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

Feng, Jinglu; Wu, Li‐Wei; Wang, Qing; Pan, Yunjia; Li, Baoli; Lin, Yu-lin; Yao, Hui

doi:10.1155/2022/2194021

Cited by 10 publications

(8 citation statements)

References 101 publications

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“…Comparison of all 10 Onagraceae plastomes revealed a high degree of conservation in genome size, gene number, structure, and IR boundaries. However, to further elucidate the phylogenetic analysis and evolution in Ludwigia and Onagraceae, additional chloroplast genomes will be necessary, as highlighted in recent studies of Iris and Aristidoideae species [104].…”

Section: Discussionmentioning

confidence: 99%

Sequencing, de novo assembly ofLudwigiaplastomes, and comparative analysis within the Onagraceae family

Barloy-Hubler,

Le Gac,

Boury

et al. 2023

Preprint

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Background: The Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera, including the genus Ludwigia L., which is comprised of 82 species. There are few genomic resources for Onagraceae, which limits phylogenetic and population genetics, as well as genomic studies. In this study, new complete plastid genomes of Ludwigia grandiflora subps. hexapetala (Lgh) and Ludwigia peploides subsp montevidensis (Lpm) were generated using a combination of different sequencing technologies. These plastomes were then compared to the published Ludwigia octovalvis (Lo) plastid genome, which was re-annotated by the authors. Results: We initially sequenced and assembled the chloroplast (cp) genomes of Lpm and Lgh using a hybrid strategy. We observed the existence of two Lgh haplotypes and two potential Lpm haplotypes. Lgh, Lpm, and Lo plastomes were similar in terms of genome size, gene number, structure, and inverted repeat (IR) boundaries, comparable to other species in the Myrtales order. A total of 45 to 65 SSRs (simple sequence repeats), were detected, depending on the species, with the majority consisting solely of A and T, which is common among angiosperms. Four chloroplast genes (matK, accD, ycf2 and ccsA) were found under positive selection pressure, which is commonly associated with plant development, and especially in aquatic plants such as Lgh, and Lpm. Conclusion: Our hybrid sequencing approach revealed the presence of two Lgh plastome haplotypes which will help to advance phylogenetic and evolutionary studies, not only specifically for Ludwigia, but also the Onagraceae family and Myrtales order. To enhance the robustness of our findings, a larger dataset of chloroplast genomes would be beneficial.

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Section: Discussionmentioning

confidence: 99%

Sequencing, de novo assembly ofLudwigiaplastomes, and comparative analysis within the Onagraceae family

Barloy-Hubler,

Le Gac,

Boury

et al. 2023

Preprint

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“…A comparison of 20 Indigofera plastomes revealed that rp s19, ycf 1, and ndh F demonstrated pronounced expansion or contraction, as reported in Salvia L., Amygdalus L., Iris L., Prunus L. subg. Cerasus Mill., and Asteraceae ( Du et al., 2021 ; Pascual-Diaz et al., 2021 ; Du et al., 2022 ; Feng et al., 2022a ; Li et al., 2022c ). These subtle differences in boundaries could potentially be used for species identification.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

et al. 2023

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IntroductionIndigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera.MethodsHere, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.Results and discussionThe chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

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“…Thus, we suggest as the most useful for phylogenetic analyses of Iris the following loci that show high variability and lack of loop structures: atpF/atpH, rps15/ycf1, atpA/atpF, trnL-UAA/trnF-GAA, trnG-UCC/trnR-UCU, psaA/ycf3. Earlier, two of these loci were recommended for phylogenetic inference based on an analysis of nucleotide diversity in Iris: rps15-ycf1 (Feng et al 2022) and trnG-UCC-trnR-UCU (Zhang et al 2021).…”

Section: Repeat Analysismentioning

confidence: 99%

Plastid genomes of four species of Iris from subgenus Scorpiris

Ortikov,

Kurbonalieva,

Alieva

et al. 2023

PDCA

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The taxonomic complexity of Iris (Iridaceae) is high, and its molecular phylogeny remains largely unknown. With the growing availability of full plastid genomes of species representing major taxonomic groups within Iris, it will become possible to produce a robust phylogenetic tree and reconstruct the evolutionary history of the genus. With this objective in mind, we sequenced and analyzed the chloroplast genomes of four species from subgenus Scorpiris native to Uzbekistan: Iris austrotschatkalica, I. pseudocapnoides, I. victoris and I. hippolyti. The phylogenetic tree obtained agreed well with those produced earlier with a limited number of chloroplast markers. We suggest as the most useful for phylogenetic analyses of Iris the following loci that show high variability and lack of loop structures: atpF/atpH, rps15/ycf1, atpA/atpF, trnL-UAA/trnF-GAA, trnG-UCC/trnR-UCU, and psaA/ycf3.

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

Cited by 10 publications

References 101 publications

Sequencing, de novo assembly ofLudwigiaplastomes, and comparative analysis within the Onagraceae family

Sequencing, de novo assembly ofLudwigiaplastomes, and comparative analysis within the Onagraceae family

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

Plastid genomes of four species of Iris from subgenus Scorpiris

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