Characterisation of the whole-genome wide hexokinase gene family unravels the functional divergence in pear (<i>Pyrus bretschneideri</i> Rehd.)

<p>Hexokinase genes <i>(HXK</i>) encode enzymes that play an important role in fruit quality and plant development because they participate in the first step of the glycolytic pathway for sugar accumulation and metabolism. In this study, the authors conducted analysis of the phylogeny, gene structure, and expression of <i>HXK</i> genes in pear (<i>Pyrus bretschneideri</i> Rehd.), comparing them with 7 other plant species. A total of 10 <i>HXK</i> protein sequences from pear and 33 <i>HXK</i>s from 7 other species were identified and clustered into 4 groups, matching their motif classification. Duplication events and motif structure variation attributed the diversification of <i>HXK</i> genes, supported by differential expression pattern of <i>PbrHXKs</i> from pear fruit transcriptome data and qRT – PCR verification. Combining pear fruit soluble sugar content data and analyses above, <i>PbrHXK1</i>and <i>PbrHXK3</i> were identified as important candidate genes in sorbitol, fructose, and glucose accumulation during pear fruit development. <i>PbrHXK1</i>and <i>PbrHXK3</i> were identified as important candidate genes in sorbitol, fructose, and glucose accumulation during pear fruit development. Subsequent research on these highly expressed <i>PbrHXKs</i> will benefit the enhancement of sugar content and quality in pear.</p

Additional file 13 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

Additional file 13: Table S13. Names and sequences (5’ to 3’) of all oligonucleotide primers used in this study

Additional file 16 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

Additional file 16: Fig. S3. KEGG analysis of genes within the 3 Mbp IBD-ER

Additional file 10 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

Additional file 10: Table S10. SNPs, SNP density, and gene density of all 29,269 high-quality SNPs on all 17 pear chromosomes

Additional file 12 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

Additional file 12: Table S12. Two significant SNPs associated with fruit firmness

Additional file 9 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

Additional file 9: Table S9. Quality control of 200,481 SNPs from the SNP array

Additional file 14 of An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus

Additional file 14: Fig. S1. Distribution of IBD tract lengths within populations (cultivated Asian-cultivated Asian, wild Asian-wild Asian, cultivated European-cultivated European, and wild European-wild European) and between populations (cultivated Asian-wild Asian, cultivated Asian-cultivated European, cultivated Asian-wild European, wild Asian-cultivated European, wild Asian-wild European, and cultivated European-wild European). WE, wild European; CA, cultivated Asian; WE, wild European; and CE, cultivated European