scholarly journals Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence

DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Nadia Kamal ◽  
Terry Mun ◽  
Dugald Reid ◽  
Jie-Shun Lin ◽  
Turgut Yigit Akyol ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Large Fraction ◽  
Lotus Japonicus ◽  
Gene Copy Number ◽  
Genetic Maps ◽  
Gene Copy ◽  
Expression Data ◽  
Perennial Legume ◽  
Herbaceous Perennial

Abstract Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and contained a large fraction of unanchored contigs. Here, we use long PacBio reads from L. japonicus Gifu combined with Hi-C data and new high-density genetic maps to generate a high-quality chromosome-scale reference genome assembly for L. japonicus. The assembly comprises 554 megabases of which 549 were assigned to six pseudomolecules that appear complete with telomeric repeats at their extremes and large centromeric regions with low gene density. The new L. japonicus Gifu reference genome and associated expression data represent valuable resources for legume functional and comparative genomics. Here, we provide a first example by showing that the symbiotic islands recently described in Medicago truncatula do not appear to be conserved in L. japonicus.

scholarly journals Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence

2020 ◽  
Author(s):  
Nadia Kamal ◽  
Terry Mun ◽  
Dugald Reid ◽  
Jie-shun Lin ◽  
Turgut Yigit Akyol ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Large Fraction ◽  
Lotus Japonicus ◽  
Gene Copy Number ◽  
Genetic Maps ◽  
Gene Copy ◽  
Expression Data ◽  
Perennial Legume ◽  
Herbaceous Perennial

AbstractAimLotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and contained a large fraction of unanchored contigs.Methods and ResultsHere, we use long PacBio reads from L. japonicus Gifu combined with Hi-C data and new high-density genetic maps to generate a high-quality chromosome-scale reference genome assembly for L. japonicus. The assembly comprises 554 megabases of which 549 were assigned to six pseudomolecules that appear complete with telomeric repeats at their extremes and large centromeric regions with low gene density.Conclusion and PerspectivesThe new L. japonicus Gifu reference genome and associated expression data represent valuable resources for legume functional and comparative genomics. Here, we provide a first example by showing that the symbiotic islands recently described in Medicago truncatula do not appear to be conserved in L. japonicus.

scholarly journals Advanced analysis and visualization of gene copy number and expression data

2009 ◽  
Vol 10 (S1) ◽  
Author(s):  
Reija Autio ◽  
Matti Saarela ◽  
Anna-Kaarina Järvinen ◽  
Sampsa Hautaniemi ◽  
Jaakko Astola
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Expression Data ◽  
Advanced Analysis

scholarly journals Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights

2021 ◽  
Author(s):  
Rodrigo P. Baptista ◽  
Yiran Li ◽  
Adam Sateriale ◽  
Mandy J. Sanders ◽  
Karen L. Brooks ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Diarrheal Disease ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Future Research ◽  
Gene Copy Number Variation ◽  
Long Read ◽  
Number Variation ◽  
Gene Structures

ABSTRACTCryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community still relies on a fragmented reference genome sequence from 2004. Incomplete reference sequences hamper experimental design and interpretation. We have generated a new C. parvum IOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species C. parvum, C. hominis and C. tyzzeri. The new C. parvum IOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers 13 of 16 possible telomeres and raises a new hypothesis for the remaining telomeres and associated subtelomeric regions. Comparative annotation revealed that most “missing” orthologs are found suggesting that species differences result primarily from structural rearrangements, gene copy number variation and SNVs in C. parvum, C. hominis and C. tyzzeri. We made >1,500 C. parvum annotation updates based on experimental evidence. They included new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete DNA methylase Dnmt2 ortholog. 190 genes under positive selection including many new candidates were identified using the new assembly and annotation as reference. Finally, possible subtelomeric amplification and variation events in C. parvum are detected that reveal a new level of genome plasticity that will both inform and impact future research.

An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis

2019 ◽  
Vol 17 (06) ◽  
pp. 1940012
Author(s):  
Yuan Liu ◽  
Yongchao Ma ◽  
Evan Salsman ◽  
Frank A. Manthey ◽  
Elias M. Elias ◽  
...  
Keyword(s):  
Reference Genome ◽  
Association Studies ◽  
Large Fraction ◽  
Snp Markers ◽  
Alternative Methods ◽  
Probability Method ◽  
Genome Wide Association Studies ◽  
Enrichment Method ◽  
Allele Distribution ◽  
Random Method

Mapping short reads to a reference genome is an essential step in many next-generation sequencing (NGS) analyses. In plants with large genomes, a large fraction of the reads can align to multiple locations of the genome with equally good alignment scores. How to map these ambiguous reads to the genome is a challenging problem with big impacts on the downstream analysis. Traditionally, the default method is to assign an ambiguous read randomly to one of the many potential locations. In this study, we explore two alternative methods that are based on the hypothesis that the possibility of an ambiguous read being generated by a location is proportional to the total number of reads produced by that location: (1) the enrichment method that assigns an ambiguous read to the location that has produced the most reads among all the potential locations, (2) the probability method that assigns an ambiguous read to a location based on a probability proportional to the number of reads the location produces. We systematically compared the performance of the proposed methods with that of the default random method. Our results showed that the enrichment method produced better results than the default random method and the probability method in the discovery of single nucleotide polymorphisms (SNPs). Not only did it produce more SNP markers, but it also produced SNP markers with better quality, which was demonstrated using multiple mainstay genomic analyses, including genome-wide association studies (GWAS), minor allele distribution, population structure, and genomic prediction.

scholarly journals Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 283
Author(s):  
Eyal Seroussi
Keyword(s):  
Copy Number ◽  
Sanger Sequencing ◽  
Cytosine Methylation ◽  
Direct Sequencing ◽  
Information Source ◽  
Gene Copy Number ◽  
Cost Effective ◽  
Gene Copy ◽  
Base Editing ◽  
Recent Developments

Determination of the relative copy numbers of mixed molecular species in nucleic acid samples is often the objective of biological experiments, including Single-Nucleotide Polymorphism (SNP), indel and gene copy-number characterization, and quantification of CRISPR-Cas9 base editing, cytosine methylation, and RNA editing. Standard dye-terminator chromatograms are a widely accessible, cost-effective information source from which copy-number proportions can be inferred. However, the rate of incorporation of dye terminators is dependent on the dye type, the adjacent sequence string, and the secondary structure of the sequenced strand. These variable rates complicate inferences and have driven scientists to resort to complex and costly quantification methods. Because these complex methods introduce their own biases, researchers are rethinking whether rectifying distortions in sequencing trace files and using direct sequencing for quantification will enable comparable accurate assessment. Indeed, recent developments in software tools (e.g., TIDE, ICE, EditR, BEEP and BEAT) indicate that quantification based on direct Sanger sequencing is gaining in scientific acceptance. This commentary reviews the common obstacles in quantification and the latest insights and developments relevant to estimating copy-number proportions based on direct Sanger sequencing, concluding that bidirectional sequencing and sophisticated base calling are the keys to identifying and avoiding sequence distortions.

scholarly journals Nongenotoxic ABCB1 activator tetraphenylphosphonium can contribute to doxorubicin resistance in MX-1 breast cancer cell line

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raimonda Kubiliute ◽  
Indre Januskeviciene ◽  
Ruta Urbanaviciute ◽  
Kristina Daniunaite ◽  
Monika Drobniene ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Line ◽  
Protein Level ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Common Mechanism ◽  
Dna Hypomethylation ◽  
Mesenchymal Transition ◽  
Molecular Features

AbstractHyperactivation of ABC transporter ABCB1 and induction of epithelial–mesenchymal transition (EMT) are the most common mechanism of acquired cancer chemoresistance. This study describes possible mechanisms, that might contribute to upregulation of ABCB1 and synergistically boost the acquisition of doxorubicin (DOX) resistance in breast cancer MX-1 cell line. DOX resistance in MX-1 cell line was induced by a stepwise increase of drug concentration or by pretreatment of cells with an ABCB1 transporter activator tetraphenylphosphonium (TPP+) followed by DOX exposure. Transcriptome analysis of derived cells was performed by human gene expression microarrays and by quantitative PCR. Genetic and epigenetic mechanisms of ABCB1 regulation were evaluated by pyrosequencing and gene copy number variation analysis. Gradual activation of canonical EMT transcription factors with later activation of ABCB1 at the transcript level was observed in DOX-only treated cells, while TPP+ exposure induced considerable activation of ABCB1 at both, mRNA and protein level. The changes in ABCB1 mRNA and protein level were related to the promoter DNA hypomethylation and the increase in gene copy number. ABCB1-active cells were highly resistant to DOX and showed morphological and molecular features of EMT. The study suggests that nongenotoxic ABCB1 inducer can possibly accelerate development of DOX resistance.

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