Abstract
BackgroundAnanas comosus var. bracteatus is an herbaceous perennial monocot cultivated as an ornamental plant for its chimeric leaves. Because of its genomic complexity, and because no genomic information is available in the public GenBank database, the complete structure of the mRNA transcript is unclear and there are limited molecular mechanism studies for Ananas comosus var. bracteatus.MethodsThree size fractionated full-length cDNA libraries (1–2 kb, 2–3 kb, and 3–6 kb) were constructed and subsequently sequenced in five single-molecule real-time (SMRT) cells (2 cells, 2 cells, and 1 cell, respectively).ResultsIn total, 19,838 transcripts were identified for alternative splicing (AS) analysis. Among them, 19,185 (96.7%) transcripts were functionally annotated. A total of 9,921 genes were identified by mapping the non-redundant isoforms to the reference genome. A total of 10,649 AS events were identified, the majority of which were intron retention events. The alternatively spliced genes had functions in the basic metabolism processes of the plant such as carbon metabolism, amino acid biosynthesis, and glycolysis. Fourteen genes related to chlorophyll biosynthesis were identified as having AS events. The distribution of the splicing sites and the percentage of conventional and non-canonical AS sites of the genes categorized in pathways related to the albino leaf phenotype (ko00860, ko00195, ko00196, and ko00710) varied greatly. The present results showed that there were 8,316 genes carrying at least one poly (A) site, which generated 21,873 poly (A) sites. These findings indicated that the quality of the gene structure and functional information of the obtained genome was greatly improved, which may facilitate further genetic study of Ananas comosus var. bracteatus.
Highlights
Ananas comosus var. bracteatus is an herbaceous perennial monocot originating from South America, and it belongs to the family Bromeliaceae, genus Ananas, and species A. comosus (L.) Merr. (Bartholomew, Paull & Rohrbach, 2003)
To address the limitation of the Illumina HiSeq platform, the transcriptome of A. comosus var. bracteatus was sequenced through the Pacific Biosciences Iso-Seq system
The leaves, stems and roots of chimeric plants as well as calluses, complete green shoots and complete white shoots derived via tissue culture were used for full-length transcriptome sequencing in the present study (Fig. 1)
Summary
SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. Bracteatus is cultivated commercially as an important ornamental plant for its colourful chimeric leaves and red fruit. Because of its genomic complexity, and because no genomic information is available in the public GenBank database, the complete structure of the mRNA transcript is unclear and there are limited molecular mechanism studies for Ananas comosus var. 19,838 transcripts were identified for alternative splicing (AS) analysis. The present results showed that there were 8,316 genes carrying at least one poly (A) site, which generated 21,873 poly (A) sites These findings indicated that the quality of the gene structure and functional information of the obtained genome was greatly improved, which may facilitate further genetic study of Ananas comosus var. These findings indicated that the quality of the gene structure and functional information of the obtained genome was greatly improved, which may facilitate further genetic study of Ananas comosus var. bracteatus
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