scholarly journals High Contiguity de novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 274 ◽  
Author(s):  
Christian Siadjeu ◽  
Boas Pucker ◽  
Prisca Viehöver ◽  
Dirk C. Albach ◽  
Bernd Weisshaar
Keyword(s):  
De Novo ◽  
Functional Annotations ◽  
Genome Sequence Assembly ◽  
Non Coding Rna ◽  
Protein Encoding ◽  
Long Read ◽  
Encoding Gene ◽  
Rna Genes ◽  
Orphan Crop ◽  
Trifoliate Yam

Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9941 non-coding RNA genes were predicted, and functional annotations were assigned.

scholarly journals High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

2020 ◽  
Author(s):  
Christian Siadjeu ◽  
Boas Pucker ◽  
Prisca Viehöver ◽  
Dirk C. Albach ◽  
Bernd Weisshaar
Keyword(s):  
De Novo ◽  
Functional Annotations ◽  
Genome Sequence Assembly ◽  
Non Coding Rna ◽  
Protein Encoding ◽  
Long Read ◽  
Encoding Gene ◽  
Rna Genes ◽  
Orphan Crop ◽  
Trifoliate Yam

AbstractTrifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 hours after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9,941 non-coding RNA genes were predicted and functional annotations were assigned.

scholarly journals Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huu Quan Nguyen ◽  
Thi Ngoc Lan Nguyen ◽  
Thi Nhung Doan ◽  
Thi Thu Nga Nguyen ◽  
Mai Huong Phạm ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Reconstruction ◽  
Single Copy ◽  
Potential Health ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Long Read ◽  
Phylogenetic Resolution ◽  
Rna Genes

AbstractAdrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla.

scholarly journals De novo computational prediction of non-coding RNA genes in prokaryotic genomes

2009 ◽  
Vol 25 (22) ◽  
pp. 2897-2905 ◽  
Author(s):  
Thao T. Tran ◽  
Fengfeng Zhou ◽  
Sarah Marshburn ◽  
Mark Stead ◽  
Sidney R. Kushner ◽  
...  
Keyword(s):  
De Novo ◽  
Computational Prediction ◽  
Non Coding Rna ◽  
Prokaryotic Genomes ◽  
Rna Genes

scholarly journals Evaluating the Genetic Capacity of Mycoplasmas for Coenzyme A Biosynthesis in a Search for New Anti-mycoplasma Targets

2021 ◽  
Vol 12 ◽  
Author(s):  
Tertius Alwyn Ras ◽  
Erick Strauss ◽  
Annelise Botes
Keyword(s):  
Acid Metabolism ◽  
Coenzyme A ◽  
De Novo ◽  
Phylogenetic Position ◽  
Biosynthesis Pathway ◽  
Functional Annotations ◽  
Disease States ◽  
Wide Range ◽  
Parasitic Lifestyle ◽  
Encoding Gene

Mycoplasmas are responsible for a wide range of disease states in both humans and animals, in which their parasitic lifestyle has allowed them to reduce their genome sizes and curtail their biosynthetic capabilities. The subsequent dependence on their host offers a unique opportunity to explore pathways for obtaining and producing cofactors – such as coenzyme A (CoA) – as possible targets for the development of new anti-mycoplasma agents. CoA plays an essential role in energy and fatty acid metabolism and is required for membrane synthesis. However, our current lack of knowledge of the relevance and importance of the CoA biosynthesis pathway in mycoplasmas, and whether it could be bypassed within their pathogenic context, prevents further exploration of the potential of this pathway. In the universal, canonical CoA biosynthesis pathway, five enzymes are responsible for the production of CoA. Given the inconsistent presence of the genes that code for these enzymes across Mycoplasma genomes, this study set out to establish the genetic capacity of mycoplasmas to synthesize their own CoA de novo. Existing functional annotations and sequence, family, motif, and domain analysis of protein products were used to determine the existence of relevant genes in Mycoplasma genomes. We found that most Mycoplasma species do have the genetic capacity to synthesize CoA, but there was a differentiated prevalence of these genes across species. Phylogenetic analysis indicated that the phylogenetic position of a species could not be used to predict its enzyme-encoding gene combinations. Despite this, the final enzyme in the biosynthesis pathway – dephospho-coenzyme A kinase (DPCK) – was found to be the most common among the studied species, suggesting that it has the most potential as a target in the search for new broad-spectrum anti-mycoplasma agents.

scholarly journals De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring

2008 ◽  
Vol 18 (6) ◽  
pp. 888-899 ◽  
Author(s):  
P. Larsson ◽  
A. Hinas ◽  
D. H. Ardell ◽  
L. A. Kirsebom ◽  
A. Virtanen ◽  
...  
Keyword(s):  
Dictyostelium Discoideum ◽  
De Novo ◽  
Genome Feature ◽  
Non Coding Rna ◽  
Rna Genes

Screening and survival analysis of melanoma immunodrug response-related genes and the function of magnetic nanoparticles in gene extraction

2021 ◽  
Vol 11 (8) ◽  
pp. 1306-1312
Author(s):  
Li Song ◽  
Ningchao Du ◽  
Haitao Luo ◽  
Furong Li
Keyword(s):  
Survival Analysis ◽  
Magnetic Nanoparticles ◽  
Drug Response ◽  
High Throughput Sequencing ◽  
Cox Proportional Hazards ◽  
Sequencing Data ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Rna Genes

This study aimed to identify the association of protein coding and long non coding RNA genes with immunotherapy response in melanoma. Based on RNA sequencing data of melanoma specimens, the expression levels of protein coding and long non coding RNA genes were calculated using the Kallisto RNA-seq quantification method, and differently expressed genes were detected using the DESeq2 method. Cox proportional hazards regression was used to evaluate the effects of gene expression on survival. According to the clinical data of 14 patients with drug response and 11 patients without drug response, 18 protein coding genes and 14 long non coding RNAs showed differential expressions (multiple of difference > 2 and P < 0.01 after correction), among which the coding genes of differential expression were significantly enriched through the process of cell adhesion (P < 0.01). The results of survival analysis showed that 18 coding genes and 14 long non coding RNA genes had significant effects on patient survival (P < 0.01). In this study, magnetic nanoparticles can be used to extract genomic DNA and total RNA due to their paramagnetism and biocompatibility, then transcriptome high-throughput sequencing was performed. The method has the advantages of removing dangerous reagents such as phenol and chloroform, replacing inorganic coating such as silica with organic oil, and shortening reaction time. Protein coding and long non coding RNA genes as well as magnetic nanoparticles may serve as potential cancer immune biomarker targets for developing future oncological treatments.

Sign in / Sign up

Export Citation Format

Share Document