Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly.
Sagar PatelZhixiu LuXiaozhu JinPadmapriya SwaminathanErliang ZengAnne Y FennellPublished in: BMC genomics (2018)
The PLAT_d and PLAT*_GC had a greater number of synteny blocks with the V. vinifera (PN40024 12X.v2) reference genome than AP or MERGE. PLAT*_GC provided the most contiguous assembly with only 1.2% scaffold N, in contrast to AP (10.7% N), PLAT_d (6.6% N) and Merge (6.4% N). A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies. An annotated de novo gene prediction for the PLAT*_GC assembly, aligned with VitisNet pathways provides new seedless grapevine specific transcriptomic resource that has excellent fidelity with the seedless short read sequence data.
Keyphrases
- genome wide
- copy number
- transcription factor
- gas chromatography
- magnetic resonance
- early onset
- high resolution
- magnetic resonance imaging
- mass spectrometry
- computed tomography
- machine learning
- single molecule
- electronic health record
- health information
- artificial intelligence
- simultaneous determination
- data analysis
- solid phase extraction