Transcriptome Analysis by Illumina High-Throughout Paired-End Sequencing Reveals the Complexity of Differential Gene Expression during <i>In Vitro</i> Plantlet Growth and Flowering in <i>Amaranthus tricolor</i> L.

<div><p><i>Amaranthus tricolor</i> L. is a C₄ plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, <i>Am. tricolor</i> readily bolts and blooms, degrading leaf quality. A preliminary <i>in vitro</i> flowering study demonstrated that the flowering control pathway in <i>Am. tricolor</i> may differ from that of <i>Arabidopsis</i>. Nevertheless, no transcriptome analysis of the flowering process in <i>Amaranthus</i> has been conducted. To study <i>Am. tricolor</i> floral regulatory mechanisms, we conducted a large-scale transcriptome analysis—based on Illumina HiSeq sequencing of cDNA libraries generated from <i>Am. tricolor</i> at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to <i>in vitro</i> flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for <i>in vitro</i> flowering in <i>Am. tricolor</i>. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from <i>Am. tricolor</i> at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in <i>Am. tricolor</i> growth and development, but the results were somewhat similar to <i>Arabidopsis</i>. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate <i>in vitro</i> plantlet growth and flowering in <i>Am. tricolor</i>, the process appears to be highly complex in this species.</p>