Supporting files for research paper "A chromosome-scale reference genome of Lathyrus sativus"

This is a supporting dataset for the research paper: "A chromosome-scale reference genome of Lathyrus sativus"

Abstract

Grass pea (Lathyrus sativus L.) is an underutilised but promising legume crop with tolerance to a wide range of abiotic and biotic stress factors, and potential for climate-resilient agriculture. Despite a long history and wide geographical distribution of cultivation, only limited breeding resources are available. This paper reports a 5.96 Gbp genome assembly of grass pea genotype LS007, of which 5.03 Gbp is scaffolded into 7 pseudo-chromosomes. The assembly has a BUSCO completeness score of 99.1% and is annotated with 31719 gene models and repeat elements. This represents the most contiguous and accurate assembly of the grass pea genome to date.

Other supporting data files related to this submission:

raw Pacific Biosciences HiFi long reads of LS007 genomic DNA, available at PRJEB70892, FASTQ

scaffolded assembly of LS007 along with annotations as an EMBL format file GCA_963859935 under project PRJEB70892 

CENH3 ChIP-seq sequencing, Illumina paired end, PRJEB54858 (run accessions ERR12509730-ERR12509733), FASTQ 

Code Availability

Source code for the gene annotation is available on github (https://github.com/gitbackspacer/grasspea_annotation)

Files in this datadepository:

README_F.txt

Readme file with MD5sums of submitted files.

lathyrus.emapper.decorated.gff

Orthology based functional annotation of protein coding genes

lathyrus_interproscan.annotations.gff3The annotation of functional domains of protein coding genes.

lathy.emapper.annotations.tab.xlsx.zip

lathy.emapper.annotations.tab.xlsx

Outputs from eggNOG-mapper for Orthology based functional annotation of LS007 Lathyrus sativus genes

lathyrus_interproscan.zip

lathyrus_interproscan.tab

Outputs from Interproscan for structure and domains of annotated LS007 Lathyrus sativus genes

repeat annotation_reversed chromosomes.zip

DANTE_LTR_full_output.gff3Full-length and partial LTR-RT elements annotated by DANTE_LTR

DANTE_filtered_output.gff3Protein coding regions of transposable elements annotated by DANTE

RM_LIB_All_concatenated.fastaCustom library of mobile elements, including LTR-RT, LINE, and Class II elements

Repeat_annotations_merged_31072023_sorted.gff3Repeat annotation based on a custom library and RepeatMasker search, as well as DANTE protein domain. The GFF3 includes annotation of mobile elements and simple repeats.

all_scaf_run_all_default_annotation.gff3Tandem repeats with a monomer size 40-3000 nt annotated by TideCluster, minimum array size 5kb

all_scaf_run_all_default_tidehunter.gff3All tandem repeats with monomer size 40-3000 identified by TideHunter.

all_scaf_run_all_short_monom_annotation.gff3Tandem repeats with monomer size 10-39 nt annotated by TideCluster with a minimum array size 5kb

all_scaf_run_all_short_monom_tidehunter.gff3All tandem repeats with monomer size 10-39 nt identified by TideHunter.