pere Kenneth Mburu Edward K. Muge John Maina Wagacha Evans N. Nyaboga |
| author_sort | Katherine Pere |
| collection | DOAJ |
| description | Plants of the genus <i>Physalis</i> are of economic interest because of their fleshy edible fruits with high nutritional value. Some species have high medicinal value with a long history of ethno-medicinal use to treat diverse diseases. There is therefore a need to correctly discriminate the different species of <i>Physalis</i> for proper utilization. Although most <i>Physalis</i> species have unique morphologies, their vegetative stages are identical, making it difficult to accurately identify them based on morphological characteristics. DNA barcoding has the potential to discriminate species accurately. In this study, ribulose bisphosphate carboxylase large (<i>rbcL</i>) and internal transcribed spacer 2 (ITS2) regions were used to discriminate <i>Physalis</i> species and to reveal their phylogenetic relationships and genetic diversity. <i>Physalis</i> plant samples were collected from seven counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. Genomic DNA was isolated from leaf samples of 64 <i>Physalis</i> accessions and used for PCR amplification and the sequencing of <i>rbcL</i> and ITS2 barcode regions. The discriminatory ability of the barcodes was based on BLASTn comparison, phylogenetic reconstruction and cluster analysis, and the determination of inter- and intra-specific distances. The nucleotide polymorphism, genetic diversity and distance of the identified <i>Physalis</i> species were determined using DnaSP and MEGA 11.0 software. Species discrimination was more robust using ITS2 sequences. The species identified and discriminated by ITS2 sequences were <i>Physalis purpurea</i>, <i>Physalis peruviana</i> and <i>Physalis cordata</i>. The <i>rbcL</i> sequences were only able to identify <i>Physalis</i> to the genus level. There was high interspecific and low intraspecific divergence within the identified <i>Physalis</i> species based on ITS2 sequences. The ITS2 barcode is an ideal DNA barcode for use in the discrimination of species, as well as in genetic diversity studies of <i>Physalis</i> accessions in Kenya. |
| first_indexed | 2024-03-08T20:52:56Z |
| format | Article |
| id | doaj.art-9a46f4b9a772468cbe2cd3b8beb4a579 |
| institution | Directory Open Access Journal |
| issn | 2673-7655 |
| language | English |
| last_indexed | 2024-03-08T20:52:56Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Crops |
| spelling | doaj.art-9a46f4b9a772468cbe2cd3b8beb4a5792023-12-22T14:01:42ZengMDPI AGCrops2673-76552023-11-013430231910.3390/crops3040027Molecular Discrimination and Phylogenetic Relationships of <i>Physalis</i> Species Based on ITS2 and <i>rbcL</i> DNA Barcode SequenceKatherine Pere0Kenneth Mburu1Edward K. Muge2John Maina Wagacha3Evans N. Nyaboga4Department of Biochemistry, University of Nairobi, Nairobi P.O. Box 30197-00100, KenyaDepartment of Life Sciences, South Eastern Kenya University, Kitui P.O. Box 170-90200, KenyaDepartment of Biochemistry, University of Nairobi, Nairobi P.O. Box 30197-00100, KenyaDepartment of Biology, University of Nairobi, Nairobi P.O. Box 30197-00100, KenyaDepartment of Biochemistry, University of Nairobi, Nairobi P.O. Box 30197-00100, KenyaPlants of the genus <i>Physalis</i> are of economic interest because of their fleshy edible fruits with high nutritional value. Some species have high medicinal value with a long history of ethno-medicinal use to treat diverse diseases. There is therefore a need to correctly discriminate the different species of <i>Physalis</i> for proper utilization. Although most <i>Physalis</i> species have unique morphologies, their vegetative stages are identical, making it difficult to accurately identify them based on morphological characteristics. DNA barcoding has the potential to discriminate species accurately. In this study, ribulose bisphosphate carboxylase large (<i>rbcL</i>) and internal transcribed spacer 2 (ITS2) regions were used to discriminate <i>Physalis</i> species and to reveal their phylogenetic relationships and genetic diversity. <i>Physalis</i> plant samples were collected from seven counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. Genomic DNA was isolated from leaf samples of 64 <i>Physalis</i> accessions and used for PCR amplification and the sequencing of <i>rbcL</i> and ITS2 barcode regions. The discriminatory ability of the barcodes was based on BLASTn comparison, phylogenetic reconstruction and cluster analysis, and the determination of inter- and intra-specific distances. The nucleotide polymorphism, genetic diversity and distance of the identified <i>Physalis</i> species were determined using DnaSP and MEGA 11.0 software. Species discrimination was more robust using ITS2 sequences. The species identified and discriminated by ITS2 sequences were <i>Physalis purpurea</i>, <i>Physalis peruviana</i> and <i>Physalis cordata</i>. The <i>rbcL</i> sequences were only able to identify <i>Physalis</i> to the genus level. There was high interspecific and low intraspecific divergence within the identified <i>Physalis</i> species based on ITS2 sequences. The ITS2 barcode is an ideal DNA barcode for use in the discrimination of species, as well as in genetic diversity studies of <i>Physalis</i> accessions in Kenya.https://www.mdpi.com/2673-7655/3/4/27DNA barcoding<i>Physalis</i>ITS2<i>rbcL</i>species discrimination |
| spellingShingle | Katherine Pere Kenneth Mburu Edward K. Muge John Maina Wagacha Evans N. Nyaboga Molecular Discrimination and Phylogenetic Relationships of <i>Physalis</i> Species Based on ITS2 and <i>rbcL</i> DNA Barcode Sequence Crops DNA barcoding <i>Physalis</i> ITS2 <i>rbcL</i> species discrimination |
| title | Molecular Discrimination and Phylogenetic Relationships of <i>Physalis</i> Species Based on ITS2 and <i>rbcL</i> DNA Barcode Sequence |
| title_full | Molecular Discrimination and Phylogenetic Relationships of <i>Physalis</i> Species Based on ITS2 and <i>rbcL</i> DNA Barcode Sequence |
| title_fullStr | Molecular Discrimination and Phylogenetic Relationships of <i>Physalis</i> Species Based on ITS2 and <i>rbcL</i> DNA Barcode Sequence |
| title_full_unstemmed | Molecular Discrimination and Phylogenetic Relationships of <i>Physalis</i> Species Based on ITS2 and <i>rbcL</i> DNA Barcode Sequence |
| title_short | Molecular Discrimination and Phylogenetic Relationships of <i>Physalis</i> Species Based on ITS2 and <i>rbcL</i> DNA Barcode Sequence |
| title_sort | molecular discrimination and phylogenetic relationships of i physalis i species based on its2 and i rbcl i dna barcode sequence |
| topic | DNA barcoding <i>Physalis</i> ITS2 <i>rbcL</i> species discrimination |
| url | https://www.mdpi.com/2673-7655/3/4/27 |
| work_keys_str_mv | AT katherinepere moleculardiscriminationandphylogeneticrelationshipsofiphysalisispeciesbasedonits2andirbclidnabarcodesequence AT kennethmburu moleculardiscriminationandphylogeneticrelationshipsofiphysalisispeciesbasedonits2andirbclidnabarcodesequence AT edwardkmuge moleculardiscriminationandphylogeneticrelationshipsofiphysalisispeciesbasedonits2andirbclidnabarcodesequence AT johnmainawagacha moleculardiscriminationandphylogeneticrelationshipsofiphysalisispeciesbasedonits2andirbclidnabarcodesequence AT evansnnyaboga moleculardiscriminationandphylogeneticrelationshipsofiphysalisispeciesbasedonits2andirbclidnabarcodesequence |