The complete chloroplast genome of weedy rye <i>Secale cereale</i> subsp. <i>segetale</i>

Du, Tianyu; Hu, Yiyu; Sun, Yanqing; Ye, Chu-Yu; Shen, Enhui

doi:10.1080/23802359.2022.2080600

Cited by 2 publications

(3 citation statements)

References 13 publications

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“…The results obtained by Du et al 11 are similar to ours. The size of the genome, the lengths of the LSC, SSC and IR sequences differ slightly.…”

Section: Discussionsupporting

confidence: 90%

“…In contrast, larger differences are seen in the number of genes. The genome we analyzed contains 73 protein-coding genes (82 in 11 ), 30 tRNA genes (41 in 11 ) four rRNA genes (8 in 11 ) and five conserved chloroplast open reading frames (ORFs)(lack of information in 11 ).…”

Section: Discussionmentioning

confidence: 99%

“…So far, only the incomplete S. cereale cpDNA sequences (NC_021761) 8 , three sequences for S. strictum (KY636137, KY636138 and OL979486) 9 and S. sylvestre ( MW557517 ) 10 are available. The chloroplast genome of S. segetale has recently been published 11 , however a comprehensive phylogenetic analysis based on whole chloroplast genomes has not been done to date. Therefore, we presume that analysis of the complete chloroplast genome sequences of Secale spp., starting with S. sylvestre 10 , will be useful and cost-effective for evolutionary and phylogenetic studies, as it was suggested by our previous studies 12 .…”

Section: Introductionmentioning

confidence: 99%

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Molecular structure, comparative and phylogenetic analysis of the complete chloroplast genome sequences of weedy rye Secale cereale ssp. segetale

Skuza

Androsiuk

Gastineau

et al. 2023

Sci Rep

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The complete chloroplast genome of Secale cereale ssp. segetale (Zhuk.) Roshev. (Poaceae: Triticeae) was sequenced and analyzed to better use its genetic resources to enrich rye and wheat breeding. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other complete chloroplast genomes of the five Secale species, and multigene phylogeny. As a result of the study, it was determined that the chloroplast genome is 137,042 base pair (bp) long and contains 137 genes, including 113 unique genes and 24 genes which are duplicated in the IRs. Moreover, a total of 29 SSRs were detected in the Secale cereale ssp. segetale chloroplast genome. The phylogenetic analysis showed that Secale cereale ssp. segetale appeared to share the highest degree of similarity with S. cereale and S. strictum. Intraspecific diversity has been observed between the published chloroplast genome sequences of S. cereale ssp. segetale. The genome can be accessed on GenBank with the accession number (OL688773).

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“…The results obtained by Du et al 11 are similar to ours. The size of the genome, the lengths of the LSC, SSC and IR sequences differ slightly.…”

Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular structure, comparative and phylogenetic analysis of the complete chloroplast genome sequences of weedy rye Secale cereale ssp. segetale

Skuza

Androsiuk

Gastineau

et al. 2023

Sci Rep

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Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants

Komluski,

Filatova,

Schlütz

et al. 2024

Preprint

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In medieval central Europe, rye was one of the most important agricultural crops. It’s properties of frost resistance, general resilience and resistance to many pathogens made it invaluable for medieval farmers. Rye has a distinct domestication history compared to other cereal crops and was not domesticated directly from its wild ancestors, like barley and wheat. Rye is considered to be a “secondary domesticate”, i.e. a crop with domestication traits that initially evolved as an arable weed but eventually was intentionally sown and propagated as a crop. To study the history of rye domestication, genetic sequences of present-day plant populations as well as material from historical samples can provide insights into the temporal and spatial signatures of domestication. In this study we combined archaeobotanical methods and ancient DNA sequencing of well-preserved, historical rye material to study patterns of genetic diversity across four centuries. We first applied archaeobotanical methods to characterize rye material acquired from construction material ranging from the 14thto 18thcentury from different locations in Germany. Next, we extracted DNA to sequence complete chloroplast genomes of six individual samples. We compared the 115,000 bp chloroplast genomes of historical rye samples to chloroplast genomes of other cereal crops and identified 217 single nucleotide variants exclusive to historical samples. By comparing the aDNA chloroplast samples with modern rye chloroplasts, we show that the genetic variation in ancient rye populations was exceptionally high compared to samples from contemporary rye cultivars. This confirms that late domestication and selective breeding have reduced genetic variation in this important crop species only in the last few centuries.HighlightsHistorical plant material covering four centuries was obtained from half-timbered houses from five locations in GermanyIntegrative archaeobotanical analyses and ancient DNA sequencing provided insights into genetic diversity of rye plants from historical farmland fields.Sequence analyses of complete assembled chloroplast genomes reveal expectational diversity in rye populations.Late domestication of rye preserved genetic diversity over centuries. The more recent intensification of rye breeding has however conferred a considerable loss of genetic diversity in this important crop.

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The complete chloroplast genome of weedy rye Secale cereale subsp. segetale

Cited by 2 publications

References 13 publications

Molecular structure, comparative and phylogenetic analysis of the complete chloroplast genome sequences of weedy rye Secale cereale ssp. segetale

Molecular structure, comparative and phylogenetic analysis of the complete chloroplast genome sequences of weedy rye Secale cereale ssp. segetale

Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants

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