Table IV. Confirmation of RNA-Seq expression profiles with qPCR

Expression levels of PsR, PdCR, PsL, and PdL were calculated, and pairwise comparisons of roots (PdCR versus PsR) and leaves (PdL versus PsL) were calculated. Expression ratios, as fold change, for RNA-Seq data were calculated for roots [RNA-Seq (R)] and leaves [RNA-Seq (L)] with the DESeq program. Ratios for qPCR analysis were calculated for roots [qPCR (R)] and leaves [qPCR (L)] using the method described by Schmittgen and Livak (2008). All expression ratios are presented as Pi deficient/Pi sufficient. Negative values indicate that Pi sufficient has a higher expression level than Pi deficient, and expression ratios of 1 indicate no difference in expression between Pi sufficient and Pi deficient. ABC, ATP-binding cassette; ACC, 1-aminocyclopropane-1-carboxylate; AGTA, Ala glyoxlate transaminase; GPX-PDE, glycerophosphodiester phosphodiesterase; HAP2B, heme activator protein homolog 2B; MGDG, monogalactosyldiacylglycerol; SPX, SYG1/Pho8/XPR1; THFD, THF deformylase; ZIM, zinc finger protein expressed in inflorescence meristem.

Sequence IdentifierRNA-Seq (R)qPCR (R)RNA-Seq (L)qPCR (L)Annotation
LAGI01_354274515461.525Purple acid phosphatase
LAGI01_589653713118Peroxidase
LAGI01_8591727301−7Ferric reductase
LAGI01_48402231221Formamidase
LAGI01_7200422513Ferric reductase3
LAGI01_21605193322MATE
LAGI01_46294171415Low-phosphate root1 (LPR1)
LAGI01_7454016411Nodulin
LAGI01_7775615311Malate synthase
LAGI01_30950121617Cytochrome P450 (76C7)
LAGI01_514701211128bHLH TF
LAGI01_668409116Unknown
LAGI01_4844691261GPX-PDE
LAGI01_429328824Phosphatase
LAGI01_316879141Phospholipase D
LAGI01_4656062247SPX3 (SPX domain3)
LAGI01_201324133ABC TP
LAGI01_571114321Sulfoqunovosyldiacylglycerol2 (SQD2)
LAGI01_515434211HAP2B
LAGI01_280634122Phosphatase
LAGI01_404364432Unknown
LAGI01_506314511Formate dehydrogenase
LAGI01_2060541224Phosphate transporter1
LAGI01_5250331321SPX3 (SPX domain3)
LAGI01_230113743Salt tolerance (SAT32)
LAGI01_232203562MGDG synthase
LAGI01_290373314CKX
LAGI01_325713311S-Adenosyl-Met synthase
LAGI01_296173211PHO1 (phosphate1)
LAGI01_145093211Transferase
LAGI01_256953111AGTA
LAGI01_4500931−62Flavonoid
LAGI01_304782512ACC synthase
LAGI01_484082511THFD
LAGI01_591962311Suc synthase
LAGI01_378051928ACC oxidase
LAGI01_3130313−31Pentatricopeptide repeat
LAGI01_149311211Methylene tetrahydrofolate
LAGI01_1871312−31Sugar transferase
LAGI01_263011121TP
LAGI01_336471−421Short-chain dehydrogenase
LAGI01_8482−2112Yellow stripe-like3
LAGI01_6205−2112DIS3-like exonuclease
LAGI01_8667−2122Auxin response factor19 (ARF19)
LAGI01_69456−2218Inositol polyphosphate 5-phosphatase
LAGI01_9188−2211Time for coffee-like
LAGI01_57082−2−213Lysosomal α-mannosidase
LAGI01_73251−2−2−22Auxin induced in root12
LAGI01_33259−2−2−41ZIM domain
LAGI01_63677−5112GA3 stimulated
LAGI01_55506−51−51GA regulated
LAGI01_2053−9−411PHO2 (phosphate2)
LAGI01_51692−15−211Unknown