Welcome To Website IAS

Hot news
Achievement

Independence Award

- First Rank - Second Rank - Third Rank

Labour Award

- First Rank - Second Rank -Third Rank

National Award

 - Study on food stuff for animal(2005)

 - Study on rice breeding for export and domestic consumption(2005)

VIFOTEC Award

- Hybrid Maize by Single Cross V2002 (2003)

- Tomato Grafting to Manage Ralstonia Disease(2005)

- Cassava variety KM140(2010)

Centres
Website links
Vietnamese calendar
Library
Visitors summary
 Curently online :  2
 Total visitors :  8646041

A data-driven genome annotation approach for cassava
Thursday, 2024/07/18 | 08:38:11

Swetha ChennaMaxim IvanovTue Kjærgaard NielsenKarina ChalenkoEvy OlsenKirsten JørgensenAlbin SandelinSebastian Marquardt

Plant Journal; 2024 Jun 3. doi: 10.1111/tpj.16856. Online ahead of print.

Abstract

Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5'- and 3'-ends as well as full-length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high-quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA-seq data but alternative genome annotation files. We found that our merged genome annotation that included cold-specific TR gene models identified about twice as many cold-induced genes. These data indicate that environmentally induced genes may be missing in off-the-shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant-environment interactions.

 

See https://pubmed.ncbi.nlm.nih.gov/38831668/

 

Figure 4: Novel genes identified in de novo annotation.

(a) Stacked bar plot showing the number of novel high confidence (HC), medium confidence (MC), low confidence (LC) genes and Single Method Confidence (SMC) identified in de novo annotation. Novel genes identified have either overlap with any of the known genes on the opposite strand (antisense, coloured red) or no overlap at all (intergenic, coloured blue). The SMC genes are supported by only strand-specific RNA-seq data.

(b) Metagene plot of RNA-seq signal over the novel genes identified. Red and blue line shows novel genes supported by all sequencing methods (HC, MC and LC) and only by RNA-seq respectively (SMC).

(c) Example of a novel HC gene identified in de novo annotation.

(d) Example of a novel MC gene identified in de novo annotation.

(e) Example of a novel LC gene identified in de novo annotation.

(f) Example of a novel SMC gene identified in de novo annotation.

 

Back      Print      View: 376

[ Other News ]___________________________________________________
  • Host plant resistance for fall armyworm management in maize: relevance, status and prospects in Africa and Asia
  • Increasing plant group productivity through latent genetic variation for cooperation
  • THP9 enhances seed protein content and nitrogen-use efficiency in maize
  • The role of soybean 14-3-3 gene (Glyma05g29080) on white mold resistance and nodulation investigations using CRISPR-Cas9 editing and RNA silencing
  • Progress in Soybean Genetic Transformation Over the Last Decade
  • Climate change challenges plant breeding
  • Breeding for disease resistance in soybean: a global perspective
  • The phosphorylation of AMPKβ1 is critical for increasing autophagy and maintaining mitochondrial homeostasis in response to fatty acids
  • Genomic selection for spot blotch in bread wheat breeding panels, full-sibs and half-sibs and index-based selection for spot blotch, heading and plant height
  • Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress
  • Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes
  • Root hair-specific transcriptome reveals response to low phosphorus in Cicer arietinum
  • Protocol for targeted modification of the rice genome using base editing
  • Understanding the Dynamics of Blast Resistance in Rice- Magnaporthe oryzae Interactions
  • Multi-omics analysis reveals the mechanism of seed coat color formation in Brassica rapa L.
  • Highly efficient transgene-free genome editing in tobacco using an optimized CRISPR/Cas9 system, pOREU3TR
  • Breeding of Rc Function Restoration Red Rice via CRISPR/Cas9 Mediated Genome Editing
  • Transposon insertions within alleles of BnaFT.A2 are associated with seasonal crop type in rapeseed
  • Natural allelic variation of GmST05 controlling seed size and quality in soybean
  • Cassava mosaic disease and its management in Southeast Asia

 

Designed & Powered by WEBSO CO.,LTD