Structure of plastid genomes of photosynthetic eukaryotes

Yurina, N. P.; Sharapova, L. S.; Odintsova, M. S.

doi:10.1134/s0006297917060049

Cited by 14 publications

(10 citation statements)

References 77 publications

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“…The same to those of other land plants [48–50], the Arachis cp genome is a single circular molecule that displays a quadripartite structure (LSC, IRa, SSC, IRb). Moreover, the genome size, gene composition and order, GC content, as well as IR-SC boundaries are also rather conserved among the Arachis cp genomes that have been acquired in this study (Additional file 1) and among thirteen earlier published Arachis cp genomes [21, 34–36].…”

Section: Discussionmentioning

confidence: 95%

“…Arachis . As for other land plant species [48–50], the cp genome size and structure, as well as gene content and order are highly conserved among the twelve acquired cp genomes. Nevertheless, substantial SNDs, indels and SSRs have been identified from the acquired genomes, and most of these SNDs, indels, and SSRs are distributed at the two single copy genome regions (LSC and SSC).…”

Section: Discussionmentioning

confidence: 99%

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Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny

Wang¹,

Li³

et al. 2019

BMC Plant Biol

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BackgroundThe cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood.ResultsHere, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species.ConclusionIn summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny

Wang¹,

Li³

et al. 2019

BMC Plant Biol

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“…It is typical of higher plants to possess a chloroplast genome that has a quadripartite structure and a relatively well-conserved gene content and arrangement (Ravi et al 2008; Wicke et al 2011; Yurina et al 2017). However, minor to major variability in chloroplast genome structure has been observed in specific plant lineages (Guisinger et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Gichira

Avoga

et al. 2019

Bot Stud

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Background Majority of the species within Senecioneae are classified in Senecio , making it the tribe’s largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus Senecio being partly linked to this ambiguity. Infrageneric relationships within Senecio remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa. Dendrosenecio , an endemic genus in Africa, is one of its segregate genera. To heighten the understanding of species divergence and phylogeny within the tribe, the complete chloroplast genomes of the first five Senecio and six Dendrosenecio species were sequenced and analyzed in this study. Results The entire length of the complete chloroplast genomes was ~ 150 kb and ~ 151 kb in Dendrosenecio and Senecio respectively. Characterization of the 11 chloroplast genomes revealed a significant degree of similarity particularly in their organization, gene content, repetitive sequence composition and patterns of codon usage. The chloroplast genomes encoded an equal number of unique genes out of which 80 were protein-coding genes, 30 transfer ribonucleic acid, and four ribosomal ribonucleic acid genes. Based on comparative sequence analyses, the level of divergence was lower in Dendrosenecio . A total of 331 and 340 microsatellites were detected in Senecio and Dendrosenecio, respectively. Out of which, 25 and five chloroplast microsatellites (cpSSR) were identified as potentially valuable molecular markers. Also, through whole chloroplast genome comparisons and DNA polymorphism tests, ten divergent hotspots were identified. Potential primers were designed creating genomic tools to further molecular studies within the tribe. Intergeneric relationships within the tribe were firmly resolved using genome-scale dataset in partitioned and unpartitioned schemes. Two main clades, corresponding to two subtribes within the Senecioneae, were formed with the genus Ligularia forming a single clade while the other had Dendrosenecio, Pericallis, Senecio and Jacobaea . A sister relationship was revealed between Dendrosenecio and Pericallis whereas Senecio, and Jacobaea were closely placed in a different clade. Conclusion Besides emphasizing on the potential of chloroplast genome data in resolving intergeneric relationships within Senecioneae, this study provides genomic resources to facilitate species identification and phylogenetic recon...

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“…The plastid genome, or plastome, of flowering plants generally shows conserved structural organization, gene arrangement, and gene content ( Palmer et al, 1987 ; Odintsova & Yurina, 2003 ; Green, 2011 ; Jansen & Ruhlman, 2012 ; Yurina, Sharapova & Odintsova, 2017 ; De Vries & Archibald, 2018 ). The plastome size of photosynthetic angiosperms usually ranges from 145–165 kbp (Genbank–Genome, 2021), and contains 110–130 unique genes ( Jansen & Ruhlman, 2012 ; Yurina, Sharapova & Odintsova, 2017 ; De Vries & Archibald, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine

Fonseca

Nazareno

Thode

et al. 2022

PeerJ

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The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are responsible for the uncommon length of the genome. At least four events of IR expansion were observed among the seven Bignoniaceae species compared, suggesting multiple expansions of the IRs over the SC regions in the family. A comparison with 6,231 other complete plastomes of flowering plants available on GenBank revealed that the plastome of B. magnifica is the longest Lamiid plastome described to date. The newly generated plastid genome was used as a source of selected genes. These genes were combined with orthologous regions sampled from other species of Bignoniaceae and all gene alignments concatenated to infer a phylogeny of the family. The tree recovered is consistent with known relationships within the Bignoniaceae.

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Structure of plastid genomes of photosynthetic eukaryotes

Cited by 14 publications

References 77 publications

Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny

Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny

Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine

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