Junpeng Shi

Sun Yat-sen University

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Jinsheng Lai

China Agricultural University

Weibin Song

Ministry of Agriculture and Rural Affairs

Xuerong Yang

Shandong Agricultural University

Haiming Zhao

China Agricultural University

Hongjun Liu

Shandong Agricultural University

Silong Sun

Shandong Agricultural University

Jian Chen

Ministry of Agriculture and Rural Affairs

Xuehui Huang

Shanghai Normal University

Qianqian Kong

China University of Mining and Technology

Qi Feng

Chinese Academy of Sciences

Cooperative Institutions

China Agricultural University

Chinese Academy of Sciences

Chinese Academy of Agricultural Sciences

Ministry of Agriculture and Rural Affairs

Sun Yat-sen University

University of Chinese Academy of Sciences

Institute of Crop Sciences

Center for Excellence in Molecular Plant Sciences

Peking University

Chinese Academy of Medical Sciences & Peking Union Medical College

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Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress

The Plant Journal (2015)

Lei Lei Junpeng Shi Jian Chen Mei Zhang Silong Sun

Summary Plants can respond to environmental changes with various mechanisms occurred at transcriptional and translational levels. Thus far, there have been relatively extensive understandings of stress responses of plants on transcriptional level, while little information is known about that on translational level. To uncover the landscape of translation in plants in response to drought stress, we performed the recently developed ribosome profiling assay with maize seedlings growing under normal and drought conditions. Comparative analysis of the ribosome profiling data and the RNA ‐seq data showed that the fold changes of gene expression at transcriptional level were moderately correlated with that of translational level globally ( R 2 = 0.69). However, less than half of the responsive genes were shared by transcription and translation under drought condition, suggesting that drought stress can introduce transcriptional and translational responses independently. We found that the translational efficiencies of 931 genes were changed significantly in response to drought stress. Further analysis revealed that the translational efficiencies of genes were highly influenced by their sequence features including GC content, length of coding sequences and normalized minimal free energy. In addition, we detected potential translation of 3063 upstream open reading frames ( uORF s) on 2558 genes and these uORF s may affect the translational efficiency of downstream main open reading frames ( ORF s). Our study indicates that plant can respond to drought stress with highly dynamic translational mechanism, that acting synergistically with that of transcription.

Ribosome profiling

Drought stress

Profiling (computer programming)

10.1111/tpj.13073

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Citations (177)

HEMU: An integrated comparative genomics database and analysis platform for Andropogoneae grasses

Plant Communications (2023)

Yuzhi Zhu Zijie Wang Zanchen Zhou Yuting Liu Xiang Gao

This study reports an online database and analysis platform HEMU, which integrates 75 genome assemblies from 20 unique species, large amounts of multi-omics data, and six sophisticated analysis toolkits. HEMU will facilitate comparative genomics analysis within the tribe Andropogoneae.

Tribe

Comparative Genomics

10.1016/j.xplc.2023.100786

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Citations (2)

Gene duplication confers enhanced expression of 27-kDa γ-zein for endosperm modification in quality protein maize

Proceedings of the National Academy of Sciences (2016)

Hongjun Liu Junpeng Shi Chuanlong Sun Hao Gong Xingming Fan

Significance More than half a century ago, Oliver Nelson and Edwin Mertz at Purdue University found the maize opaque2 ( o2 ) mutation produces doubling of the endosperm lysine content, creating the foundation for quality protein maize (QPM) breeding. QPM has the potential to benefit millions of people in developing countries who consume maize as their sole protein source. However, breeding new QPM hybrids takes longer than regular hybrids, primarily because of the complex and unknown components of o2 endosperm modification; this has limited expansion of QPM worldwide. We identified a quantitative trait locus, a gene duplication at the 27-kDa γ-zein locus, which confers enhanced expression of this protein and leads to endosperm modification. This knowledge can effectively be applied in QPM breeding.

10.1073/pnas.1601352113

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Citations (67)

Patterns of genomic changes with crop domestication and breeding

Current Opinion in Plant Biology (2015)

Junpeng Shi Jinsheng Lai

Crop domestication and further breeding improvement have long been important areas of genetics and genomics studies. With the rapid advancing of next-generation sequencing (NGS) technologies, the amount of population genomics data has surged rapidly. Analyses of the mega genomics data have started to uncover a previously unknown pattern of genome-wide changes with crop domestication and breeding. Selection during domestication and breeding drastically reshaped crop genomes, which have ended up with regions of greatly reduced genetic diversity and apparent enrichment of potentially beneficial alleles located in both genic and non-genic regions. Increasing evidences suggest that epigenetic modifications also played an important role during domestication and breeding.

Molecular breeding

Population genomics

10.1016/j.pbi.2015.01.008

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Citations (82)

A retrotransposon in an HKT1 family sodium transporter causes variation of leaf Na⁺ exclusion and salt tolerance in maize

New Phytologist (2017)

Ming Zhang Yibo Cao Zhiping Wang Zhi‐Qiang Wang Junpeng Shi

Soil salinity is one of several major abiotic stresses that constrain maize productivity worldwide. An improved understanding of salt-tolerance mechanisms will thus enhance the breeding of salt-tolerant maize and boost productivity. Previous studies have indicated that the maintenance of leaf Na+ concentration is essential for maize salt tolerance, and the difference in leaf Na+ exclusion has previously been associated with variation in salt tolerance between maize varieties. Here, we report the identification and functional characterization of a maize salt-tolerance quantitative trait locus (QTL), Zea mays Na+ Content1 (ZmNC1), which encodes an HKT-type transporter (designated as ZmHKT1). We show that a natural ZmHKT1 loss-of-function allele containing a retrotransposon insertion confers increased accumulation of Na+ in leaves, and salt hypersensitivity. We next show that ZmHKT1 encodes a plasma membrane-localized Na+ -selective transporter, and is preferentially expressed in root stele (including the parenchyma cells surrounding the xylem vessels). We also show that loss of ZmHKT1 function increases xylem sap Na+ concentration and causes increased root-to-shoot Na+ delivery, indicating that ZmHKT1 promotes leaf Na+ exclusion and salt tolerance by withdrawing Na+ from the xylem sap. We conclude that ZmHKT1 is a major salt-tolerance QTL and identifies an important new gene target in breeding for improved maize salt tolerance.

Retrotransposon

10.1111/nph.14882

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Citations (260)

A high-quality, phased genome assembly of broomcorn millet reveals the features of its subgenome evolution and 3D chromatin organization

Plant Communications (2023)

Zhiheng Wang Shihui Huang Zhengyue Yang Jinsheng Lai Xiang Gao

10.1016/j.xplc.2023.100557

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HITAC-seq enables high-throughput cost-effective sequencing of plasmids and DNA fragments with identity

Journal of genetics and genomics/Journal of Genetics and Genomics (2021)

Xiang Gao Weipeng Mo Junpeng Shi Ning Song Pei Liang

DNA sequencing is vital for many aspects of biological research and diagnostics. Despite the development of second and third generation sequencing technologies, Sanger sequencing has long been the only choice when required to precisely track each sequenced plasmids or DNA fragments. Here, we report a complete set of novel barcoding and assembling system, Highly-parallel Indexed Tagmentation-reads Assembled Consensus sequencing (HITAC-seq), that could massively sequence and track the identities of each individual sequencing sample. With the cost of much less than that of single read of Sanger sequencing, HITAC-seq can generate high-quality contiguous sequences of up to 10 kilobases or longer. The capability of HITAC-seq was confirmed through large-scale sequencing of thousands of plasmid clones and hundreds of amplicon fragments using approximately 100 pg of input DNAs. Due to its long synthetic length, HITAC-seq was effective in detecting relatively large structural variations, as demonstrated by the identification of a ∼1.3 kb Copia retrotransposon insertion in the upstream of a likely maize domestication gene. Besides being a practical alternative to traditional Sanger sequencing, HITAC-seq is suitable for many high-throughput sequencing and genotyping applications.

Sanger sequencing

Massive parallel sequencing

Sequencing by ligation

Amplicon

Single cell sequencing

Retrotransposon

Illumina dye sequencing

Sequence assembly

10.1016/j.jgg.2021.05.009

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Citations (4)

De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis

Nature Genetics (2023)

Baobao Wang Mei Hou Junpeng Shi Lixia Ku Wei Song

Inbred strain

10.1038/s41588-022-01283-w

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Citations (68)

Evolution and Domestication Footprints Uncovered from the Genomes of Coix

Molecular Plant (2019)

Hongbing Liu Junpeng Shi Zexi Cai Yumin Huang Menglu Lv

Coix

Synteny

10.1016/j.molp.2019.11.009

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Citations (40)

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

Nature Genetics (2018)

Silong Sun Yingsi Zhou Jian Chen Junpeng Shi Haiming Zhao

Abstract Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.

Germ plasm

Coding region

10.1038/s41588-018-0182-0

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Citations (356)