Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck)

Abstract

Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control.

Gene coexpression network analysis of fruit transcriptomes uncovers a possible mechanistically distinct class of sugar/acid ratio-associated genes in sweet orange

“…To compare the fruit sugar/acid ratios in the four varieties of sweet orange, Newhall, Xinhui, Bingtang and Succari, we re-analyzed the fruit sugar and acid accumulation data reported previously [ 14 ]. At 45 DPA, the four varieties had sugar/acid ratios of 2.3–3.3, but because of similar increase in sugar levels and different acid levels at 142 DPA, they exhibited different sugar/acid ratios at 142 DPA (Fig.…”

“…( a ) Comparison of sugar and acid levels and sugar/acid ratios in different sweet orange varieties. Sugar and acid levels were adapted from a prior manuscript [ 14 ], and the sugar/acid ratios were calculated using the sugar and acid levels in each fruit for each variety. Values are means and SE of three fruits.…”

“…In this study, we use citrus as a model to reanalyze the fruit transcriptome data recently published from our group [ 14 ]. Citrus, representing one of the largest fresh fruit and juice industry in the world, has the potential for use as an economically important tree fruit model organism to study non-climacteric fruit development.…”

“…Towards this, we have identified a total of 72 genes strongly correlated with the sugar/acid ratios, and yet most of them do not correlate with either sugar or acid contents alone. Furthermore, since our first report of using systems biology approach in unraveling the citrus host response to the attack by one of the most constructive disease Huanglongbing [ 22 ], the gene coexpression-based approach has been increasingly used by us and other groups to further understand the gene networks involved in Huanglongbing pathogenesis and fruit development or predict gene annotations [ 14 , 23 – 25 ]. Therefore, in this study we also use the network approach to analyze the fruit transcriptome data, leading us to conclude that these 72 sugar/acid ratio-related genes belong to four modules of the fruit development gene coexpression network, two of which have no overlap with the sugar- and acid-related network modules.…”

Spatiotemporal Transcriptome Analysis Provides Insights into Bicolor Tepal Development in Lilium “Tiny Padhye”

“…This strategy has been used to identify regulators and co-expression networks in Arabidopsis thaliana (Appel et al, 2014), strawberry ( Fragaria spp.) (Hollender et al, 2014), apple ( Malus × domestica ) (Bai et al, 2015), and sweet orange ( Citrus sinensis L. Osbeck) (Huang et al, 2016). …”