Dataset Information

The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data.

ABSTRACT: Tea is a globally consumed non-alcohol beverage with great economic importance. However, lack of the reference genome has largely hampered the utilization of precious tea plant genetic resources towards breeding. To address this issue, we previously generated a high-quality reference genome of tea plant using Illumina and PacBio sequencing technology, which produced a total of 2,124?Gb short and 125?Gb long read data, respectively. A hybrid strategy was employed to assemble the tea genome that has been publicly released. We here described the data framework used to generate, annotate and validate the genome assembly. Besides, we re-predicted the protein-coding genes and annotated their putative functions using more comprehensive omics datasets with improved training models. We reassessed the assembly and annotation quality using the latest version of BUSCO. These data can be utilized to develop new methodologies/tools for better assembly of complex genomes, aid in finding of novel genes, variations and evolutionary clues associated with tea quality, thus help to breed new varieties with high yield and better quality in the future.

SUBMITTER: Xia E

PROVIDER: S-EPMC6629666 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data.

Xia Enhua E Li Fangdong F Tong Wei W Yang Hua H Wang Songbo S Zhao Jian J Liu Chun C Gao Liping L Tai Yuling Y She Guangbiao G Sun Jun J Cao Haisheng H Gao Qiang Q Li Yeyun Y Deng Weiwei W Jiang Xiaolan X Wang Wenzhao W Chen Qi Q Zhang Shihua S Li Haijing H Wu Junlan J Wang Ping P Li Penghui P Shi Chengying C Zheng Fengya F Jian Jianbo J Huang Bei B Shan Dai D Shi Mingming M Fang Congbing C Yue Yi Y Wu Qiong Q Ge Ruoheng R Zhao Huijuan H Li Daxiang D Wei Shu S Han Bin B Jiang Changjun C Yin Ye Y Xia Tao T Zhang Zhengzhu Z Zhao Shancen S Bennetzen Jeffrey L JL Wei Chaoling C Wan Xiaochun X

Scientific data 20190715 1

Tea is a globally consumed non-alcohol beverage with great economic importance. However, lack of the reference genome has largely hampered the utilization of precious tea plant genetic resources towards breeding. To address this issue, we previously generated a high-quality reference genome of tea plant using Illumina and PacBio sequencing technology, which produced a total of 2,124 Gb short and 125 Gb long read data, respectively. A hybrid strategy was employed to assemble the tea genome that h ...[more]

PMID: 31308375

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Project description:BackgroundThe marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. In the case of T. pseudonana, optical restriction site mapping was employed to further clarify and contextualize chromosome-level scaffolds. While both genomes are considered highly accurate and reasonably contiguous, they still contain many unresolved regions and unordered/unlinked scaffolds.ResultsWe have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. pseudonana and P. tricornutum genomes. Fine-scale assessment of our long-read derived genome assemblies allowed us to resolve previously uncertain genomic regions, further characterize complex structural variation, and re-evaluate the repetitive DNA content of both genomes. We also identified 1862 previously undescribed genes in T. pseudonana. In P. tricornutum, we used transposable element detection software to identify 33 novel copia-type LTR-RT insertions, indicating ongoing activity and rapid expansion of this superfamily as the organism continues to be maintained in culture. Finally, Bionano optical mapping of P. tricornutum chromosomes was combined with long-read sequence data to explore the potential of long-read sequencing and optical mapping for resolving haplotypes.ConclusionDespite its potential to yield highly contiguous scaffolds, long-read sequencing is not a panacea. Even for relatively small nuclear genomes such as those investigated herein, repetitive DNA sequences cause problems for current genome assembly algorithms. Determining whether a long-read derived genomic assembly is 'better' than one produced using traditional sequence data is not straightforward. Our revised reference genomes for P. tricornutum and T. pseudonana nevertheless provide additional insight into the structure and evolution of both genomes, thereby providing a more robust foundation for future diatom research.

Dataset Information

The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data.

Publications

The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data.

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