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| 1 | Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement显示文摘Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut. | Xiaoping Chen Qing Lu Hao Liu Jianan Zhang Yanbin Hong Haofa Lan Haifen Li Jinpeng Wang Haiyan Liu Shaoxiong Li Manish K.Pandey Zhikang Zhang Guiyuan Zhou Jigao Yu Guoqiang Zhang Jiaqing Yuan Xingyu Li Shijie Wen Fanbo Meng Shanlin Yu Xiyin Wang Kadambot H.M.Siddique Zhong-Jian Liu Andrew H.Paterson Rajeev K.Varshney Xuanqiang Liang | 2019 | Molecular Plant2019，12，7： | 23 |
| 2 | The associated evolution among the extensive RNA editing,GC-biased mutation,and PPR family expansion in the organelle genomes of Selaginellaceae显示文摘Extensive C-to-U editing has been reported from plastid genomes(plastomes)and mitochondrial genomes(mitogenomes)of spikemoss.While“reverse”U-to-C editing was recorded in other seed-free plants such as hornworts,quillworts,and ferns,it was not observed in spikemosses.However,no comprehensive study on the association between RNA editing and other genomic features was conducted for the organelle genomes of spikemosses.Here,we report thousands of C-to-U editing sites from plastomes and mitogenomes of two species:1767 and 2394 edits in Selaginella remotifolia,and 4091 and 2786 edits in Selaginella nipponica,respectively.Comparative analyses revealed two different editing frequencies among plastomes,but one similar frequency in mitogenomes.The different editing frequency in the Selaginella organelle genomes is related to the nonsynonymous substitution rate and the genome structural complexity.The high guanine and cytosine(GC)content caused by GC-biased mutations in organelle genomes might be related to the absence of U-to-C editing in Selaginellaceae.Using RNA-seq and whole-genome data,we screened the pentatricopeptide repeat(PPR)family and discovered that the number of aspartic acid-tyrosine-tryptophan(DYW)domain-containing PPR proteins corresponded roughly to the editing abundance in the Selaginella organelle genomes.Consequently,we hypothesize that associated evolution among RNA editing,GC-biased mutation in organelle genomes,and the PPR protein family encoded in the nuclear genome,is probably triggered by the aberrant DNA repair system in Selaginellaceae.Our study provides new insights into the association between organelle and nuclear genomes in Selaginellaceae,which would contribute to understanding the evolution of post-transcriptional modifications of organelle genomes in land plants. | Jong-Soo Kang Jigao Yu Xian-Chun Zhang Qiao-Ping Xiang | 2023 | Journal of Systematics and Evolution2023，61，5： | 0 |
| 3 | Paleo-polyploidization in Lycophytes显示文摘Lycophytes and seed plants constitute the typical vascular plants.Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants.Here,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model lycophyte.In addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed plants.Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants. | Jinpeng Wang Jigao Yu Pengchuan Sun Chao Li Xiaoming Song Tianyu Lei Yuxian Li Jiaqing Yuan Sangrong Sun Hongling Ding Xueqian Duan Shaoqi Shen Yanshuang Shen Jing Li Fanbo Meng Yangqin Xie Jianyu Wang Yue Hou Jin Zhang Xianchun Zhang Xiu-Qing Li Andrew HPaterson Xiyin Wang | 2020 | Genomics, Proteomics & Bioinformatics2020，18，3： | 0 |
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