Lost and Found: Return of the Inverted Repeat in the Legume Clade Defined by Its Absence

Choi, In‐Su; Jansen, Robert K.; Ruhlman, Tracey A.

doi:10.1093/gbe/evz076

Cited by 76 publications

(136 citation statements)

References 75 publications

(87 reference statements)

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“…Gene conversion during speciation is thought to be responsible for small IR expansions or contractions. (Wang et al, 2008;Goulding et al, 1996;Khakhlova & Bock, 2006;Meng et al, 2018;Choi, Jansen & Ruhlman, 2019).…”

Section: Ir Expansion Analysismentioning

confidence: 99%

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

Huang

Cano

et al. 2020

PeerJ

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The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

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Section: Ir Expansion Analysismentioning

confidence: 99%

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

Huang

Cano

et al. 2020

PeerJ

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“…Seeds were germinated and grown in the greenhouse at UT Austin and emergent leaves were collected in liquid nitrogen from single individuals. All DNA protocols followed Choi et al (2019), including isolation, sequencing, assembly, and annotation of plastomes. Completed plastome sequences were submitted to NCBI and GenBank accession numbers are given in Table S1.…”

Section: Additional Taxon Selection and Plastome Sequencingmentioning

confidence: 99%

Caught in the Act: Variation in plastid genome inverted repeat expansion within and between populations of Medicago minima

Choi

Jansen

Ruhlman

2020

Ecology and Evolution

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A plastid genome (plastome) containing large and small single-copy regions (LSC and SSC, respectively) separated by a large inverted repeat (IR) is widely acknowledged to represent the ancestral form of the plastome monomer of land plants. The typical plastome IR is on the order of 25-30 kb with most size variation driven by expansion and contraction of IR boundaries (Jansen & Ruhlman, 2012; Ruhlman & Jansen, 2014). The ancestral form is not, however, ubiquitous among photosynthetic plants. In disparate lineages, the IR has massively expanded, contracted, and been entirely lost (Ruhlman & Jansen, 2018; Zhu et al., 2016). Major IR expansions identified among Pelargonium species yielded the largest plastomes, which contain IRs that ranged up

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“…Moreover, the repeats of plastid genomes will be helpful for identifying polymorphisms at the species level for deducing distant phylogenetic relationships among Campanulaceae species. Repeats were previously inferred to associate with plastome structural variation [98][99][100][101]. In this study, the plastomes of all studied species possessed large amount of repeats and longer repeats, and presented the structural variations.…”

Section: Plos Onementioning

confidence: 61%

Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications

Wang

2020

PLoS ONE

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The conflicts exist between the phylogeny of Campanulaceae based on nuclear ITS sequence and plastid markers, particularly in the subdivision of Cyanantheae (Campanulaceae). Besides, various and complicated plastid genome structures can be found in species of the Campanulaceae. However, limited availability of genomic information largely hinders the studies of molecular evolution and phylogeny of Campanulaceae. We reported the complete plastid genomes of three Cyanantheae species, compared them to eight published Campanulaceae plastomes, and shed light on a deeper understanding of the applicability of plastomes. We found that there were obvious differences among gene order, GC content, gene compositions and IR junctions of LSC/IRa. Almost all protein-coding genes and amino acid sequences showed obvious codon preferences. We identified 14 genes with highly positively selected sites and branch-site model displayed 96 sites under potentially positive selection on the three lineages of phylogenetic tree. Phylogenetic analyses showed that Cyananthus was more closely related to Codonopsis compared with Cyclocodon and also clearly illustrated the relationship among the Cyanantheae species. We also found six coding regions having high nucleotide divergence value. Hotpot regions were considered to be useful molecular markers for resolving phylogenetic relationships and species authentication of Campanulaceae.

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Lost and Found: Return of the Inverted Repeat in the Legume Clade Defined by Its Absence

Cited by 76 publications

References 75 publications

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

Caught in the Act: Variation in plastid genome inverted repeat expansion within and between populations of Medicago minima

Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications

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