Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya

Background Carica papaya is a trioecious plant species with a genetic sex-determination system defined by sex chromosomes. Under unfavorable environmental conditions male and hermaphrodite exhibit sex-reversal. Previous genomic research revealed few candidate genes for sex differentiation in this species. Nevertheless, more analysis is still needed to identify the mechanism responsible for sex flower organ development in papaya. Results The aim of this study was to identify differentially expressed genes among male, female and hermaphrodite flowers in papaya during early (pre-meiosis) and later (post-meiosis) stages of flower development. RNA-seq was used to evaluate the expression of differentially expressed genes and RT-qPCR was used to verify the results. Putative functions of these genes were analyzed based on their homology with orthologs in other plant species and their expression patterns. We identified a Male Sterility 1 gene (CpMS1) highly up-regulated in male and hermaphrodite flower buds compared to female flower buds, which expresses in small male flower buds (3–8 mm), and that might be playing an important role in male flower organ development due to its homology to MS1 genes previously identified in other plants. This is the first study in which the sex-biased expression of genes related to tapetum development in the anther developmental pathway is being reported in papaya. Besides important transcription factors related to flower organ development and flowering time regulation, we identified differential expression of genes that are known to participate in ABA, ROS and auxin signaling pathways (ABA-8-hydroxylases, AIL5, UPBEAT 1, VAN3-binding protein). Conclusions CpMS1 was expressed in papaya male and hermaphrodite flowers at early stages, suggesting that this gene might participate in male flower organ development processes, nevertheless, this gene cannot be considered a sex-determination gene. Due to its homology with other plant MS1 proteins and its expression pattern, we hypothesize that this gene participates in anther development processes, like tapetum and pollen development, downstream gender specification. Further gene functional characterization studies in papaya are required to confirm this hypothesis. The role of ABA and ROS signaling pathways in papaya flower development needs to be further explored as well.Ope

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