Table 4. Forty most abundant mRNA sequences (contigs) in the transcriptome of developing sweet cherry ‘Regina’ fruit. Additional information about these sequences is given in Supplementary Table S4.

Contig ID	Length (bp)	FPKM total	B2G best hit e-value	B2G best hit definition	Tentative function or process
Pa_24402	537	523 781	1.3×10−135	Glucan endo-1,3-beta-glucosidase; TLP; allergen Pru av 2	Stress
Pa_20288	606	269 571	6.9×10−35	Extensin-3	Cell wall
Pa_49067	411	250 297	2.9×10−49	Extensin-3	Cell wall
Pa_47876b	472	169 152	1.8×10−31	Proline-rich extensin-like protein EPR1	Cell wall
Pa_11846a	690	160 873	3.6×10−112	Major allergen Pru av 1	Stress
Pa_25400	432	152 331		No hit	Unknown
Pa_47716	483	140 243	5.4×10−28	Dehydrin COR47; cold-induced COR47 protein	Stress
Pa_29501a,b	581	112 730	5.3×10−79	Nonspecific lipid-transfer protein; allergen Pru av 3	Transport
Pa_53685	298	109 269		No hit	Unknown
Pa_50270	369	104 741		No hit	Unknown
Pa_10726	820	99 920	8.1×10−42	Protein E6	Unknown
Pa_39995	357	94 862	1.8×10−27	Phosphoprotein ECPP44	Stress
Pa_49183	405	85 504		no hit	Unknown
Pa_13183	905	76 502	0	Phosphoenolpyruvate carboxykinase	Gluconeogenesis
Pa_46196	679	75 477	4.2×10−107	Probable xyloglucan endotransglucosylase/hydrolase	Cell wall
Pa_21625	829	69 722	2.4×10−138	Glucan endo-1,3-beta-glucosidase; TLP; allergen Pru av 2	Stress
Pa_28260a	537	65 818	1.2×10−21	Conserved hypothetical protein	Unknown
Pa_11084	806	62 814	3.0×10−13	Metallothionein-like protein type 3	Transport
Pa_35173a	469	62 774	4.0×10−14	Arabinogalactan peptide 15	Cell wall
Pa_21347a,b	750	58 838	1.2×10−100	Major allergen Pru ar 1	Stress
Pa_21722	398	57 020	3.0×10−12	Polygalacturonase inhibitor 1; PGIP-1	Stress
Pa_06786	1089	55 517	0	Leucoanthocyanidin dioxygenase	Flavonoid bs.
Pa_11167b	1090	54 012	4.5×10−59	Extensin-1	Cell wall
Pa_30361	338	53 527	1.6×10−47	Chalcone synthase 2; Naringenin-chalcone synthase 2	Flavonoid bs.
Pa_59559	240	48 770		No hit	Unknown
Pa_13457a	894	48 742	2.1×10−18	Major latex allergen Hev b 5	Stress
Pa_44191	283	47 095		No hit	Unknown
Pa_54252	291	46 745		No hit	Unknown
Pa_16626	537	46 455	1.0×10−61	Ribulose bisphosphate carboxylase small chain	Photosynth.
Pa_11118	1257	44 566	1.4×10−151	Catalase isozyme 1	ROS detoxification
Pa_23720a	638	41 644	7.9×10−17	Universal stress protein A-like protein	Stress
Pa_05806	1627	41 123	0	Polyubiquitin	Protein turn-over
Pa_18352	1480	37 174	2.7×10−104	Cysteine proteinase RD21a	Protein turn-over
Pa_32379b	348	36 122	6.6×10−55	Glycine-rich cell wall structural protein; precursor	Cell wall
Pa_01373	771	35 506	4.0×10−62	Probable xyloglucan endotransglucosylase/hydrolase	Cell wall
Pa_21518a	645	35 305	3.6×10−40	Metallothionein-like protein type 2	Transport
Pa_21558	303	35 275	1.8×10−29	Tubulin alpha chain	Cytoskeleton
Pa_10497a	1760	35 073	4.0×10−175	S-adenosylmethionine decarboxylase proenzyme	Stress
Pa_29840	342	34 516	1.3×10−43	Elongation factor 1-alpha	Translation
Pa_44188	348	33 983		No hit	Unknown

Abbreviations: bs., biosynthesis; FPKM, fragments (reads) per kilobase of contig per million fragments mapped; ROS, reactive oxygen species.

^aContig was predicted to contain a full-length open reading frame.

^bExpression preferentially in exocarp (FPKM values in mesocarp 24 and 80 DAFB below 1% of the total sum of FPKM values in all samples).