Comparison of Three Assembly Strategies for a Heterozygous Seedless Grapevine Genome Assembly

Authors

Sagar Patal, South Dakota State UniversityFollow
Zhixiu Lu, University of South Dakota
Xiaozhu Jin, South Dakota State University
Padmapriya Swaminathan, South Dakota State UniversityFollow
Erliang Zeng, University of South Dakota
Anne Y. Fennell Dr, South Dakota State UniversityFollow

Document Type

Article

Publication Date

2018

Abstract

Background
De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera ‘Sultanina’ genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC).
Results
The three new assemblies were greater in size than the AP assembly. PLAT*_GC had the greatest number of scaffolds aligning with a minimum of 95% identity and ≥1000 bp alignment length to V. vinifera (PN40024 12X.v2) reference genome. SNP analysis also identified additional high quality SNPs. A greater number of sequence reads mapped back with zero-mismatch to the PLAT_d, MERGE, and PLAT*_GC (>94%) than was found in the AP assembly (87%) indicating a greater fidelity to the original sequence data in the new assemblies than in AP assembly. A de novo gene prediction conducted using seedless RNA-seq data predicted > 30,000 coding sequences for the three new de novo assemblies, with the greatest number (30,544) in PLAT*_GC and only 26,515 for the AP assembly. Transcription factor analysis indicated good family coverage, but some genes found in the VCOST.v3 annotation were not identified in any of the de novo assemblies, particularly some from the MYB and ERF families.
Conclusions
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.

Publication Title

BMC Genomics

Volume

19

Issue

57

Format

application/pdf

DOI of Published Version

10.1186/s12864-018-4434-2

Rights

Copyright © 2018 the Author(s)

Recommended Citation

Patel, S., Lu, Z., Jin, X. et al. BMC Genomics (2018) 19: 57. https://doi.org/10.1186/s12864-018-4434-2

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Comments

The data-set associated with this publication can be found here: https://openprairie.sdstate.edu/vitis_vinifera_sultanina/1/