Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(4), P. 2278 - 2278

Published: Feb. 14, 2024

The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports such events have emerged in some lineages. In this study, we conducted a comprehensive comparison the complete plastomes from twenty-two species, covering seventeen genera three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) Papaveraceae. Our results revealed high level variability genome size Papaveraceae, ranging 151,864 bp to 219,144 length, which might be triggered by expansion IR region large number repeat sequences. Moreover, detected numerous large-scale rearrangements, primarily occurring Fumarioideae Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, several tRNA genes, particularly associated structural variation their plastomes. Furthermore, found that exhibited higher GC content more sequences than those Papaveroideae. showed Papaveroideae generally displayed relatively conserved plastome, exception Eomecon chionantha, while Hypecooideae harbored reconfigurable plastomes, showing size, content, order. This study provides insights into plastome evolution Papaveraceae may contribute development effective molecular markers.

Language: Английский

Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: June 24, 2024

Abstract In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for first time. The spans approximately 154,120 bp, comprising four sections: Large Single-Copy (LSC) (85,538 bp), Small (SSC) (17,984 and two Inverted Repeat (IR) regions (25,299 bp). A comparative study N. ’s with ten other species from various genera in Ranunculaceae family reveals substantial structural variations. contraction inverted repeat region influences boundaries single-copy regions, resulting a shorter size than species. When comparing those its related species, significant divergence is observed, particularly except damascena . Among these, A. glaucifolium displays highest average pairwise (0.2851) , followed by raddeana (0.2290) coerulea (0.1222). Furthermore, identified 12 distinct hotspot characterized elevated Pi values (> 0.1). These include trn H -GUG-psb mat K -trn Q -UUG, psb R -UCU, atp F -atp I rpo B -psb D ycf3-ndh J ndh C -cem pet -psa N- GUU-ndh V -GAC-rps12, ycf2-trn -CAU, -ycf1 Approximately, 24 tandem 48 palindromic forward repeats were detected plastome. analysis revealed 32 microsatellites majority being mononucleotide repeats. plastome, phenylalanine had number codons (1982 codons), while alanine least common amino acid 260 codons. phylogenetic tree, constructed using protein-coding genes, monophyletic clade damascene closely aligned Cimicifugeae tribe exhibiting robust support. This provides valuable genetic information precise identification, resolution, evolutionary studies

Language: Английский

Efficient assembly of plant genomes: A case study with evolutionary implications inRanunculus(Ranunculaceae)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 11, 2023

Abstract Currently, it is still a challenge - in terms of laboratory effort and cost, as well assembly quality to unravel the sequence large complex genomes from non-model/crop plants. This often hampers study evolutionarily intricate species groups. The species-rich genus Ranunculus (Ranunculaceae) an important angiosperm group for polyploidy, apomixis, reticulate evolution, biogeography. However, neither mitochondrial, nor high-quality nuclear genome sequences are available. limits phylogenomic, functional, taxonomic analyses thus far. Here, we tested Illumina short- read, Oxford Nanopore Technology (ONT) or PacBio/HiFi long-read, hybrid-read strategies. We used diploid progenitor R. cassubicifolius ( auricomus complex), selected best assemblies completeness, contiguity, scores. first assembled plastome (156 kbp, 85 genes) mitogenome (1.18 Mbp, 40 using Illumina-PacBio-hybrid strategies, respectively. also present updated phylogeny Ranunculaceae, including studies gene loss (e.g., infA , ycf15 rps ) with evolutionary implications. For genome, favored PacBio-based three-times polished filtered reads subsequently scaffolded into 8 pseudochromosomes by chromatin conformation data (Hi-C) representative sequence. obtained haploid 2.69 Gbp, 94.1% complete BUSCO ‘embryophyta_odb10’ genes found, 31,322 annotated genes. genomic information presented here will improve phylogenomic this complex, enable advanced evolutionary, biogeographic beyond Ranunculaceae future. Significance Statement model system flowering plants biogeography research. mitochondrial sequence, plastid evolution Ranunculaceae. Using Illumina, ONT, PacBio data, developed efficient strategy that can be applied other non-model Results useful improving population analyses, better functional at species, family level.

Language: Английский