Chromatin Architectures Are Associated with Response to Dark Treatment in the Oil Crop Sesamum indicum, Based on a High-Quality Genome Assembly

Li，Chaoqiong1; Li，Xiaoli1,2; Liu，Hongzhan1; Wang，Xueqin1; Li，Weifeng3; Chen，Mao Sheng4; Niu，Long Jian5,6

2020-05-01

10.1093/pcp/pcaa026

PLANT AND CELL PHYSIOLOGY   影响因子和分区

0032-0781

1471-9053

Eukaryotic chromatin is tightly packed into hierarchical structures, allowing appropriate gene transcription in response to environmental and developmental cues. Here, we provide a chromosome-scale de novo genome assembly of sesame with a total length of 292.3 Mb and a scaffold N50 of 20.5 Mb, containing estimated 28,406 coding genes using Pacific Biosciences long reads combined with a genome-wide chromosome conformation capture (Hi-C) approach. Based on this high-quality reference genome, we detected changes in chromatin architectures between normal growth and dark-treated sesame seedlings. Gene expression level was significantly higher in 'A' compartment and topologically associated domain (TAD) boundary regions than in 'B' compartment and TAD interior regions, which is coincident with the enrichment of H4K3me3 modification in these regions. Moreover, differentially expressed genes (DEGs) induced by dark treated were enriched in the changed TAD-related regions and genomic differential contact regions. Gene Ontology (GO) enrichment analysis of DEGs showed that genes related to 'response to stress' and 'photosynthesis' functional categories were enriched, which corresponds to dark treatment. These results suggested that chromatin organization is associated with gene transcription in response to dark treatment in sesame. Our results will facilitate the understanding of regulatory mechanisms in response to environmental cues in plants.

Chromatin architecture Dark treatment Genome Hi-C Sesame

SCI

英语

通讯

WOS:000537456600011

PLANT & ANIMAL SCIENCE

2-s2.0-85084695665

Scopus

1.College of Life Science and Agronomy,Zhoukou Normal University,Zhoukou,466001,China
2.Key Laboratory of Plant Genetics and Molecular Breeding,Zhoukou Normal University,Zhoukou,466001,China
3.Sesame Experiment Station,Zhoukou Academy of Agricultural Sciences,Zhoukou,466001,China
4.CAS Key Laboratory of Tropical Plant Resources and Sustainable Use,Innovative Academy of Seed Design,Chinese Academy of Sciences,Xishuangbanna Tropical Botanical Garden,666303,China
5.Department of Biology,Southern University of Science and Technology,Shenzhen,518055,China
6.Department of Biology,Nankai University,China

Li，Chaoqiong,Li，Xiaoli,Liu，Hongzhan,et al. Chromatin Architectures Are Associated with Response to Dark Treatment in the Oil Crop Sesamum indicum, Based on a High-Quality Genome Assembly[J]. PLANT AND CELL PHYSIOLOGY,2020,61(5):978-987.

Li，Chaoqiong.,Li，Xiaoli.,Liu，Hongzhan.,Wang，Xueqin.,Li，Weifeng.,...&Niu，Long Jian.(2020).Chromatin Architectures Are Associated with Response to Dark Treatment in the Oil Crop Sesamum indicum, Based on a High-Quality Genome Assembly.PLANT AND CELL PHYSIOLOGY,61(5),978-987.

Li，Chaoqiong,et al."Chromatin Architectures Are Associated with Response to Dark Treatment in the Oil Crop Sesamum indicum, Based on a High-Quality Genome Assembly".PLANT AND CELL PHYSIOLOGY 61.5(2020):978-987.