The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color

文献类型： 外文期刊

第一作者： Feng, Lijun

作者： Feng, Lijun;Mao, Meiqin;Yang, Wei;Adje, Mark Owusu;Xue, Yanbin;Zhou, Xuzixin;Zhang, Huiling;Luo, Jiaheng;Tang, Ruimin;Tan, Lin;Lin, Dongpu;Zhang, Xiaopeng;Zang, Yaoqiang;Li, Xi;Sun, Lingxia;Jiang, Fuxing;Ma, Jun;Wang, Juntao;He, Yehua;Chen, Changming;Luan, Aiping;Lin, Wenqiu;Xu, Wentian

作者机构：

关键词： Ananas comosus var; bracteatus f; tricolor; assembly; genetic variation; anthocyanin biosynthesis genes; photosynthesis genes

期刊名称：G3-GENES GENOMES GENETICS （ 影响因子：3.542； 五年影响因子：3.545 ）

ISSN： 2160-1836

年卷期： 2022 年 12 卷 2 期

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收录情况： SCI

摘要： Ananas comosus var. bracteatus f. tricolor (GL1) is a red pineapple accession whose mostly green leaves with chimeric white leaf margins turn red in spring and autumn and during flowering. It is an important ornamental plant and ideal plant research model for anthocyanin metabolism, chimeric leaf development, and photosynthesis. Here, we generated a highly contiguous chromosome-scale genome assembly for GL1 and compared it with other 3 published pineapple assemblies (var. comosus accessions MD2 and F153, and var. bracteatus accession CB5). The GL1 assembly has a total size of similar to 461 Mb, with a contig N50 of similar to 2.97 Mb and Benchmarking Universal Single-Copy Ortholog score of 97.3%. More than 99% of the contigs are anchored to 25 pseudochromosomes. Compared with the other 3 published pineapple assemblies, the GL1 assembly was confirmed to be more continuous. Our evolutionary analysis showed that the Bromeliaceae and Poaceae diverged from their nearest common ancestor similar to 82.36 million years ago (MYA). Population structure analysis showed that while GL1 has not undergone admixture, bracteatus accession CB5 has resulted from admixture of 3 species of Ananas. Through classification of orthogroups, analysis of genes under positive selection, and analysis of presence/absence variants, we identified a series of genes related to anthocyanin metabolism and development of chimeric leaves. The structure and evolution of these genes were compared among the published pineapple assemblies with reveal candidate genes for these traits. The GL1 genome assembly and its comparisons with other 3 pineapple genome assemblies provide a valuable resource for the genetic improvement of pineapple and serve as a model for understanding the genomic basis of important traits in different pineapple varieties and other pan-cereal crops.

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