Supporting data for "Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)"

Dataset type: Genomic, Transcriptomic
Data released on August 31, 2018

Zhao H; Chen C; Fei B; Wang S; Shi C; Liu X; Zhang H; Lou Y; Chen L; Sun H; Zhou X; Wang S; Zhang C; Xu H; Li L; Yang Y; Wei Y; Yang W; Gao Q; Yang H; Gao Z; Zhao S; Jiang Z (2018): Supporting data for "Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)" GigaScience Database. http://dx.doi.org/10.5524/100498

DOI10.5524/100498

Bamboo is one of the most important non-timber forest products worldwide. However, a chromosome-level reference genome is lacking, and the evolutionary landscape of alternative splicing (AS) in bamboo remains unclear despite emerging data and improved technologies. Here, we provide a chromosome-level de novo genome assembly of the moso bamboo (Phyllostachys edulis) using additional abundance data and different assembly strategies. The significantly improved genome is a Scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version, and 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 266,771 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. Via comparison with orthologous genes in related plants, we observed dramatic evolutionary characteristics, suggesting that the AS genes are concentrated in more conserved genes that tend to accumulate higher expressed transcripts and share less specificity. Furthermore, gene family expansion, abundant AS and positive selection were identified in crucial genes involved in lignin biosynthesis, indicating that moso bamboo's specificity in being a woody plant in the grass family. These fundamental studies provide useful information for future studies performing in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.

Additional details

Read the peer-reviewed publication(s):

Zhao, H., Gao, Z., Wang, L., Wang, J., Wang, S., Fei, B., … Jiang, Z. (2018). Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis). GigaScience. doi:10.1093/gigascience/giy115

Accessions (data included in GigaDB):

BioProject: PRJEB2955
BioProject: PRJEB2956





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMEA168979738705kikko-chiku Phyllostachys edulis Description:Genomic DNA extracted from moso bamboo
Alternative names:PHO1
Alternative accession-BioProject:PRJEB2955
...
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SAMN0612783138705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
SAMN0612783238705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
SAMN0612783338705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
SAMN0612783438705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
SAMN0612783538705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
SAMN0612783638705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
SAMN0612783738705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
SAMN0612783838705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
SAMN0612783938705kikko-chiku Phyllostachys edulis Description:RNA extracted from a mixed sample of m...
Pooling details:A mixed sample of same tissue coll...
Alternative accession-BioProject:PRJEB2956
...
+
Displaying 1-10 of 28 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
scriptUNKNOWN20.54 KB2018-08-29
scriptUNKNOWN0.33 KB2018-08-29
scriptUNKNOWN6.39 KB2018-08-29
scriptUNKNOWN0.36 KB2018-08-29
scriptUNKNOWN9.3 KB2018-08-29
scriptUNKNOWN16.36 MB2018-08-29
scriptUNKNOWN0.28 KB2018-08-29
scriptUNKNOWN2.7 MB2018-08-29
scriptUNKNOWN0.28 KB2018-08-29
otherAGP393.13 KB2018-08-29
Displaying 1-10 of 137 File(s).
Funding body Awardee Award ID Comments
State administration of forestry and grassland H Zhao No. 201504106 Special Fund for Forest Scientific Research in the Public Welfare from State Forestry Administration of China
Ministry of Science of Technology of The People’s Republic of China H Zhao No. 2015BAD04B03 Sub-Project of National Science and Technology Support Plan of the Twelfth Five-Year in China
Ministry of Science of Technology of The People’s Republic of China Z Gao No. 2015BAD04B01 Sub-Project of National Science and Technology Support Plan of the Twelfth Five-Year in China

Protocols.io:

Date Action
August 31, 2018 Dataset publish
November 3, 2018 Manuscript Link added : 10.1093/gigascience/giy115