Changmian Ji

Chinese Academy of Tropical Agricultural Sciences

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Zhe Liang

Chinese Academy of Agricultural Sciences

Mingcheng Wang

Huanghuai University

Anping Guo

Chinese Academy of Tropical Agricultural Sciences

Ray Ming

Fujian Agriculture and Forestry University

Yunxie Wei

Hainan University

Songbi Chen

Tropical Crops Genetic Resources Institute

Xinhui Xiao

Tropical Crops Genetic Resources Institute

Jianchun Guo

State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation

Xiaoying Yang

University of California, Los Angeles

Wenquan Wang

Zhongshan Hospital

Cooperative Institutions

Chinese Academy of Sciences

Fujian Agriculture and Forestry University

Ministry of Agriculture and Rural Affairs

Chinese Academy of Tropical Agricultural Sciences

State Forestry and Grassland Administration

Chinese Academy of Agricultural Sciences

University of Chinese Academy of Sciences

Henan Agricultural University

Sanya University

Nanjing Agricultural University

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Additional file 12 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

Figshare (2021)

Wei Hu Changmian Ji Zhe Liang Jianqiu Ye Wenjun Ou

Additional file 12: Table S12. Comparation of starch content between accessions carrying heterozygous blocks with high frequency and accessions carrying homozygous blocks in cultivars.

Variation (astronomy)

10.6084/m9.figshare.17030762

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Additional file 17 of Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

Figshare (2021)

Wei Hu Changmian Ji Zhe Liang Jianqiu Ye Wenjun Ou

Additional file 17: Table S17. Genomic regions and genes that exhibit a decrease in both heterozygosity and nucleotide diversity during domestication from wild progenitors to cultivars (Top 0.99).

Variation (astronomy)

10.6084/m9.figshare.17030776

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The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth

Journal of Advanced Research (2023)

Honglin Luo Yongde Zhang Fuyan Liu Yongzhen Zhao Jinxia Peng

Golden pompano (Trachinotus ovatus) is economically significant important for offshore cage aquaculture in China and Southeast Asian countries. Lack of high-quality genomic data and accurate gene annotations greatly restricts its genetic breeding progress. To decode the mechanisms of sex determination and rapid growth in golden pompano and facilitate the sex- and growth-aimed genetic breeding. Genome assemblies of male and female golden pompano were generated using Illumina, PacBio, BioNano, genetic maps and Hi-C sequencing data. Genomic comparisons, whole genome re-sequencing of 202 F1 individuals, QTL mapping and gonadal transcriptomes were used to analyze the sex determining region, sex chromosome evolution, SNP loci, and growth candidate genes. Zebrafish model was used to investigate the functions of growth candidate gene. Female (644.45 Mb) and male (652.12 Mb) genomes of golden pompano were assembled and annotated at the chromosome level. Both genomes are highly conserved and no new or highly differentiated sex chromosomes occur. A 3.5 Mb sex determining region on LG15 was identified, where Hsd17b1, Micall2 and Lmx1a were putative candidates for sex determination. Three SNP loci significantly linked to growth were pinpointed, and a growth-linked gene gpsstr1 was identified by locus BSNP1369 (G→C, 17489695, Chr23). Loss of sstr1a (homologue of gpsstr1) in zebrafish caused growth retardation. This study provides insights into sex chromosome evolution, sex determination and rapid growth of golden pompano.

SNP

10.1016/j.jare.2023.11.030

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Phylogenetic Analyses and Transcriptional Survey Reveal the Characteristics, Evolution, and Expression Profile of NBS-Type Resistance Genes in Papaya

Agronomy (2023)

Qian Jiang Yu Wang Ai‐Sheng Xiong Hui Zhao Ruizong Jia

Carica papaya maintains an abnormally small but complete NLR family while showing weak disease resistance. To better understand their origin, evolution, and biological function, we identified 59 NLR genes via a customized RGAugury and investigated their characteristics, evolutionary history, and expression profiles based on the improved papaya genome and large-scale RNA-seq data. The results indicated that duplication is a major evolutionary force driving the formation of the papaya NLR family. Synteny analyses of papaya and other angiosperms showed that both insertion and inheritance-derived NLRs are present in papaya. Transcriptome-based expression and network analyses revealed that NLRs are actively involved in biotic stress responses. For example, a papaya-specific inserted TNL was up-regulated strongly by the fungal infection. Both transcriptome and qRT-PCR analyses confirmed the expression divergence of an RNL and an RCNL, a pair of tandem duplication genes involved in different co-expression modules. Furthermore, we observed an inserted gene cluster composed of five duplicated CNLs, showing dosage effects and functional differentiation of disease-resistance genes during evolution. This research will enhance our knowledge of the special NLR family in papaya, which may serve as a model plant for disease-resistance genetic studies.

Carica

Synteny

10.3390/agronomy13040970

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Citations (1)

A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement

SSRN Electronic Journal (2019)

Hong Zhang Xuming Li Haiyan Yu Yongbing Zhang Meihua Li

Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat genome using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C and a high-density genetic map. The final 12 chromosome-level scaffolds cover ~94.13% of the estimated genome (398.57Mb). Compared to the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. The genomic comparison analysis between Payzawat and DHL92 reveal that six genes relevant for cell wall biosynthesis may explain a considerable proportion of the skin thickness QTL STHQF12.4 on pseudochromosome 12. In addition, we have identified selective sweeps underlying the genes related to fruit size, seed size and leaf size during the multiple domestication of cultivated melon, and these findings serve as a foundation for the future studies of melon molecular breeding programs.

Trait

Melon

Basis (linear algebra)

10.2139/ssrn.3436230

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P4.07E.06 Distinct Genomic and Immune Microenvironment Features of Solid or Micropapillary Predominant Subtype in Stage I Lung Adenocarcinomas

Journal of Thoracic Oncology (2024)

Lei Zhang Qiang Huang Jiadi Luo Changmian Ji Yong Zhang

10.1016/j.jtho.2024.09.688

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Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

Genome biology (2021)

Wei Hu Changmian Ji Zhe Liang Jianqiu Ye Wenjun Ou

Abstract Background Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. Results We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB. Conclusions This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.

Outcrossing

Balancing selection

10.1186/s13059-021-02524-7

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Citations (23)

Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya

International Journal of Molecular Sciences (2023)

Yunsu Dai Yu Wang Liwang Zeng Ruizong Jia Linwen He

MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.

Carica

MADS-box

Functional divergence

Segmental duplication

10.3390/ijms241814039

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Citations (5)

Peanut Evolution: Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut (Adv. Sci. 4/2020)

Advanced Science (2020)

Dongmei Yin Changmian Ji Qingxin Song Wan‐Ke Zhang Xing‐Guo Zhang

The wild allotetraploid peanut species Arachis monticola is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. In article number 1901672, Dongmei Yin, Jinsong Zhang, Wei Hu, Z. Jeffrey Chen, and co-workers present a fully-annotated sequence of the A. monticola genome and comparative genomics of the Arachis species, which reveal asymmetric subgenome evolution and genome-assisted improvement of peanut production and resistance.

Arachis

Arachis hypogaea

Lineage (genetic)

10.1002/advs.202070018

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A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement

iScience (2019)

Hong Zhang Xuming Li Haiyan Yu Yongbing Zhang Meihua Li

Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding.

Sequence assembly

Melon

10.1016/j.isci.2019.10.049

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Citations (42)