A global survey of the transcriptome of allopolyploid Brassica napus based on single‐molecule long‐read isoform sequencing and Illumina‐based RNA sequencing data

Abstract

SUMMARY Brassica napus is a recent allopolyploid derived from the hybridization of Brassica rapa (ArAr) and Brassica oleracea (CoCo). Because of the high sequence similarity between the An and Cn subgenomes, it is difficult to provide an accurate landscape of the whole transcriptome of B. napus. To overcome this problem, we applied a single‐molecule long‐read isoform sequencing (Iso‐Seq) technique that can produce long reads to explore the complex transcriptome of B. napus at the isoform level. From the Iso‐Seq data, we obtained 147 698 non‐redundant isoforms, capturing 37 403 annotated genes. A total of 18.1% (14 934/82 367) of the multi‐exonic genes showed alternative splicing (AS). In addition, we identified 549 long non‐coding RNAs, the majority of which displayed tissue‐specific expression profiles, and detected 7742 annotated genes that possessed isoforms containing alternative polyadenylation sites. Moreover, 31 591 AS events located in open reading frames (ORFs) lead to potential protein isoforms by in‐frame or frameshift changes in the ORF. Illumina RNA sequencing of five tissues that were pooled for Iso‐Seq was also performed and showed that 69% of the AS events were tissue‐specific. Our data provide abundant transcriptome resources for a transcript isoform catalog of B. napus, which will facilitate genome reannotation, strengthen our understanding of the B. napus transcriptome and be applied for further functional genomic research.

Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

“…Benchmarking of Universal Single-Copy Orthologs (BUSCO) analysis revealed that the transcriptome assemblies of the two species contain more than 94% of the eudicotyledonous “near-universal single-copy orthologs”. This number is similar to or more than that for transcriptome assemblies of other Brassicaceae (Chandler et al 2020; Yao et al 2020; Fernandez-Pozo et al 2021). Furthermore, we found members of all 16 miRNA families that were found to have originated before the emergence of eudicots and conserved in eudicots (Montes et al 2014).…”

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

“…We discovered two conserved motifs (AUAAA and UGUA) upstream of the poly(A) cleavage site (Figure 5E); these motifs were also present in maize, red clover (Trifolium pratense L.), sorghum (Sorghum bicolor), Brassica napus, and poplar (Populus alba var. pyramidalis) (Abdel- Ghany et al, 2016;Wang et al, 2016;Chao et al, 2018;Hu et al, 2020;Yao et al, 2020). Additionally, to investigate the preferential nucleotides at the poly(A) cleavage sites, we analyzed the nucleotide composition of 50 downstream and 50 upstream nucleotides at all APA cleavage sites.…”

Characterization and Fine Mapping of a Yellow-Virescent Gene Regulating Chlorophyll Biosynthesis and Early Stage Chloroplast Development in Brassica napus

“…In addition, it expressed higher in all tissues of ZS9 than in yvl ( Figure 5D ). Apart from qRT-PCR, we further analyze the expression pattern of BnaA03.CHLH using RNA-seq data of Zhongshuang11 tissues (including root, stem, leaf, bud, silique, sepal, ovule, pericarp and callus), previously published by our group ( Li et al 2019 ; Yao et al 2020 ). The transcript abundance level of BnaA03.CHLH in leaf was consistent with the relative expression patterns observed in qRT-PCR (Figure S9).…”