Abstract
BackgroundBamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies.ResultsHere, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo.ConclusionsThese fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.
Highlights
We are sorry for the typo error and we have revised the sentence in the Abstract section, as follows: “we provide a comprehensive alternative splicing (AS) profile based on the identification of 266,711 uniform AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and PacBio sequencing platforms.”
We are sorry for the typo error and we have revised the sentence, as follows: “Since AS possess strong specificity to different tissues or developmental stages, we identified 181,105 tissue-specific AS events (67.57%), which account for two-thirds of the AS events.”
Based on the genome-wide identification of orthologous genes in the selected 8 plants (Amborella trichopoda, A. thaliana, Elaeis guineensis, B. distachyon, O. sativa, Spirodela polyrhiza, S. bicolor and Ph. edulis) and the species divergence time in a phylogeny tree (Fig. 3a), we identified eight orthologous gene datasets
Summary
Dear Dr Scott, Re: Manuscript reference No GIGA-D-18-00076 Please find attached a revised version of our manuscript “Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)”, which we would like to resubmit for publication as a research article in GigaScience. We are sorry for the typo error and we have revised the sentence, as follows: “we provide a comprehensive AS profile based on the identification of 266,711 uniform AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and PacBio sequencing platforms.”. We have added the reference of BUSCO, and re-organized and re-numbered the Additional Table, as follows: “According to the completeness assessment of the annotation using BUSCO [1], moso bamboo (95.2%) was more complete than Z. mays (92.2%) but close to O. sativa (95.6%) (Fig. 1d and Additional Table S20)”. Response: Thank you for this excellent suggestion We have revised this sentence, as follows: “the distribution of the TE genes in the 8 datasets was examined and a substantially negative correlation was observed, indicating that the more conserved genes had more TE insertions.”. We have added the related description in the figure legend of Figure 2, as follows: “IR, A3SS, A5SS, and ES represents intron retention, alternative 3’ splice site donor, alternative 5’ splice site acceptor, and exon skipping, respectively.”
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