The Emerging Importance of Type I MADS Box Transcription Factors for Plant Reproduction

Masiero, Simona; Colombo, Lucia; Grini, Paul E.; Schnittger, Arp; Kater, Martin M.

doi:10.1105/tpc.110.081737

Cited by 199 publications

(158 citation statements)

References 86 publications

(154 reference statements)

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“…Interactions among type I MADS-box genes are important for the initiation of endosperm development 56 . We also determined the expression levels of all orchid MADS-box genes (Supplementary Table 26) and found that 20 of these genes were preferentially expressed in flower tissue.…”

Section: Mads-box Gene Family Analysismentioning

confidence: 99%

The genome sequence of the orchid Phalaenopsis equestris

et al. 2014

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Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers

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Section: Mads-box Gene Family Analysismentioning

confidence: 99%

The genome sequence of the orchid Phalaenopsis equestris

et al. 2014

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“…tauschii had an excess of such TFs as MYB-related genes (103, in contrast with 66 in Brachypodium and 95 in maize), and these are also thought to be involved in various stress responses 17 . The M-type MADS-box genes (58, in contrast with 23 in Brachypodium and 34 in maize) are involved in regulation in plant reproduction 18 ( Fig. 2b and Supplementary Table 18).…”

Section: Research Lettermentioning

confidence: 99%

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

Jia

Zhao

Kong

et al. 2013

Nature

683

637

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About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n 5 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n 5 4x 5 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n 5 6x 5 42; AABBDD) 1,2 . Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker's flour 2 . Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.We selected Ae. tauschii accession AL8/78 for genome sequencing because it has been extensively characterized genetically (Supplementary Information). Using a whole genome shotgun strategy, we generated 398 Gb of high-quality reads from 45 libraries with insert sizes ranging from 200 bp to 20 kb (Supplementary Information). A hierarchical, iterative assembly of short reads employing the parallelized sequence assembler SOAPdenovo 3 achieved contigs with an N50 length (minimum length of contigs representing 50% of the assembly) of 4,512 bp (Table 1). Paired-end information combined with an additional 18.4 Gb of Roche/454 long-read sequences was used sequentially to generate 4.23-Gb scaffolds (83.4% were non-gapped contiguous sequences) with an N50 length of 57.6 kb (Supplementary Information). The assembly represented 97% of the 4.36-Gb genome as estimated by K-mer analysis (Supplementary Information). We also obtained 13,185 Ae. tauschii expressed sequence tag (EST) sequences using Sanger sequencing, of which 11,998 (91%) could be mapped to the scaffolds with more than 90% coverage (Supplementary Information).To aid in gene identification, we performed RNA-Seq (53.2 Gb for a 117-Mb transcriptome assembly) on 23 libraries representing eight tissues including pistil, root, seed, spike, stamen, stem, leaf and sheath (Supplementary Information). Using both evidence-based and de novo gene predictions, we identified 34,498 high-confidence protein-coding loci. FGENESH 4 and GeneID models were supported by a 60% overlap with either our ESTs and RNA-Seq reads, or with homologous proteins. More than 76% of the gene models had a significant match (E value # 10 25; alignment length $ 60%) in the ...

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“…Also, the function of the different Type I genes is generally poorly characterized. However, several Type I genes have been reported to play a role in female gametogenesis, embryogenesis, and seed development (Portereiko et al, 2006;Bemer et al, 2010;Masiero et al, 2011).…”

Section: Iii2 Type I Mads-box Genesmentioning

confidence: 99%

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

et al. 2017

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Conserved genomic context provides critical information for comparative evolutionary analysis. With the increase in numbers of sequenced plant genomes, synteny analysis can provide new insights into gene family evolution. Here, we exploit a network analysis approach to organize and interpret massive pairwise syntenic relationships. Specifically, we analyzed synteny networks of the MADS-box transcription factor gene family using 51 completed plant genomes. In combination with phylogenetic profiling, several novel evolutionary patterns were inferred and visualized from synteny network clusters. We found lineage-specific clusters that derive from transposition events for the regulators of floral development (APETALA3 and PI) and flowering time (FLC) in the Brassicales and for the regulators of root development (AGL17) in Poales. We also identified two large gene clusters that jointly encompass many key phenotypic regulatory Type II MADS-box gene clades (SEP1, SQUA, TM8, SEP3, FLC, AGL6, and TM3). Gene clustering and gene trees support the idea that these genes are derived from an ancient tandem gene duplication that likely predates the radiation of the seed plants and then expanded by subsequent polyploidy events. We also identified angiosperm-wide conservation of synteny of several other less studied clades. Combined, these findings provide new hypotheses for the genomic origins, biological conservation, and divergence of MADS-box gene family members.

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The Emerging Importance of Type I MADS Box Transcription Factors for Plant Reproduction

Cited by 199 publications

References 86 publications

The genome sequence of the orchid Phalaenopsis equestris

The genome sequence of the orchid Phalaenopsis equestris

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

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