The cp genome characterization of Adenium obesum: Gene content, repeat organization and phylogeny

Al-Anazi, Khalid Mashay; Ali, M. Ajmal; Kim, Soo-Yong; Rahman, M. Oliur; Farah, Mohammad Abul; Al-Hemaid, Fahad M.A.; Elangbam, Meena; Gurung, Arun Bahadur; Lee, Dong Kun

doi:10.1016/j.sjbs.2021.03.048

Cited by 5 publications

(2 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…F. longipetiolata had a relatively high A or T content and A/T polymerization at the SSR sites of cpDNA. These might be reasons for the high content of AT in the cp genome of F. longipetiolata, similar to the rich results of AT in other cp genomes [66,67]. Consistent with previous reports [68,69], the SSRs found in the cp genome of F. longipetiolata were mainly located in the LSC region and were enriched in the non-coding region.…”

Section: Discussionsupporting

confidence: 90%

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Liang

Wang

Zhang

et al. 2022

Life

View full text Add to dashboard Cite

Fagus longipetiolata Seemen is a deciduous tree of the Fagus genus in Fagaceae, which is endemic to China. In this study, we successfully sequenced the cp genome of F. longipetiolata, compared the cp genomes of the Fagus genus, and reconstructed the phylogeny of Fagaceae. The results showed that the cp genome of F. longipetiolata was 158,350 bp, including a pair of inverted repeat (IRA and IRB) regions with a length of 25,894 bp each, a large single-copy (LSC) region of 87,671 bp, and a small single-copy (SSC) region of 18,891 bp. The genome encoded 131 unique genes, including 81 protein-coding genes, 37 transfer RNA genes (tRNAs), 8 ribosomal RNA genes (rRNAs), and 5 pseudogenes. In addition, 33 codons and 258 simple sequence repeats (SSRs) were identified. The cp genomes of Fagus were relatively conserved, especially the IR regions, which showed the best conservation, and no inversions or rearrangements were found. The five regions with the largest variations were the rps12, rpl32, ccsA, trnW-CCA, and rps3 genes, which spread over in LSC and SSC. The comparison of gene selection pressure indicated that purifying selection was the main selective pattern maintaining important biological functions in Fagus cp genomes. However, the ndhD, rpoA, and ndhF genes of F. longipetiolata were affected by positive selection. Phylogenetic analysis revealed that F. longipetiolata and F. engleriana formed a close relationship, which partially overlapped in their distribution in China. Our analysis of the cp genome of F. longipetiolata would provide important genetic information for further research into the classification, phylogeny and evolution of Fagus.

show abstract

Section: Discussionsupporting

confidence: 90%

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Liang

Wang

Zhang

et al. 2022

Life

View full text Add to dashboard Cite

show abstract

“…Phylogenetic Analysis. CP genomes have been used to determine evolutionary relationships [100][101][102][103][104]. In the present study, a ML tree was constructed using 27 whole CP genome sequences to determine the evolutionary relationships of I. tectorum, I. japonica, I. dichotoma, and I. domestica with S. angustifolium as the outgroup (Figure 8).…”

Section: Identification Of Highly Variablementioning

confidence: 99%

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Feng

Wang

et al. 2022

BioMed Research International

View full text Add to dashboard Cite

Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.

show abstract

Plastogenomics Provides a Tool to Study Phylogenetic Interrelationships of Monilophytes: A Review

Kumar

Giri

Uniyal

2022

Ferns

View full text Add to dashboard Cite

The cp genome characterization of Adenium obesum: Gene content, repeat organization and phylogeny

Cited by 5 publications

References 68 publications

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Plastogenomics Provides a Tool to Study Phylogenetic Interrelationships of Monilophytes: A Review

Contact Info

Product

Resources

About