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

Abstract

Amaranthus tricolor 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, Am. tricolor readily bolts and blooms, degrading leaf quality. A preliminary in vitro flowering study demonstrated that the flowering control pathway in Am. tricolor may differ from that of Arabidopsis. Nevertheless, no transcriptome analysis of the flowering process in Amaranthus has been conducted. To study Am. tricolor floral regulatory mechanisms, we conducted a large-scale transcriptome analysis—based on Illumina HiSeq sequencing of cDNA libraries generated from Am. tricolor 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 in vitro flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for in vitro flowering in Am. tricolor. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from Am. tricolor at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in Am. tricolor growth and development, but the results were somewhat similar to Arabidopsis. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate in vitro plantlet growth and flowering in Am. tricolor, the process appears to be highly complex in this species.

Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis

“…For example, in case of transcriptome analysis of Cymbidium sinence , only 49.88 % of the unigenes could be annotated [ 22 ]. Further, significant match could be assigned to only 55 % of the unigenes in bamboo transcriptome [ 23 ] while in case of Amaranthus tricolor only 52.89 % of the unigenes showed significant similarity [ 24 ].…”

De novo assembly, transcriptome characterization, lignin accumulation and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development

“…With the introduction of NGS, transcriptome sequencing has become an important tool in research because of its low cost and high throughput 26 27 . Short reads from Illumina high-throughput paired-end sequencing can be well assembled and used for transcriptome analysis and gene identification 28 . In the present study, larger amount raw reads were obtained from celery leaves collected at Stage 1, Stage 2, and Stage 3, respectively.…”

Reference genes forRT‐qPCRnormalisation in different tissues, developmental stages and stress conditions of amaranth

“…; Liu et al . ). Some of the libraries available on NCBI databases on amaranth are derived from experiments conducted on plants exposed to either different types of stress, such as drought, water stress, bacteria, salt stress and insect herbivores (Accession PRJNA65409); different development stages or experiments conducted on various tissues (accession PRJNA263128).…”