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

Wang, Baobao; Hou, Meifang; Shi, Junpeng; Ku, Lixia; Song, Wei; Ning, Qiang; Li, Xin; Li, Changyu; Zhao, Bin; Zhang, Ruyang; Xu, Hui; Bai, Zhijing; Xia, Zhanchao; Wang, Hai; Wei, Hongbin; Jing, Yifeng; Dai, Zhouyan; Wang, Hu Hailing; Zhu, Xinyu; Li, Chunhui; Sun, Xuan; Wang, Shuaishuai; Wen, Yuh‐Sheng; Hou, Gege; Qi, Zhi; Dai, He; Li, Xuming; Zheng, Hongkun; Zhang, Zuxin; Liu, Yu; Wang, Tianyu; Jiang, Taijiao; Wan, Zhong; Chen, Yanhui; Zhao, Jiuran; Lai, Jinsheng; Wang, Haiyang

doi:10.1038/s41588-023-01308-y

Cited by 3 publications

(2 citation statements)

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“…The multiple sequence alignments (MSA) were computed using famsa (Deorowicz et al, 2016) from pan-genome relationships derived from the software package Pandagma (Cannon, 2023), which uses an all-vs-all approach to align the canonical transcripts in a given pan-gene group. Pandagma generated the MSA on 51 maize reference genomes including two versions of B73 (Hufford et al, 2021;Jiao et al, 2017), a set of 25 diverse maize lines called the Nested Association Mapping (NAM) panel (Hufford et al, 2021), 12 lines used in Chinese breeding programs (Wang et al, 2023), 4 European lines (Haberer et al, 2020), and an additional set of 8 high-quality maize lines available at MaizeGDB. The maize genome Zm-B73-REFERENCE-NAM-5.0 is used as the reference genome and the B73v5 annotation set contains 39,755 gene models and 75,539 transcripts.…”

Section: Pan-genome Multiple Sequence Alignmentsmentioning

confidence: 99%

PanEffect: A pan-genome visualization tool for variant effects in maize

Andorf,

Haley,

Hayford

et al. 2023

Preprint

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Understanding the effects of genetic variants is crucial for accurately predicting traits and phenotypic outcomes. Recent advances have utilized protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect. We implemented PanEffect at MaizeGDB to enable a comprehensive examination of the potential effects of coding variants across 51 maize genomes. The tool allows users to visualize over 550 million possible amino acid substitutions in the B73 maize reference genome and also to observe the effects of the 2.3 million natural variations in the maize pan-genome. Each variant effect score, calculated from the Evolutionary Scale Modeling (ESM) protein language model, shows the log-likelihood ratio difference between B73 and all variants in the pan-genome. These scores are shown using heatmaps spanning benign outcomes to strong phenotypic consequences. Additionally, PanEffect displays secondary structures and functional domains along with the variant effects, offering additional functional and structural context. Using PanEffect, researchers now have a platform to explore protein variants and identify genetic targets for crop enhancement.Availability and implementation: The PanEffect code is freely available on GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/PanEffect). A maize implementation of PanEffect and underlying datasets are available at MaizeGDB (https://www.maizegdb.org/effect/maize/).

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Section: Pan-genome Multiple Sequence Alignmentsmentioning

confidence: 99%

PanEffect: A pan-genome visualization tool for variant effects in maize

Andorf,

Haley,

Hayford

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…In recent years, advances in sequencing technologies and bioinformatics have made pan-genome analysis feasible and affordable. The availability of multiple high-quality reference genomes and the emergence of powerful computational tools have enabled the construction and comparison of pan-genomes for various plant species (Cai et al, 2021;Li et al, 2023;Liu et al, 2020;Qin et al, 2021;Wang et al, 2023a;Wang et al, 2022b;Zhang et al, 2021). These pangenomic investigations have provided valuable insights into the evolutionary dynamics, genetic diversity, and functional variation within/among species, highlighting the importance of studying the pan-genome for a comprehensive understanding of plant biology.…”

Section: Introductionmentioning

confidence: 99%

Pan-genome analysis of different morphotypes reveals genomic basis ofBrassica oleraceadomestication and differential organogenesis

Guo,

Wang,

Wang

et al. 2023

Preprint

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The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed with high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant (SV) hotspot regions enriched with auxin and flowering-related genes. Population genomic analyses reveal that early domestication of B. oleracea focused on leaf or stem selection. Gene flows resulting from agricultural practices and variety improvement are detected among different morphotypes. Selective sweep analysis identifies an auxin-responsive SAUR gene and a CLE family gene as the crucial players in the leaf-stem differentiation during the early stage of B. oleracea domestication, and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further discover that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.

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PanEffect: a pan-genome visualization tool for variant effects in maize

Andorf,

Haley,

Hayford

et al. 2024

Bioinformatics

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Understanding the effects of genetic variants is crucial for accurately predicting traits and functional outcomes. Recent approaches have utilized artificial intelligence and protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect. We implemented PanEffect at MaizeGDB to enable a comprehensive examination of the potential effects of coding variants across 50 maize genomes. The tool allows users to visualize over 550 million possible amino acid substitutions in the B73 maize reference genome and to observe the effects of the 2.3 million natural variations in the maize pan-genome. Each variant effect score, calculated from the Evolutionary Scale Modeling (ESM) protein language model, shows the log-likelihood ratio difference between B73 and all variants in the pan-genome. These scores are shown using heatmaps spanning benign outcomes to potential functional consequences. Additionally, PanEffect displays secondary structures and functional domains along with the variant effects, offering additional functional and structural context. Using PanEffect, researchers now have a platform to explore protein variants and identify genetic targets for crop enhancement. Availability The PanEffect code is freely available on GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/PanEffect). A maize implementation of PanEffect and underlying datasets are available at MaizeGDB (https://www.maizegdb.org/effect/maize/). Supplementary information Supplementary data are available at Bioinformatics online.

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

Abstract: In the version of this article initially published, Fig. 2b was from an earlier version of the figure, with the cancer types shown in incorrect order. The figure has been amended in the HTML and PDF versions of the article.

Cited by 3 publications

References 0 publications

PanEffect: A pan-genome visualization tool for variant effects in maize

PanEffect: A pan-genome visualization tool for variant effects in maize

Pan-genome analysis of different morphotypes reveals genomic basis ofBrassica oleraceadomestication and differential organogenesis

PanEffect: a pan-genome visualization tool for variant effects in maize

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