9 Works

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Joaquin Canizares, Yimin Xu, Esther Van Der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni & Zhangjun Fei
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter...

Additional file 4 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 4: Table S3.qPCR results of gDNA after DNase treatment. (recording data values of Additional file 1: Fig. S6B).

Additional file 5 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 5: Table S4.Normalized abundance of marker genes in each GC cell type. (recording data values of Additional file 1: Fig. S7D).

Additional file 2 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 2: Table S1. Coverage uniformity across gene body and gene number detected by SHERRY2 when testing different conditions on bulk RNA. (data values of Additional file 1: Fig. S1).

Additional file 2 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 2: Table S1. Coverage uniformity across gene body and gene number detected by SHERRY2 when testing different conditions on bulk RNA. (data values of Additional file 1: Fig. S1).

Additional file 3 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 3: Table S2.Comparison of SHERRY and SHERRY2 performances on bulk RNA. (recording data values of Additional file 1: Fig. S2).

Additional file 3 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 3: Table S2.Comparison of SHERRY and SHERRY2 performances on bulk RNA. (recording data values of Additional file 1: Fig. S2).

Additional file 4 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 4: Table S3.qPCR results of gDNA after DNase treatment. (recording data values of Additional file 1: Fig. S6B).

Additional file 5 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 5: Table S4.Normalized abundance of marker genes in each GC cell type. (recording data values of Additional file 1: Fig. S7D).

Registration Year

  • 2022
    8
  • 2019
    1

Resource Types

  • Dataset
    9

Affiliations

  • Agricultural Genomics Institute at Shenzhen
    9
  • New York University Langone Medical Center
    8
  • Zhejiang University
    8
  • Air Force Medical University
    8
  • Huazhong University of Science and Technology
    8
  • Beihang University
    8
  • Shanghai University of Traditional Chinese Medicine
    8
  • Northwest University
    8
  • Fudan University
    8
  • Capital Medical University
    8