We are analyzing https://link.springer.com/article/10.1186/s12870-021-03202-3.

Title:
Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives | BMC Plant Biology
Description:
Background Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. Results We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. Conclusions Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.
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Keywords {🔍}

species, pubmed, article, repeat, plastome, repeats, google, scholar, genes, table, cas, fig, sequences, plastomes, melilotus, gene, genome, sequence, ycf, irlc, genomic, regions, inverted, repetitive, medicago, accd, chloroplast, content, substitution, plastid, data, clpp, dna, rearrangements, variations, tandem, rates, central, evol, loss, dentata, found, biol, analysis, individuals, coding, trigonella, intron, trna, copy,

Topics {✒️}

mpi-mp chloroplast references article download pdf repeat-mediated recombination-dependent replication synthesis-dependent strand annealing 8/codeml free-ratio model experienced repeat-mediated perturbations high-throughput sequencing technologies hmmer profile search full-length transcriptome assembly significant positive correlation repeat-mediated illegitimate recombination bmc plant biol recombination-dependent replication play inverted-repeat-lacking clade double-strand break trigonella foenum-graecum voucher recombination-dependent dna repair percent repetitive dna repeat-mediated trna duplicate increased locus-specific rates privacy choices/manage cookies codon-based maximum likelihood bmc evol biol chumley tw front plant sci trna duplication detected colon represent length full access minimum repeat size inverted region involving plant mol biol genome resequencing data extensive genomic rearrangements guangpeng ren recombination-dependent replication total genomic dna distinct plastome configurations integrating search large single copy creative commons licence abundant repetitive dna important legume forage abundant repeat type genome resequencing reads article wu modified ctab procedure sci rep-uk molecular phylogenetic analysis tobacco plastome published related subjects

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         description:Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.
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      headline:Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives
      description:Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.
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          Trigonella
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         Agriculture
         Tree Biology
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      name:State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
      name:State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
      name:State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
      name:State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
      name:State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
      name:State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
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