Exploratory karyological and genome size studies in Chilean<i>Sophora</i>species

Espejo, Jaime; Baeza, C.; Loureiro, João; Santos, Conceição; Boshier, David; Ruíz, Eduardo

doi:10.1080/0028825x.2016.1144622

Cited by 3 publications

(1 citation statement)

References 32 publications

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“…These results may indicate a latitudinal difference in the species that needs further investigation. The genome size of this diploid species has been previously estimated to be 2C = 1.61 pg (Espejo & al., 2016). Our results are similar to those reported.…”

Section: Ene (Conc)mentioning

confidence: 99%

IAPT chromosome data 40

Marhold,

Kučera,

de Abreu

et al. 2023

TAXON

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Section: Ene (Conc)mentioning

confidence: 99%

IAPT chromosome data 40

Marhold,

Kučera,

de Abreu

et al. 2023

TAXON

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Evidence for both long-distance dispersal and isolation in the Southern Oceans: molecular phylogeny of Sophora sect Edwardsia (Fabaceae)

Shepherd

Heenan

2017

New Zealand Journal of Botany

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A first insight into the genomic background of Ilex pubescens (Aquifoliaceae) by flow cytometry and genome survey sequencing

Zhou

et al. 2023

BMC Genomics

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Background Ilex pubescens is an important traditional Chinese medicinal plant with many naturally occurring compounds and multiple pharmacological effects. However, the lack of reference genomic information has led to tardiness in molecular biology research and breeding programs of this plant. Results To obtain knowledge on the genomic information of I. pubescens, a genome survey was performed for the first time by next generation sequencing (NGS) together with genome size estimation using flow cytometry. The whole genome survey of I. pubescens generated 46.472 Gb of sequence data with approximately 82.2 × coverage. K-mer analysis indicated that I. pubescens has a small genome of approximately 553 Mb with 1.93% heterozygosity rate and 39.1% repeat rate. Meanwhile, the genome size was estimated to be 722 Mb using flow cytometry, which was possibly more precise for assessment of genome size than k-mer analysis. A total of 45.842 Gb clean reads were assembled into 808,938 scaffolds with a relatively short N50 of 760 bp. The average guanine and cytosine (GC) content was 37.52%. In total, 197,429 microsatellite motifs were detected with a frequency of 2.8 kb, among which mononucleotide motifs were the most abundant (up to 62.47% of the total microsatellite motifs), followed by dinucleotide and trinucleotide motifs. Conclusion In summary, the genome of I. pubescens is small but complex with a high level of heterozygosity. Even though not successfully applied for estimation of genome size due to its complex genome, the survey sequences will help to design whole genome sequencing strategies and provide genetic information support for resource protection, genetic diversity analysis, genetic improvement and artificial breeding of I. pubescens.

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Exploratory karyological and genome size studies in ChileanSophoraspecies

Cited by 3 publications

References 32 publications

IAPT chromosome data 40

IAPT chromosome data 40

Evidence for both long-distance dispersal and isolation in the Southern Oceans: molecular phylogeny of Sophora sect Edwardsia (Fabaceae)

A first insight into the genomic background of Ilex pubescens (Aquifoliaceae) by flow cytometry and genome survey sequencing

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