scholarly journals Estimation of Genome Size in the Endemic Species Reseda pentagyna and the Locally Rare Species Reseda lutea Using comparative Analyses of Flow Cytometry and K-Mer Approaches

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1362
Author(s):  
Fahad Al-Qurainy ◽  
Abdel-Rhman Z. Gaafar ◽  
Salim Khan ◽  
Mohammad Nadeem ◽  
Aref M. Alshameri ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Genome Size ◽  
General Formula ◽  
Genome Sequencing ◽  
Endemic Species ◽  
Rare Species ◽  
Sequencing Data ◽  
Repeat Content ◽  
Taxonomic Studies ◽  
Paired End Sequencing

Genome size is one of the fundamental cytogenetic features of a species, which is critical for the design and initiation of any genome sequencing projects and can provide essential insights in studying taxonomy, cytogenetics, phylogenesis, and evolutionary studies. However, this key cytogenetic information is almost lacking in the endemic species Reseda pentagyna and the locally rare species Reseda lutea in Saudi Arabia. Therefore, genome size was analyzed by propidium iodide PI flow cytometry and compared to k-mer analysis methods. The standard method for genome size measures (flow cytometry) estimated the genome size of R. lutea and R. pentagyna with nuclei isolation MB01 buffer were found to be 1.91 ± 0.02 and 2.09 ± 0.03 pg/2 °C, respectively, which corresponded approximately to a haploid genome size of 934 and 1.022 Mbp, respectively. For validation, K-mer analysis was performed on both species’ Illumina paired-end sequencing data from both species. Five k-mer analysis approaches were examined for biocomputational estimation of genome size: A general formula and four well-known programs (CovEST, Kmergenie, FindGSE, and GenomeScope). The parameter preferences had a significant impact on GenomeScope and Kmergenie estimates. While the general formula estimations did not differ considerably, with an average genome size of 867.7 and 896. Mbp. The differences across flow cytometry and biocomputational predictions may be due to the high repeat content, particularly long repetitive regions in both genomes, 71% and 57%, which interfered with k-mer analysis. GenomeScope allowed quantification of high heterozygosity levels (1.04 and 1.37%) of R. lutea and R. pentagyna genomes, respectively. Based on our observations, R. lutea may have a tetraploid genome or higher. Our results revealed fundamental cytogenetic information for R. lutea and R. pentagyna, which should be used in future taxonomic studies and whole-genome sequencing.

scholarly journals Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 270 ◽  
Author(s):  
Yamkela Mgwatyu ◽  
Allison Anne Stander ◽  
Stephan Ferreira ◽  
Wesley Williams ◽  
Uljana Hesse
Keyword(s):  
Flow Cytometry ◽  
Genome Size ◽  
Internal Standard ◽  
Size Estimation ◽  
Sequencing Data ◽  
Aspalathus Linearis ◽  
Paired End Sequencing ◽  
Size Estimates ◽  
Genome Projects ◽  
Isolation Buffer

Plant genomes provide information on biosynthetic pathways involved in the production of industrially relevant compounds. Genome size estimates are essential for the initiation of genome projects. The genome size of rooibos (Aspalathus linearis species complex) was estimated using DAPI flow cytometry and k-mer analyses. For flow cytometry, a suitable nuclei isolation buffer, plant tissue and a transport medium for rooibos ecotype samples collected from distant locations were identified. When using radicles from commercial rooibos seedlings, Woody Plant Buffer and Vicia faba as an internal standard, the flow cytometry-estimated genome size of rooibos was 1.24 ± 0.01 Gbp. The estimates for eight wild rooibos growth types did not deviate significantly from this value. K-mer analysis was performed using Illumina paired-end sequencing data from one commercial rooibos genotype. For biocomputational estimation of the genome size, four k-mer analysis methods were investigated: A standard formula and three popular programs (BBNorm, GenomeScope, and FindGSE). GenomeScope estimates were strongly affected by parameter settings, specifically CovMax. When using the complete k-mer frequency histogram (up to 9 × 105), the programs did not deviate significantly, estimating an average rooibos genome size of 1.03 ± 0.04 Gbp. Differences between the flow cytometry and biocomputational estimates are discussed.

Novelties in Phoradendron killipii (Viscaceae): an endemic and rare species from Colombia

Phytotaxa ◽  
2021 ◽  
Vol 490 (3) ◽  
pp. 285-290
Author(s):  
JHON S. MURILLO-SERNA ◽  
GRETA A. DETTKE ◽  
ISABEL CARMONA-GALLEGO ◽  
FERNANDO ALZATE
Keyword(s):  
Endemic Species ◽  
Rare Species ◽  
Original Material ◽  
Distribution And Ecology ◽  
Taxonomic Studies ◽  
First Time

Phoradendron killipii is an endemic species from Colombia, initially known only from the original material. Ten herbarium sheets of this species were found during taxonomic studies of Colombian Viscaceae, allowing to figure out some aspects that remained unclear since P. killipii was published, until now. The morphology of P. killipii fruits and staminate inflorescences is described here for the first time, confirming its generic identity. Evidence of the dioecy of the species and some aspects of its distribution and ecology are also discussed.

scholarly journals Analysis of chromosome karyotype and genome size in echiuran Urechis unicinctus Drasche, 1880 (Polychaeta, Urechidae)

2019 ◽  
Vol 13 (1) ◽  
pp. 75-85
Author(s):  
Zhenkui Qin ◽  
Xueyu Li ◽  
Danwen Liu ◽  
Qing Wang ◽  
Li Lu ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Molecular Biology ◽  
Genome Size ◽  
Genome Sequencing ◽  
Taxonomic Study ◽  
Whole Genome ◽  
Urechis Unicinctus ◽  
Coelomic Cells ◽  
2C Dna Content ◽  
Chicken Erythrocytes

Karyotype and genome size are two primary cytogenetic characteristics of species, which are of great significance to the study of cytogenetics, taxonomy, phylogenesis, evolution as well as molecular biology. However, this basic cytogenetic information in echiurans is lacking. Therefore, we analyzed characteristics of karyotype and genome size in the echiuran worm Urechisunicinctus Drasche, 1880. In this study, coelomic cells of U.unicinctus were used for analyzing the genome size by a flow cytometry with chicken erythrocytes as DNA standard, and the 2C DNA content was determined to be 1.85 pg, which was corresponded to the genome size of 904.58 Mbp approximately. Furthermore, trochophores of U.unicinctus were dissociated and cells were utilized for preparing the chromosomes stained with DAPI, and the karyotype was determined as 2n = 30 (10m + 6sm + 6st + 8t), FN=52. Our data provided the basic cytogenetic information of U.unicinctus, which could be utilized in taxonomic study and whole-genome sequencing in future.

scholarly journals Detection of complex structural variation from paired-end sequencing data

2017 ◽  
Author(s):  
Joseph G. Arthur ◽  
Xi Chen ◽  
Bo Zhou ◽  
Alexander E. Urban ◽  
Wing Hung Wong
Keyword(s):  
Genome Sequencing ◽  
Genome Analysis ◽  
Structural Variation ◽  
State Of The Art ◽  
Whole Genome ◽  
Structural Variants ◽  
Sequencing Data ◽  
Complex Structural Variation ◽  
Complex Structural ◽  
Paired End Sequencing

AbstractDetecting structural variants (SVs) from sequencing data is key to genome analysis, but methods using standard whole-genome sequencing (WGS) data are typically incapable of resolving complex SVs with multiple co-located breakpoints. We introduce the ARC-SV method, which uses a probabilistic model to detect arbitrary local rearrangements from WGS data. Our method performs well on simple SVs while surpassing state-of-the-art methods in complex SV detection.

scholarly journals High-precision and cost-efficient sequencing for real-time COVID-19 surveillance

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sung Yong Park ◽  
Gina Faraci ◽  
Pamela M. Ward ◽  
Jane F. Emerson ◽  
Ha Youn Lee
Keyword(s):  
Los Angeles ◽  
Whole Genome Sequencing ◽  
Real Time ◽  
Genome Sequencing ◽  
High Precision ◽  
High Throughput Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Public Health Response ◽  
Cost Efficient

AbstractCOVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneously achieved high precision, simple workflow, and low cost. We developed a high-precision, cost-efficient SARS-CoV-2 whole genome sequencing platform for COVID-19 genomic surveillance, CorvGenSurv (Coronavirus Genomic Surveillance). CorvGenSurv directly amplified viral RNA from COVID-19 patients’ Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens and sequenced the SARS-CoV-2 whole genome in three segments by long-read, high-throughput sequencing. Sequencing of the whole genome in three segments significantly reduced sequencing data waste, thereby preventing dropouts in genome coverage. We validated the precision of our pipeline by both control genomic RNA sequencing and Sanger sequencing. We produced near full-length whole genome sequences from individuals who were COVID-19 test positive during April to June 2020 in Los Angeles County, California, USA. These sequences were highly diverse in the G clade with nine novel amino acid mutations including NSP12-M755I and ORF8-V117F. With its readily adaptable design, CorvGenSurv grants wide access to genomic surveillance, permitting immediate public health response to sudden threats.

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