Complete Chloroplast Genome Sequences of Two Ehretia Trees (Ehretia cymosa and Ehretia obtusifolia): Genome Structures and Phylogenetic Analysis

Alawfi, Mohammad S.; Alzahrani, Dhafer A.; Albokhari, Enas

doi:10.3390/f14071486

Cited by 3 publications

(1 citation statement)

References 86 publications

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“…The chloroplast genome of plants plays a crucial role in elucidating chloroplast functions, species identification, population genetics, phylogenetics, and conservation of plant resources [13][14][15][16]. In this study, we conducted a comprehensive analysis of the complete cp genome sequence of V. japonicum using second-generation sequencing technology.…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)

Zhu,

Liu,

et al. 2023

Forests

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Viburnum japonicum (Thunb.) Sprengel is an endangered species endemic to coastal regions of eastern Asia (China, Japan, and South Korea). However, its systematic position has been controversial. In this study, we present the complete chloroplast (cp) genome of V. japonicum (GenBank OP644292) sequenced using the Illumina NovaSeq platform. The cp genome has a total length of 158,606 bp and a G+C contents of 38.08%. It consists of a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs) regions measuring 87,060 bp, 18,510 bp, and 26,516 bp, respectively. A total of 131 genes were identified, including 87 protein-coding genes, 36 transfer RNA genes (tRNAs), and 8 ribosomal RNA genes(rRNAs). Additionally, a total of 44 dispersed repeats were detected, including three types: forward, palindromic, and reverse. Among the 38 SSR loci that were discovered, the majority were mononucleotide loci composed of A/T. Furthermore, we found that 15 genes (accD, atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps12, rps16, trnA-UGC, trnI, trnK-UUU, and trnL-UAA) contain one intron, while clpP and ycf3 have two introns. The relative synonymous codon usage (RSCU) analysis detected 31 high-frequency codons, where A/U bases accounted for 93.55% of the total, indicating an asymmetry in chloroplast gene and a presence for A/U bases. Comparative analysis of genome structure and sequences data of V. japonicum chloroplast genomes in comparison with other closely related species demonstrated a high level of conservation in their structure and organization. Furthermore, three mutation hotspots (psbH, rps19, and trnL) were identified, which could be valuable for future phylogenetic and population genetic research. Phylogenetic analysis revealed that the two accessions of V. japonicum are closely related to a group of V. setigerum, V. erosum, and V. fordiae within the Viburnum genus. In conclusion, this study provides important insights for accurately identifying and understanding the phylogeny of Viburnum species through the complete cp genome sequencing of V. japonicum.

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Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)

Zhu,

Liu,

et al. 2023

Forests

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Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

Ren,

Peng,

et al. 2024

Forests

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The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources.

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The Complete Chloroplast Genome Sequence of the Medicinal Moss Rhodobryum giganteum (Bryaceae, Bryophyta): Comparative Genomics and Phylogenetic Analyses

Shen,

Liu,

Hao

et al. 2024

Genes

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Rhodobryum giganteum (Bryaceae, Bryophyta), a rare medicinal bryophyte, is valued for its cardiovascular therapeutic properties in traditional Chinese medicine. This study presents the first complete chloroplast genome sequence of R. giganteum, including its assembly and annotation. The circular chloroplast genome of R. giganteum is 124,315 bp in length, displaying a typical quadripartite structure with 128 genes: 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Analyses of codon usage bias, repetitive sequences, and simple sequence repeats (SSRs) revealed an A/U-ending codon preference, 96 repetitive sequences, and 385 SSRs in the R. giganteum chloroplast genome. Nucleotide diversity analysis identified 10 high mutational hotspots. Ka/Ks ratio analysis suggested potential positive selection in rpl20, rps18, petG, and psbM genes. Phylogenetic analysis of whole chloroplast genomes from 38 moss species positioned R. giganteum within Bryales, closely related to Rhodobryum laxelimbatum. This study augments the chloroplast genomic data for Bryales and provides a foundation for molecular marker development and genetic diversity analyses in medicinal bryophytes.

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Complete Chloroplast Genome Sequences of Two Ehretia Trees (Ehretia cymosa and Ehretia obtusifolia): Genome Structures and Phylogenetic Analysis

Cited by 3 publications

References 86 publications

Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)

Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)

Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

The Complete Chloroplast Genome Sequence of the Medicinal Moss Rhodobryum giganteum (Bryaceae, Bryophyta): Comparative Genomics and Phylogenetic Analyses

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