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

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.

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Genome survey and SSR analysis of Apocynum venetum

Bioscience Reports ◽

10.1042/bsr20190146 ◽

2019 ◽

Vol 39 (6) ◽

Cited By ~ 8

Author(s):

Guo-qi Li ◽

Li-xiao Song ◽

Chang-qing Jin ◽

Miao Li ◽

Shi-pei Gong ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Size ◽

Genome Sequencing ◽

Repeated Sequences ◽

Economic Plant ◽

Whole Genome ◽

Sequencing Analysis ◽

Total Length ◽

Genome Survey ◽

Apocynum Venetum

AbstractApocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measure the genome size of A. venetum, and bioinformatics methods were employed for the evaluation of the genome size, heterozygosity ratio, repeated sequences, and GC content in order to provide a foundation for subsequent whole-genome sequencing. The sequencing analysis results indicated that the preliminary estimated genome size of A. venetum was 254.40 Mbp, and its heterozygosity ratio and percentage of repeated sequences were 0.63 and 40.87%, respectively, indicating that it has a complex genome. We used k-mer = 41 to carry out a preliminary assembly and obtained contig N50, which was 3841 bp with a total length of 223949699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227322054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous. We recommend the use of the ‘2+3’ (Illumina+PacBio) sequencing combination to supplement the Hi-C technique and resequencing technique in future whole-genome research in A. venetum.

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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 ◽

10.3390/plants10071362 ◽

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.

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Decoding of Finger Millet Genome: A Milestone of Millet Genomics

Signal Transduction Insights ◽

10.1177/1178643418820541 ◽

2019 ◽

Vol 8 ◽

pp. 117864341882054 ◽

Cited By ~ 2

Author(s):

Subramani Pandian ◽

Manikandan Ramesh

Keyword(s):

Molecular Structure ◽

Molecular Biology ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Finger Millet ◽

Whole Genome ◽

Important Milestone

Whole genome sequencing is an important milestone of the genomics-assisted molecular biology studies. Sequencing the whole genome of plants unravels the complex molecular structure of these complex organisms. In this respect, whole genome sequencing of important small millet that is finger millet was subsequently released by 2 independent groups. This commentary outlines the major applications of these reports, which also provided some opinion about this.

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Erratum for O’Donnell et al., “Early Detection of Emergent Extensively Drug-Resistant Tuberculosis by Flow Cytometry-Based Phenotyping and Whole-Genome Sequencing”

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00764-19 ◽

2019 ◽

Vol 63 (6) ◽

Author(s):

Max R. O’Donnell ◽

Michelle H. Larsen ◽

Tyler S. Brown ◽

Paras Jain ◽

Vanisha Munsamy ◽

...

Keyword(s):

Flow Cytometry ◽

Early Detection ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Drug Resistant ◽

Drug Resistant Tuberculosis ◽

Resistant Tuberculosis ◽

Extensively Drug Resistant

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Reconstructing fungal natural product biosynthetic pathways

Natural Product Reports ◽

10.1039/c4np00084f ◽

2014 ◽

Vol 31 (10) ◽

pp. 1339-1347 ◽

Cited By ~ 36

Author(s):

C. M. Lazarus ◽

K. Williams ◽

A. M. Bailey

Keyword(s):

Molecular Biology ◽

Heterologous Expression ◽

Natural Product ◽

Genome Sequencing ◽

Vital Role ◽

Whole Genome ◽

Biosynthetic Pathways ◽

Expression Systems ◽

Natural Product Research ◽

Heterologous Expression Systems

Molecular biology plays a vital role in contemporary natural product research. Responding to developments in whole genome sequencing, heterologous expression systems are being refined to accommodate whole fungal biosynthetic pathways.

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Determination of DNA content and relative 2C genome sizes of some promising commercial varieties of sugarcane using flow cytometer

Current Botany ◽

10.19071/cb.2017.v8.3207 ◽

2017 ◽

Vol 8 ◽

Author(s):

A. Mondal S.K. Ghosal ◽

T. Pal Kalyan Kumar De

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Cane Yield ◽

Sugarcane Varieties ◽

Yield Information ◽

A Genome ◽

2C Dna Content

In the present study, 2C DNA content and the genome sizes (in picograms-pg and megabase pairs-Mbp respectively) of 19 promising commercial varieties of sugarcane, the derivatives of man-made interspecific hybrids between cultivated and wild species were analyzed using flow cytometry. In this work, 2C nuclear DNA content was determined. Knowing the 2C nuclear DNA content, the unknown chromosome numbers of the varieties could be predicted. Large differences (65 % variation) in DNA content (2C) of 19 varieties were detected, ranging, from 3.80 pg to 10.96 pg, which corresponds to a genome size ranging from 3724.00 Mbp to 10740.80 Mbp due to the variation of ploidy level and are considered the most complex genomes among crop plants. However, the relationship between chromosome number and genome size was highly significant (P < 0.001). In the present study, internode diameter, Sugar juice content and cane yield/ha are also positively correlated with DNA content. The estimated genome sizes would also yield information critical for sugarcane breeding and genome sequencing programs. Keywords: Genome size, Sugarcane varieties, Flow cytometry, DNA content.

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DNA content estimation of Fig and Black Mulberry using flow cytometry

Revista Brasileira de Fruticultura ◽

10.1590/0100-29452018568 ◽

2018 ◽

Vol 40 (2) ◽

Author(s):

Zeynel Dalkiliç ◽

Gonca Günver Dalkiliç

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Dna Content ◽

Dna Contents ◽

2C Dna Content ◽

Dapi Fluorescence

Abstract In this study, fig and black mulberry DNA contents were estimated using DAPI fluorescence stain in flow cytometry. The 2C DNA contents of the fig and black mulberry were found as 0.82 pg and 8.34 pg, respectively. The calculated 1C value of genome size of fig is 401.8 Mbp and that of black mulberry is 4086.6 Mbp. The ratio of 2C DNA content and 1C genome of the black mulberry was 10.17 times that of the fig although fig is diploid and black mulberry is decosaploid.

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Diagnostic molecular biology with whole genome sequencing versus diagnostic electron microsopy - a change of paradigm in diagnostic EM?

European Microscopy Congress 2016: Proceedings ◽

10.1002/9783527808465.emc2016.6460 ◽

2016 ◽

pp. 308-309

Author(s):

Susanne Richter

Keyword(s):

Molecular Biology ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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Genome Size Versus Genome Assemblies: Are the Genomes Truly Expanded in Polyploid Fungal Symbionts?

Genome Biology and Evolution ◽

10.1093/gbe/evaa217 ◽

2020 ◽

Vol 12 (12) ◽

pp. 2384-2390

Author(s):

Pepijn W Kooij ◽

Jaume Pellicer

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Genome Assembly ◽

Sequence Data ◽

Fungal Genome ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Whole Genome ◽

Fungus Growing Ants ◽

Genome Assemblies

Abstract Each day, as the amount of genomic data and bioinformatics resources grows, researchers are increasingly challenged with selecting the most appropriate approach to analyze their data. In addition, the opportunity to undertake comparative genomic analyses is growing rapidly. This is especially true for fungi due to their small genome sizes (i.e., mean 1C = 44.2 Mb). Given these opportunities and aiming to gain novel insights into the evolution of mutualisms, we focus on comparing the quality of whole genome assemblies for fungus-growing ants cultivars (Hymenoptera: Formicidae: Attini) and a free-living relative. Our analyses reveal that currently available methodologies and pipelines for analyzing whole-genome sequence data need refining. By using different genome assemblers, we show that the genome assembly size depends on what software is used. This, in turn, impacts gene number predictions, with higher gene numbers correlating positively with genome assembly size. Furthermore, the majority of fungal genome size data currently available are based on estimates derived from whole-genome assemblies generated from short-read genome data, rather than from the more accurate technique of flow cytometry. Here, we estimated the haploid genome sizes of three ant fungal symbionts by flow cytometry using the fungus Pleurotus ostreatus (Jacq.) P. Kumm. (1871) as a calibration standard. We found that published genome sizes based on genome assemblies are 2.5- to 3-fold larger than our estimates based on flow cytometry. We, therefore, recommend that flow cytometry is used to precalibrate genome assembly pipelines, to avoid incorrect estimates of genome sizes and ensure robust assemblies.

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