While the size of chromosomes can be measured under a microscope, obtaining the exact size of a genome remains a challenge. Biochemical methods and k-mer distribution-based approaches allow only estimations. An alternative approach to estimate the genome size based on high contiguity assemblies and read mappings is presented here. Analyses of Arabidopsis thaliana and Beta vulgaris data sets are presented to show the impact of different parameters. Oryza sativa, Brachypodium distachyon, Solanum lycopersicum, Vitis vinifera, and Zea mays were also analyzed to demonstrate the broad applicability of this approach. Further, MGSE was also used to analyze Escherichia coli, Saccharomyces cerevisiae, and Caenorhabditis elegans datasets to show its utility beyond plants. Mapping-based Genome Size Estimation (MGSE) and additional scripts are available on GitHub: https://github.com/bpucker/MGSE . MGSE predicts genome sizes based on short reads or long reads requiring a minimal coverage of 5-fold.

In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain-pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pig.....

The genome of the cornflower (Centaurea cyanus ) was sequenced with long reads (ONT) to reveal the full sequences of genes in the flavonoid biosynthesis. Of particular interest are genes responsible f...

Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...

Abstract. The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bo

Abstract. Cassava (Manihot esculenta Grantz) is a vital staple crop for millions of people, particularly in Sub-Saharan Africa, where it is a primary sourc

Background The rapid advancement of sequencing technologies has drastically increased the availability of plant genomic and transcriptomic data, shifting the challenge from data generation to function...

While the size of chromosomes can be measured under a microscope, obtaining the exact size of a genome remains a challenge. Biochemical methods and k-mer distribution-based approaches allow only estim...

This review examines dark anthocyanin pigmentation in plants by outlining its distribution, exploring the genetic mechanisms behind its development, and discussing its ecological role together with i...

Withanolides are plant steroids with potent bioactivities found in many medicinal plants including Withania somnifera, but their biosynthetic pathway is largely unknown. Here, the authors report the g...

Withanolides are plant steroids with potent bioactivities found in many medicinal plants including Withania somnifera, but their biosynthetic pathway is largely unknown. Here, the authors report the g...

This review examines dark anthocyanin pigmentation in plants by outlining its distribution, exploring the genetic mechanisms behind its development, and discussing its ecological role together with i...

While the size of chromosomes can be measured under a microscope, obtaining the exact size of a genome remains a challenge. Biochemical methods and k-mer distribution-based approaches allow only estim...

Cassava brown streak disease (CBSD) caused by the ipomoviruses CBSV and UCBSV, poses a significant threat to cassava crops and the destruction of tuberous roots leads to substantial yield losses. Viru...

Abstract. Cassava (Manihot esculenta Grantz) is a vital staple crop for millions of people, particularly in Sub-Saharan Africa, where it is a primary sourc

Background The rapid advancement of sequencing technologies has drastically increased the availability of plant genomic and transcriptomic data, shifting the challenge from data generation to function...

Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...

The genome of the cornflower (Centaurea cyanus ) was sequenced with long reads (ONT) to reveal the full sequences of genes in the flavonoid biosynthesis. Of particular interest are genes responsible f...

Abstract. The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bo

In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain-pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pig.....