Complete Chloroplast Genome Sequences of &lt;em&gt;Clematis&lt;/em&gt;: IR Expansion and Relative Rates of Synonymous Substitutions

Choi, Kyoung Su; Jeong, Keum Seon; Ha, Young‐Ho; Choi, Kyung

doi:10.20944/preprints201804.0106.v1

Cited by 4 publications

(4 citation statements)

References 2 publications

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“…Recently, as the availability of plastid genomes increases, IR border shifts become more frequently reported, yet large-scale expansion and contraction of IR are considered uncommon phenomena 81 , principally observed in heterotrophs 83 and a few autotrophs 84 . However, unlike the case of rearrangement that frequently occurred in the CP genome of which IR remarkably shifted, for instance, Pelargonium 85 , conifers 79 , 86 , Clemati 87 , legumes 59 , Asarum 88 , etc., the genome structure and gene order within the apioid superclade are significantly conserved 81 . Hence, the large-scale alteration of IR within this clade has great benefit for the study of the underlying mechanism causing large-scale expansion and contraction of IR 81 .…”

Section: Discussionmentioning

confidence: 93%

Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

Yuan

Sha

Xiong

et al. 2021

Sci Rep

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Ligusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

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Section: Discussionmentioning

confidence: 93%

Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

Yuan

Sha

Xiong

et al. 2021

Sci Rep

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“…In B. itoana plastome, rps15 and rpl32 are resided in IRs, typically located in SSC. Previous studies proved that two copies of genes in IR offer more opportunities to correct the aberrant mutations (Zhu et al 2016;Choi et al 2018). Thus, we could reasonably speculate that IRs may shelter these genes from being deleted in B. itoana plastome.…”

Section: Unusual Retention Of Genes In B Itoana Plastomementioning

confidence: 54%

Peer Review #3 of "Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements (v0.1)"

Logacheva¹

2019

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Plastomes of heterotrophs went through varying degrees of degradation along with the transition from autotrophic to heterotrophic lifestyle. Here we identified the plastome of mycoheterotrophic species Burmannia itoana and compared it with those of its reported relatives including three autotrophs and one heterotroph (Thismia tentaculata) in Dioscoreales. B. itoana yields a rampantly degraded plastome reduced in size and gene numbers at the advanced stages of degradation. Its length is 44, 463 bp with a quadripartite structure. B. itoana plastome contains 33 tentatively functional genes and six tentative pseudogenes, including several unusually retained genes. These unusual retention suggest that the inverted repeats regions (IRs) and possibility of being compensated may prolong retention of genes in plastome at the advanced stage of degradation. Otherwise, six rearrangements including four inversions (Inv1/Inv2/Inv3/Inv4) and two translocations (Trans1/Trans2) were detected in B. itoana plastome versus its autotrophic relative Burmannia disticha. We speculate that Inv1 may be mediated by recombination of distinct tRNA genes, while Inv2 is likely consequence of extreme gene losses due to the shift to heterotrophic lifestyle. The other four rearrangements involved in IRs and SSC may attribute to multiple waves of IRs and overlapping inversions. Our study fills the gap of knowledge about plastomes of heterotroph in Burmannia and provides a new evidence for the convergent degradation patterns of plastomes en route to heterotrophic lifestyle.

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“…In B. itoana plastome, rps15 and rpl32 are resided in IRs, typically located in SSC. Previous studies proved that two copies of genes in IR offer more opportunities to correct the aberrant mutations (Zhu et al, 2016; Choi et al, 2018). Thus, we could reasonably speculate that IRs may shelter these genes from being deleted in B. itoana plastome.…”

Section: Discussionmentioning

confidence: 99%

Plastome of mycoheterotrophicBurmannia itoanaMak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements

Qian

Yao

et al. 2019

PeerJ

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Plastomes of heterotrophs went through varying degrees of degradation along with the transition from autotrophic to heterotrophic lifestyle. Here, we identified the plastome of mycoheterotrophic species Burmannia itoana and compared it with those of its reported relatives including three autotrophs and one heterotroph (Thismia tentaculata) in Dioscoreales. B. itoana yields a rampantly degraded plastome reduced in size and gene numbers at the advanced stages of degradation. Its length is 44,463 bp with a quadripartite structure. B. itoana plastome contains 33 tentatively functional genes and six tentative pseudogenes, including several unusually retained genes. These unusual retention suggest that the inverted repeats (IRs) regions and possibility of being compensated may prolong retention of genes in plastome at the advanced stage of degradation. Otherwise, six rearrangements including four inversions (Inv1/Inv2/Inv3/Inv4) and two translocations (Trans1/Trans2) were detected in B. itoana plastome vs. its autotrophic relative B. disticha. We speculate that Inv1 may be mediated by recombination of distinct tRNA genes, while Inv2 is likely consequence of extreme gene losses due to the shift to heterotrophic lifestyle. The other four rearrangements involved in IRs and small single copy region may attribute to multiple waves of IRs and overlapping inversions. Our study fills the gap of knowledge about plastomes of heterotroph in Burmannia and provides a new evidence for the convergent degradation patterns of plastomes en route to heterotrophic lifestyle.

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Complete Chloroplast Genome Sequences of <em>Clematis</em>: IR Expansion and Relative Rates of Synonymous Substitutions

Abstract: Genus

Cited by 4 publications

References 2 publications

Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

Peer Review #3 of "Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements (v0.1)"

Plastome of mycoheterotrophicBurmannia itoanaMak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements

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