Cytogenetic analysis of Bienertia sinuspersici Akhani as the first step in genome sequencing

Sevilleno, Samantha Serafin; Ju, Yoon Ha; Kim, Jung Sun; Mancia, Franklin Hinosa; Byeon, Eun Ju; Cabahug, Raisa Aone M.; Hwang, Yoon‐Jung

doi:10.1007/s13258-019-00908-5

Cited by 3 publications

(1 citation statement)

References 68 publications

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“…C0t-1 DNA has some interesting applications outside of its use in blocking the binding of repetitive DNA sequences in exome captures. It can be used in fluorescence in situ hybridization (FISH) to locate repetitive DNA sequences within chromosomes (Chang et al, 2008; Sevilleno et al, 2020) or it can be sequenced to analyze the repetitive DNA (low c0t DNA) contents within a genome. This approach has been used to analyze repetitive DNA contents within chicken (Wicker et al, 2005), banana (Hřibová et al, 2008), and beet (Zakrzewski et al, 2010) genomes.…”

Section: Discussionmentioning

confidence: 99%

Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker

Kesälahti,

Kumpula,

Cervantes

et al. 2024

Preprint

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Large and highly repetitive genomes are common. However, research interests usually lie within the non-repetitive parts of the genome, as they are more likely functional, and can be used to answer questions related to adaptation, selection, and evolutionary history. Exome capture is a cost-effective method for providing sequencing data from protein-coding parts of the genes. C0t-1 DNA blockers consist of repetitive DNA and are used in exome captures to prevent the hybridization of repetitive DNA sequences to capture baits or bait-bound genomic DNA. Universal blockers target repetitive regions shared by many species, while species-specific c0t-1 DNA is prepared from the DNA of the studied species, thus perfectly matching the repetitive DNA contents of the species. So far the use of species-specific c0t-1 DNA has been limited to a few model species. Here, we evaluated the performance of blocker treatments in exome captures of Pinus sylvestris, a widely distributed conifer species with a large (> 20 Gbp) and highly repetitive genome. We compared treatment with a commercial universal blocker to treatments with species-specific c0t-1 (30,000 ng and 60,000 ng). Species-specific c0t-1 captured more unique exons than the initial set of targets, reduced sequencing of tandem repeats, and produced more target regions with high read coverage and narrower depth distribution than the universal blocker. Based on our results, we recommend optimizing exome captures by using at least 60,000 ng species-specific c0t-1 DNA. It is relatively easy and fast to prepare and can also be used with existing bait set designs.

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Section: Discussionmentioning

confidence: 99%

Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker

Kesälahti,

Kumpula,

Cervantes

et al. 2024

Preprint

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Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review

Maravilla

Rosato

Rosselló

2021

Plants

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The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.

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In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C₃, C₄, CAM, and SCC₄ model plants

Won

Soundararajan

Irulappan

et al. 2023

PeerJ

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Single-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C3, C4, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC4 plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC4 species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC4 plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC4 system in comparison with other C3, C4, and CAM model plants.

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Cytogenetic analysis of Bienertia sinuspersici Akhani as the first step in genome sequencing

Cited by 3 publications

References 68 publications

Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker

Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker

Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review

In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C₃, C₄, CAM, and SCC₄ model plants

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Cytogenetic analysis of Bienertia sinuspersici Akhani as the first step in genome sequencing

Cited by 3 publications

References 68 publications

Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker

Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker

Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review

In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants

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Product

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In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C₃, C₄, CAM, and SCC₄ model plants