Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development

Abstract

Background Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

Impact of Agroclimatic Variables on Proteogenomics in Sugar Cane (Saccharum spp.) Plant Productivity

“…Next-generation sequencing (NGS) technology has accelerated the genome sequencing and resequencing of polyploidy crops to determine molecular markers’ genetic and physical mapping in specific loci/genes. These identified markers may be used to conduct molecular marker-assisted selection (MAS) breeding or evaluate the genetic links between different accessions using genotyping technologies to improve agronomic traits. − The evolution of transcriptome sequences has improved gene interpretation by providing insight into the domestication and control of gene function networks via gene expression and sequence patterns ,− for modern breeding and genome editing.…”

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

“…We analyzed SSR on transcripts over 500 bp selected from new transcripts with MIcroSAtellite identification toolsoftware which could identify 7 types of SSR, they are Mono nucleotide (p1), Di nucleotide (p2), Tri nucleotide (p3), Tetra nucleotide (p4), Penta nucleotide (p5), Hexa nucleotide (p6), compound SSR (c) and compound SSR with overlapping positions (c*) [ 42 ]. It can be seen that there are significant differences in the number and density distribution of different types of SSR (Table 2 , Fig.…”

Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing in Vicia sativa

“…The prediction principle of this method was to use BLAST software (version 2.2.26) to compare the sequences in pairs. The alignment results met the following conditions: the lengths of both sequences were greater than 1000 bp, and contained two HSPs (High-scoring Segment Pairs) in the alignment; The AS gap was greater than 100 bp and at least 100 bp away from the end of 3′/5′; Allowing an overlap of 5 bp of the all alternative transcripts, then were considered as candidate AS events [ 28 ].…”