Additional file 1: Table S1. of Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci

Pearson correlation (first cell) and P-value (second cell) of all the traits measured over four years in the ‘Old Home’ x ‘Louise Bonne de Jersey’ OHxLBJ segregating pear population. Branches: branches per tree; Height: total tree height; Inflorescence: inflorescences per tree; Nodes: nodes per tree; Spurs: spurs per tree; TCAtrunk: trunk cross-sectional area 20 cm above graft unit; TCAroot: TCA of rootstock; TCAsec: TCA secondary growth of the main axis; TCAtert: TCA tertiary growth of the main axis. (PDF 164 kb

Additional file 2: Figure S1. of Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci

Alignment of linkage groups from ‘Louise Bonne de Jersey’ (LBJ) and ‘Old Home’ (OH) pears with the maps of ‘Moonglow’ (Moon) and PEAR1 (Montanari et al., 2013). The markers are named using the NCBI dbSNP accessions and their positions are indicated in centiMorgan. Microsatellite markers mapped in the ‘Moonglow’ x PEAR1 population are underlined. The linkage group (LG) numbering system is consistent with the apple LG numbering. Identified QTLs are shown with blue symbols coming from OH and brown symbols from LBJ. The Dw1 flanking marker Hi01c04 (underlined and red) mapped to LG5 of OH. (PDF 306 kb

Additional file 4: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

BLASTP comparison of manually edited gene models to the revised ‘Hongyang’ gene models. List of best reciprocal BLASTp matches between the revised Actinidia chinensis ‘Hongyang’ genes [18]and the Red5 gene set (XLSX 436 kb

Additional file 8: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Sequenced cDNA’s used to verify the gene models.Fasta formatted predicted protein sequences of 550 bidirectionally sequenced expressed sequence tag clones from A. chinensis var. chinensis used in evaluating manually annotated gene models of Red5. (FASTA 220 kb

Additional file 1: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Map back rates to the Red5 genome sequence.Summary of the numbers of input reads reads that align to the RED5 genome construction (XLSX 10 kb

Additional file 6: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Revised ‘Hongyang’ genes omitted from the manually edited gene set. Average RNA-Seq read coverage of the 1069 KIR V2 models perfectly aligned to the Red5 genome without a protein match in the Red5 gene set. (XLSX 114 kb

Additional file 3: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Comparison of predicted paired end distance to genome.Heatmaps of alignment distance scores for the alignment of the read pairs from the 9Kb long-insert mate-paired-end (LIMP) library to each of the 29 chromosomes within the Red5 whole genome assembly and. Individual chromosome plots were prepared using hagfish_blockplot from the software program ‘hagfish’ ( https://github.com/mfiers/hagfish/ ). Individual images were cropped for height (not length) then cut and pasted into a table format for easier viewing. Each image depicted the entire length of the chromosome but all images are of standard length irrespective of chromosome length. Green regions indicate mate pairs aligning to the whole genome sequence within the expected distance of the library. Black indicates regions without mate pair alignment. Pinkish-red indicates regions where the distance between mated paired end reads is shorter (assembly compression relative to physical genome) or longer (assembly expansion relative to physical genome). (PPTX 432 kb

Additional file 7: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Details of sequenced cDNA’s generated. Fasta formatted sequences of 812 bidirectionally sequenced expressed sequence tag clones from A. chinensis var. chinensis used in evaluating manually annotated gene models of Red5. (FASTA 1204 kb

Additional file 10: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

The manual annotation process.Flow diagram of manual annotation process. A. Timeline showing the manual annotation process. *see materials and methods. B. Annotation followed a 5 step process. The annotator training was completed in the form of both workshops and YouTube training videos. ** https://www.youtube.com/playlist?list=PLcBe8nhQVgUg1zqOsdeRuVq9QVsLfj_Y9 . (PPTX 47 kb

Additional file 11: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Parental tests of the Red5 genotype. Results from F1 Sibling test for the first cross. (DOCX 14 kb