Data from: Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

Wu, Shan1; Lau, Kin H.2; Cao, Qinghe1; Hamilton, John P.2; Sun, Honghe1; Zhou, Chenxi3; Eserman, Lauren4; Gemenet, Dorcus5; Olukolu, Bode6; Wang, Haiyan2; Crisovan, Emily2; Godden, Grant T.2; Jiao, Chen1; Wang, Xin1; Kitavi, Mercy7; Manrique-Carpintero, Norma2; Vaillancourt, Brieanne2; Wiegert-Rininger, Krystle2; Yang, Xinsun8; Bao, Kan1; Zheng, Yi; Schaff, Jennifer6; Kreuze, Jan5; Gruneberg, Wolfgang5; Khan, Awais5; Ghislain, Marc7; Ma, Daifu9; Jiang, Jiming2; Mwanga, Robert O.M.10; Leebens-Mack, Jim4; Coin, Lachlan J.M.3; Yencho, G. Craig6; Buell, C. Robin2; Fei, Zhangjun1

Published Nov 02, 2018 on Dryad. https://doi.org/10.5061/dryad.b9m61cg

Data files

Nov 02, 2018 version files 6.77 GB

gt4sp_v3_asm_anno_readme.txt

4.70 KB
I_trifida_NSP306_FPKM_expression_matrix_v3_anno.xlsx

4.33 MB
I_trifida_NSP306_stress_FPKM_expression_matrix_v3_anno.xlsx

7.20 MB
I_triloba_NSP323_FPKM_expression_matrix_v3_anno.xlsx

3.82 MB
I_triloba_NSP323_stress_FPKM_expression_matrix_v3_anno.xlsx

7.80 MB
NSP306_trifida_chr_v3.fa

500.59 MB
NSP306_trifida_chr_v3.hm.fa

502.23 MB
NSP306_trifida_v3.hc.func_anno.txt

2.33 MB
NSP306_trifida_v3.hc.gene_models.cdna.fa

75.38 MB
NSP306_trifida_v3.hc.gene_models.cds.fa

58.77 MB
NSP306_trifida_v3.hc.gene_models.gff3

42.85 MB
NSP306_trifida_v3.hc.gene_models.pep.fa

20.08 MB
NSP306_trifida_v3.hc.repr.gene_models.txt

872.14 KB
NSP306_trifida_v3.working.gene_models.cdna.fa

83.78 MB
NSP306_trifida_v3.working.gene_models.cds.fa

66.93 MB
NSP306_trifida_v3.working.gene_models.gff3

52.27 MB
NSP306_trifida_v3.working.gene_models.pep.fa

22.97 MB
NSP323_triloba_chr_v3.fa

469.54 MB
NSP323_triloba_chr_v3.hm.fa

471.08 MB
NSP323_triloba_v3.hc.func_anno.txt

2.48 MB
NSP323_triloba_v3.hc.gene_models.cdna.fa

86.21 MB
NSP323_triloba_v3.hc.gene_models.cds.fa

64.10 MB
NSP323_triloba_v3.hc.gene_models.gff3

47.41 MB
NSP323_triloba_v3.hc.gene_models.pep.fa

21.88 MB
NSP323_triloba_v3.hc.repr.gene_models.txt

848.52 KB
NSP323_triloba_v3.working.gene_models.cdna.fa

92.17 MB
NSP323_triloba_v3.working.gene_models.cds.fa

69.75 MB
NSP323_triloba_v3.working.gene_models.gff3

54.49 MB
NSP323_triloba_v3.working.gene_models.pep.fa

23.88 MB
trifi_aln_8x8_parents_freebayes_mRNA_regions.vcf.gz

1.89 GB
trilo_aln_8x8_parents_freebayes_mRNA_regions.vcf.gz

2.02 GB

Abstract

Abstract missing

Usage notes

I_triloba_NSP323_stress_FPKM_expression_matrix_v3_anno.xlsx

FPKM values of v3 high confidence gene models for 15 I. triloba abiotic and biotic stress RNA-seq libraries. The libraries are described in the 'Library Key' worksheet.

I_triloba_NSP323_FPKM_expression_matrix_v3_anno.xlsx

FPKM values of v3 high confidence gene models for 6 I. triloba RNA-seq libraries (flower, flowerbud, leaf, root1, root2, stem).

NSP323_triloba_v3.hc.func_anno.txt

Putative functional annotation of high confidence gene models.

NSP323_triloba_v3.hc.gene_models.cdna.fa

Nucleotide sequences of the high confidence gene model transcript sequences (cDNA).

NSP323_triloba_v3.hc.gene_models.cds.fa

Nucleotide sequences of the high confidence gene model coding sequences (CDS).

NSP323_triloba_v3.hc.gene_models.gff3

High confidence gene model annotation in GFF3 format.

NSP323_triloba_v3.hc.gene_models.pep.fa

Amino acid sequences corresponding to the high confidence gene model coding sequences.

NSP323_triloba_v3.hc.repr.gene_models.txt

List of representative high confidence gene models (longest CDS).

NSP323_triloba_v3.working.gene_models.cdna.fa

Nucleotide sequences of the working gene model transcript sequences (cDNA).

NSP323_triloba_v3.working.gene_models.cds.fa

Nucleotide sequences of the working gene model coding sequences (CDS).

NSP323_triloba_v3.working.gene_models.gff3

Working gene model annotation in GFF3 format.

NSP323_triloba_v3.working.gene_models.pep.fa

Amino acid sequences corresponding to the working gene model coding sequences.

NSP323_triloba_chr_v3.fa

Ipomoea triloba (NSP323) Genome Assembly (v3) - FASTA format

NSP323_triloba_chr_v3.hm.fa

Ipomoea triloba (NSP323) Hard Masked Genome Assembly (v3) - FASTA format

trilo_aln_8x8_parents_freebayes_mRNA_regions.vcf.gz

Quality-filtered variant calls for the MDP clones based on alignment of genomic reads to I. triloba.

I_trifida_NSP306_stress_FPKM_expression_matrix_v3_anno.xlsx

FPKM values of v3 high confidence gene models for 15 I. trifida abiotic and biotic stress RNA-seq libraries. The libraries are described in the 'Library Key' worksheet.

I_trifida_NSP306_FPKM_expression_matrix_v3_anno.xlsx

FPKM values of v3 high confidence gene models for 8 I. trifida RNA-seq libraries (callus_flower, callus_stem, flower, flowerbud, leaf, root1, root2, stem).

NSP306_trifida_v3.hc.func_anno.txt