Title Participants Abstract "Origin and evolution of the triploid cultivated banana genome" "Xiuxiu Li, Sheng Yu, Zhihao Cheng, Xiaojun Chang, Yingzi Yun, Mengwei Jiang, Xuequn Chen, Xiaohui Wen, Hua Li, Wenjun Zhu, Shiyao Xu, Yanbing Xu, Xianjun Wang, Chen Zhang, Qiong Wu, Jin Hu, Zhenguo Lin, Jean-Marc Aury, Yves Van de Peer, Zonghua Wang, Xiaofan Zhou, Jihua Wang, Peitao Lü, Liangsheng Zhang" "Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas." "Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package" "Fabricio De Almeida Silva, Yves Van de Peer" "Comparative genomics has become an indispensable part of modern biology due to the advancements in high-throughput sequencing technologies and the accumulation of genomic data in public databases. However, the quality of genomic data and the choice of parameters used in software tools used for comparative genomics can greatly impact the accuracy of results. Here, we present cogeqc, an R/Bioconductor package that provides researchers with a toolkit to assess genome assembly and annotation quality, orthogroup inference, and synteny detection. The package offers context-guided assessments of assembly and annotation statistics by comparing observed statistics to those of closely-related species on NCBI. To assess orthogroup inference, cogeqc calculates a protein domain-aware orthogroup score that aims at maximising the number of shared protein domains within the same orthogroup. The assessment of synteny detection consists in representing anchor gene pairs as a synteny network and analysing its graph properties, such as clustering coefficient, node count, and scale-free topology fit. The application of cogeqc to real datasets allowed for an evaluation of multiple parameter combinations for orthogroup inference and synteny detection, providing researchers in need for comparative genomics with guidelines to aid in the selection of the most appropriate tools and parameters for their specific data. We demonstrate that the default parameters in orthogroup identification and synteny detection tools are not always the most suitable, highlighting the importance of performing assessments for each dataset. The assessment metrics provided by cogeqc will help researchers generate more accurate and reliable results." "The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil" "Mehrshad Ebadi, Quinten Bafort, Eshchar Mizrachi, Pieter Audenaert, Pieter Simoens, Marc Van Montagu, Dries Bonte, Yves Van de Peer" "The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that polyploidization can help overcome environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete or outlive nonpolyploids at times of environmental upheaval remain elusive, especially for autopolyploids, in which heterosis effects are limited. On the longer term, WGD might increase both mutational and environmental robustness due to redundancy and increased genetic variation, but on the short—or even immediate—term, selective advantages of WGDs are harder to explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show that duplicated GRNs—and thus duplicated genomes—show higher signal output variation than nonduplicated GRNs. This increased variation leads to niche expansion and can provide polyploid populations with substantial advantages to survive environmental turmoil. In contrast, under stable environments, GRNs might be maladaptive to changes, a phenomenon that is exacerbated in duplicated GRNs. We believe that these results provide insights into how genome duplication and (auto)polyploidy might help organisms to adapt quickly to novel conditions and to survive ecological uproar or even cataclysmic events." "Studying whole-genome duplication using experimental evolution of Spirodela polyrhiza" "Tian Wu, Annelore Natran, Lucas Prost, Eylem Aydogdu Lohaus, Yves Van de Peer, Quinten Bafort" "In this chapter, we present the use of Spirodela polyrhiza in experiments designed to study the evolutionary impact of whole-genome duplication (WGD). We shortly introduce this duckweed species and explain why it is a suitable model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related duckweed experiment. These steps include strain selection, ploidy determination, different methods of making polyploid duckweeds, replication, culturing conditions, preservation, and the ways to quantify phenotypic and transcriptomic change." "Inference of ancient polyploidy using transcriptome data" "Jia Li, Yves Van de Peer, Zhen Li" "Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and likely enabled adaptation under harsh conditions. Besides genomic data, transcriptome data have been widely employed to detect WGDs, due to their efficient accessibility to the gene space of a species. Age distributions based on synonymous substitutions (so-called KS age distributions) for paralogs assembled from transcriptome data have identified numerous WGDs in plants, paving the way for further studies on the importance of WGDs for the evolution of seed and flowering plants. However, it is still unclear how transcriptome-based age distributions compare to those based on genomic data. In this chapter, we implemented three different de novo transcriptome assembly pipelines with two popular assemblers, i.e., Trinity and SOAPdenovo-Trans. We selected six plant species with published genomes and transcriptomes to evaluate how assembled transcripts from different pipelines perform when using KS distributions to detect previously documented WGDs in the six species. Further, using genes predicted in each genome as references, we evaluated the effects of missing genes, gene family clustering, and de novo assembled transcripts on the transcriptome-based KS distributions. Our results show that, although the transcriptome-based KS distributions differ from the genome-based ones with respect to their shapes and scales, they are still reasonably reliable for unveiling WGDs, except in species where most duplicates originated from a recent WGD. We also discuss how to overcome some possible pitfalls when using transcriptome data to identify WGDs." "syntenet : an R/Bioconductor package for the inference and analysis of synteny networks" "Fabricio De Almeida Silva, Tao Zhao, Kristian K Ullrich, M Eric Schranz, Yves Van de Peer" "The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids" "JiaU+2010Yu Xue, Zhen Li, ShuaiU+2010Ya Hu, Shu-Min Kao, Tao Zhao, JieU+2010Yu Wang, Yue Wang, Min Chen, Yichun Qiu, HaiU+2010Yun Fan, Yang Liu, ZhuU+2010Qing Shao, Yves Van de Peer" "Genomic insights into adaptation to karst limestone and incipient speciation in East Asian Platycarya spp. (Juglandaceae)" "Yu Cao, Fabricio De Almeida Silva, Wei-Ping Zhang, Ya-Mei Ding, Dan Bai, Wei-Ning Bai, Bo-Wen Zhang, Yves Van de Peer, Da-Yong Zhang" "Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of microTom tomato" "Jia-Yu Xue, Hai-Yun Fan, Zhen Zeng, Yu-Han Zhou, Shuai-Ya Hu, Sai-Xi Li, Ying-Juan Cheng, Xiang-Ru Meng, Fei Chen, Zhu-Qing Shao, Yves Van de Peer" "MicroTom tomato has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g., arbuscular mycorrhizal symbiosis and fruit development. Additionally, non-coding RNAs, including miRNAs, lncRNAs and circRNAs were also identified, together with their potential targets. Interacting networks between different types of non-coding RNAs (miRNA-lncRNA), and non-coding RNAs and genes (miRNA-mRNA and lncRNA-mRNA) were constructed as well. Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit. Lastly, we established a database (http://eplant.njau.edu.cn/microTomBase/) with genomic and transcriptomic data, as well as details of gene co-expression and interacting networks on microTom, and this database should be of great value to those who wants to adopt microTom as a model plant for research." "A panoramic view of the genomic landscape of the genus Streptomyces" "Marios Nikolaidis, Andrew Hesketh, Nikoletta Frangou, Dimitris Mossialos, Yves Van de Peer, Stephen G. Oliver, Grigorios D. Amoutzias"