Genetic variability of Begonia longifolia Blume from Indonesia based on Nuclear DNA internal transcribed spacer (ITS) sequence data

Ningrum, Wahyu Dewi Astuti; Atmaja, Muhammad Bima; Daryono, Budi Setiadi; Purnomo, Purnomo

doi:10.13057/biodiv/d211239

Cited by 4 publications

(4 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The majority of research on the molecular phylogeny of Begonia was based on chloroplast ( psb A -trn H, mat K, and rbc L) sequences and nuclear (ITS and ITS2) fragments. However, the phylogenetic relationship of Begonia was not completely resolved by these sequences [ 16 , 17 ]. Plant phylogeny based on the whole chloroplast genome has become popular in recent years [ 18 , 19 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

Xiong,

Huang,

et al. 2023

BMC Genomics

View full text Add to dashboard Cite

Background The Begonia species are common shade plants that are mostly found in southwest China. They have not been well studied despite their medicinal and decorative uses because gene penetration, decreased adaptability, and restricted availability are all caused by frequent interspecific hybridization. Result To understand the patterns of mutation in the chloroplast genomes of different species of Begonia, as well as their evolutionary relationships, we collected seven Begonia species in China and sequenced their chloroplast genomes. Begonia species exhibit a quadripartite structure of chloroplast genomes (157,634 − 169,694 bp), consisting of two pairs of inverted repeats (IR: 26,529 − 37,674 bp), a large single copy (LSC: 75,477 − 86,500 bp), and a small single copy (SSC: 17,861 − 18,367 bp). 128–143 genes (comprising 82–93 protein-coding genes, 8 ribosomal RNAs, and 36–43 transfer RNAs) are found in the chloroplast genomes. Based on comparative analyses, this taxon has a relatively similar genome structure. A total of six substantially divergent DNA regions (trnT-UGU-trnL-UAA, atpF-atpH, ycf4-cemA, psbC-trnS-UGA, rpl32-trnL-UAG, and ccsA-ndhD) are found in the seventeen chloroplast genomes. These regions are suitable for species identification and phylogeographic analysis. Phylogenetic analysis shows that Begonia species that were suited to comparable environments grouped in a small clade and that all Begonia species formed one big clade in the phylogenetic tree, supporting the genus’ monophyly. In addition, positive selection sites were discovered in eight genes (rpoC1, rpoB, psbE, psbK, petA, rps12, rpl2, and rpl22), the majority of which are involved in protein production and photosynthesis. Conclusion Using these genome resources, we can resolve deep-level phylogenetic relationships between Begonia species and their families, leading to a better understanding of evolutionary processes. In addition to enhancing species identification and phylogenetic resolution, these results demonstrate the utility of complete chloroplast genomes in phylogenetically and taxonomically challenging plant groupings.

show abstract

Section: Discussionmentioning

confidence: 99%

Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

Xiong,

Huang,

et al. 2023

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…This score implied a close phylogenetic relationship between Olele sample and five accessions of P. acidula, while the phylogenetic relationship between Biluhu sample and five P. acidula accessions is pretty far. According to Qin et al (2017) and Ningrum et al (2020), the genetic distance threshold for ITS2 in intraspecies of seed plants is 3.76%. Based on the value, it can be said that Olele sample and the fifth P. acidula accession were classified as intraspecies, while Biluhu sample was classified as different species.…”

Section: Genetic Diversitymentioning

confidence: 99%

Diversity of Santigi (<i>Pemphis acidula</i> J.R.Forst. & G.Forst.), A Mangrove Association in Tomini Bay, Sulawesi, Indonesia

Baderan,

Rahim,

Angio

et al. 2024

J.Tropical Biodiversity Biotechnology

View full text Add to dashboard Cite

Pemphis acidula is a wild plant in rocky or sandy coastal areas and mangrove ecosystems. Different geographic characteristics may affect plant adaptability and have an impact on the emergence of various genotypes. This study was performed to reveal the phenetic relationship and genetic variation of P. acidula in 3 different areas in Tomini Bay, Gorontalo Province, Indonesia. We took 3 samples from each location and analysed them using 14 morphological characters and molecular approaches based on ISSR markers and ITS gene. The results showed that P. acidula on Olele had bigger sizes in some morphological features compared to the plants in other study areas. The phenetic analysis showed that P. acidula at Biluhu and Dulanga were more closely related, although P. acidula at the 3 locations had 100% similarity. Genetic variation analysis showed the highest genetic similarity based on ISSR markers was found in Dulanga and Biluhu samples (76.8%). Phylogenetic based on ITS gene revealed that Olele samples were in the same clade with P. acidula accession from GenBank (genetic distance 0-0.19%), while Biluhu samples were a sister group (genetic distance 24.97-25.03%) even though their percentage identity corresponds to P. acidula (81.34%). Plant adaptation to different habitat conditions may affect the genetic diversity of P. acidula.

show abstract

“…The majority of studies on the molecular phylogeny of Begonia were based on chloroplast (psbA-trnH, matK, rbcL) sequences and nuclear (ITS and ITS2) fragments. However, the phylogenetic relationship of Begonia was not completely resolved by these sequences [16,17]. Plant phylogeny based on the whole chloroplast genome has become popular in recent years [18,19].…”

Section: Phylogenetic Relationshipmentioning

confidence: 99%

Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

Xiong

Huang

et al. 2023

Preprint

View full text Add to dashboard Cite

Background The Begonia species are common shade plants that are mostly found in southwest China. They have not been well studied despite their medicinal and decorative uses because gene penetration, decreased adaptability, and restricted availability are all caused by frequent interspecific hybridization. Result To understand the patterns of mutation in the chloroplast genomes of different species of Begonia, as well as their evolutionary relationship, we collected seven Begonia species in China and sequenced their chloroplast genomes. Begonia species exhibit a quadripartite structure of chloroplast genomes (157,634 − 169,694 bp), consisting of two pairs of inverted repeats (IR: 26,529 − 37,674 bp), a large single copy (LSC: 75,477 − 86,500 bp), and a small single copy (SSC: 17,861 − 18,367 bp). 128–142 genes (comprising 82–93 protein-coding genes, 8 ribosomal RNAs, and 36–43 transfer RNAs) are found in the chloroplast genomes. Based on comparative analyses, this taxon has a relatively similar genome structure. A total of ten substantially divergent DNA regions (rpl32, trnS-GCU, trnT-UGU-trnL-UAA, atpF-atpH, ycf4-cemA, rps19-trnG-UCC, trnD-GUC-trnY-GUA, trnC-GCA-petN, trnE-UUC-trnT-GGU and petD-rpoA) are found in the seventeen chloroplast genomes. These regions are suitable for species identification and phylogeographic analysis. Phylogenetic analysis shows that Begonia species that were suited to comparable environments grouped in a small clade and that all Begonia species formed one big clade in the phylogenetic tree, supporting the genus' monophyly. In addition, positive selection sites are discovered in eight genes (rpoC1, rpoB, psbE, psbK, petA, rps12, rpl2 and rpl22), the majority of which are involved in protein production and photosynthesis. Conclusion Using these genome resources, we can resolve deep-level phylogenetic relationships between Begonia species and their families, leading to a better understanding of evolutionary processes. In addition to enhancing species identification and phylogenetic resolution, these results demonstrate the utility of complete chloroplast genomes in phylogenetically and taxonomically challenging plant groupings.

show abstract

Genetic variability of Begonia longifolia Blume from Indonesia based on Nuclear DNA internal transcribed spacer (ITS) sequence data

Cited by 4 publications

References 26 publications

Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

Diversity of Santigi (<i>Pemphis acidula</i> J.R.Forst. & G.Forst.), A Mangrove Association in Tomini Bay, Sulawesi, Indonesia

Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

Contact Info

Product

Resources

About