Haplotype-resolved genome sequence of Cassava (Manihot esculenta) cultivar COL40

Pucker, Boas; Thoben, Corinna; Sheat, Samar; Winter, Stephan

doi:10.24355/dbbs.084-202409230712-0

Research Data Mon Oct 7 2024 CC BY 4.0

Published

Haplotype-resolved genome sequence of Cassava (Manihot esculenta) cultivar COL40

Pucker, Boas ; Thoben, Corinna ; Sheat, Samar ; Winter, Stephan

A high quality genome assembly of Cassava COL40 cultivar (completeness > 98 %; QV > 57) is presented together with predicted polypeptide sequences (completeness > 96 %) and functional annoation. The genome sequence of Cassava COL40 was assembled with Hifiasm from PacBio HiFi sequencing data. The assembly was scaffolded into pseudochromosomes and gene models were predicted with BRAKER3 by incorporating RNA-Seq hints of the COL40 cultivar and other Cassava cultivars and polypeptide sequences from Manihot esculenta and Viridiplantae as external hints. The predicted polypeptide sequences were functionally annotated by InterProScan5 and transposable elements (TEs) were predicted by EDTA (TE proportion > 58 %).

Category

Date Created:: 04.10.2023
Date Created:: 16.06.2023
Date Issued:: 07.10.2024
DOI:: 10.24355/dbbs.084-202409230712-0
Language:: English
Type of Resource:: Text
DDC:: 580 Pflanzen (Botanik)
Hosting institution:: 02 - Life Sciences
Comment:: The haplotype-resolved assembly of COL40 a cassava (Manihot esculenta) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elements on chromosome 12 Corinna Thoben, Boas Pucker, Stephan Winter, Bethany Fallon Econopouly, Samar Sheat bioRxiv 2024.09.30.615795; doi: https://doi.org/10.1101/2024.09.30.615795 [Preprint]
Comment:: This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A). This study was funded by the Bill & Melinda Gates Foundation through the Next Generation Cassava Breeding Project, agreement no. 84941-11220 (under prime agreement no. OPP1175661).

Data Origin:: Other Prior to sampling, the plants were transferred to the dark for 24 hours after which fully-expanded leaves (between 3rd to 5th leaf) were taken and flash frozen in liquid N2. Leaves (10-15g) were sent to Arizona Genomics Institute (AGI) for high-molecular-weight (HMW) genomic DNA (gDNA) extraction, library preparation, and sequencing. HMW gDNA extraction was done following a modified CTAB protocol. The HiFi express template prep kit 2.0 was used for PacBio HiFi SMRTbell library construction. Fragments between 10 kb and 25 kb were selected for HiFi sequencing on the Sequel II instrument. SeqII v.2.0 chemistry was used with two SMRT cells 8M v1 in circular consensus sequencing (CCS) mode for a 30-hour run time per cell. The HiFi reads are available in the European Nucleotide Archive (ENA): ERS20926319.
Methods/Processes:: The genome sequence was assembled with Hifiasm. Genetic markers of the composite genetic map of Manihot esculenta Crantz were mapped to the assembly and given to ALLMAPs to perform scaffolding on each haplophase seaparately. The 21 RNA-Seq libraries of the COL40 cultivar and 24 external RNA-Seq libraries from other cultivars were mapped to the COL40 assembly with HISAT2 version 2.2.1 and "--dta" option. Samtools was applied for conversion and sorting of the mapping files. Together with external protein hints from Manihot esculenta Crantz v8.1 and the OrthoDB 11 Viridiplantae database the mapped RNA-Seq libraries were given to BRAKER3 as external hints to perform the structural annotation. The predicted polypeptide sequences were functionally annotated using InterProScan5. Transposable elements (TEs) were annotated with EDTA.