The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Ming, Ray; Hou, Shaobin; Feng, Yun; Yu, Qingyi; Dionne‐Laporte, Alexandre; Saw, Jimmy H.; Senin, Pavel; Wang, Wei; Ly, Benjamin V.; Lewis, Kanako L.; Salzberg, Steven L.; Feng, Lu; Jones, M.; Skelton, Rachel L.; Murray, Jan E.; Chen, Cuixia; Qian, Wubin; Shen, Junguo; Du, Peng; Eustice, Moriah; Tong, Eric; Tang, Haibao; Lyons, Eric; Paull, Robert E.; Michael, Todd P.; Wall, Kerr; Rice, Danny W.; Albert, Henrik H.; Wang, Ming Li; Zhu, Yun; Schatz, Michael C.; Nagarajan, Niranjan; Acob, Ricelle A.; Guan, Peizhu; Blas, Andrea L.; Wai, Ching Man; Ackerman, Christine M.; Ren, Yan; Liu, Chao; Wang, Jianmei; Wang, Jianping; Na, Jong Kuk; Shakirov, Eugene V.; Haas, Brian J.; Thimmapuram, Jyothi; Nelson, David R.; Wang, Xiyin; Bowers, John E.; Gschwend, Andrea R.; Delcher, Arthur L.; Singh, Ratnesh; Suzuki, Jon Y.; Tripathi, Savarni; Neupane, Kabi R.; Wei, Hairong; Irikura, Beth; Paidi, Maya Devi; Jiang, Ning; Zhang, Wenli; Presting, Gernot G.; Windsor, Aaron J.; Navajas-Pérez, Rafael; Torres, M.; Feltus, F. Alex; Porter, Brad W.; Li, Yingjun; Burroughs, Adam; Luo, Ming‐Cheng; Liu, Lei; Christopher, David A.; Mount, Stephen M.; Moore, Paul H.; Sugimura, Tak; Jiang, Jiming; Schuler, Mary A.; Friedman, Vikki; Mitchell-Olds, Thomas; Shippen, Dorothy E.; dePamphilis, Claude W.; Palmer, Jeffrey D.; Freeling, Michael; Paterson, Andrew H.; Gonsalves, D.; Wang, Lei; Alam, Maqsudul

doi:10.1038/nature06856

Cited by 954 publications

(732 citation statements)

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“…The accuracy rate is very high at 99.99995%, and a relatively high proportion of the errors (two-thirds) are small insertions or deletions (indels). The accuracy rate is similar to those obtained with WGS Sanger approaches 5,36 and is higher than those reported for most NGS-based assemblies. The estimated residual within-genome heterozygosity for the Oropetium genome is very low at 0.087%, which probably contributed to the high contiguity of the assembly.…”

Section: Methodssupporting

confidence: 81%

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

VanBuren

Bryant

Edger

et al. 2015

Nature

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Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly 1 . The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE) 2 . Here we report the whole-genome sequencing and assembly of the desiccationtolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.The genomes of Arabidopsis 3 , rice 4 , poplar, grape and Sorghum 5 were first sequenced using high-quality and reiterative Sanger-based approaches producing a series of 'gold standard' reference genomes. The advent of next-generation sequencing (NGS) technologies reduced costs of sequencing substantially, which has enabled sequencing of over 100 plant genomes 1 . The quality of plant genome assemblies depends on genome size, ploidy, heterozygosity and sequence coverage, but most NGS-based genomes have on the order of tens of thousands of short contigs distributed in thousands of scaffolds. The short read lengths of NGS, inherent biases and non-random sequencing errors have resulted in highly fragmented draft genome assemblies that are not complete, which means they are missing biologically meaningful sequences including entire genes, regulatory regions, transposable elements, centromeres, telomeres and haplotype-specific structural variations. It is becoming clear from ENCODE projects that complete genomes are needed to better understand the importance of the non-coding regions of genomes 2 .More than 40% of calories consumed by humans are derived from grasses, and the grass family (Poaceae) is arguably the most important plant family with regard to global food security 6 . The size and complexity of most grass genomes has challenged progress in gene discovery and comparative genomics, although draft genomes are now available for most agriculturally important grasses 1 . The largest genome assemblies, such as maize (2,300 megabases (Mb)) 7 , barley (5,100 Mb) 8 and wheat (hexaploid, 1...

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Section: Methodssupporting

confidence: 81%

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

VanBuren

Bryant

Edger

et al. 2015

Nature

Self Cite

280

248

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“…The expansion in the genome size in G. max and also P. trichocarpa (Tuskan et al, 2006), which has the second highest number of predicted MCC paralogs (77) in our repertoire of Meds, may account for the increased number of detectable MCC paralogs in these dicots as compared with Arabidopsis. Likewise, C. papaya, reported to have fewer genes than any other sequenced angiosperm (Ming et al, 2008), had the least number of MCC paralogs among dicots. Similarly, in monocots, the reported similar gene numbers across a broad diversity of grasses (International Brachypodium Initiative, 2010) was reflected in the number of MCC paralogs identified.…”

Section: Evidence Of Animal Med26 In Plantsmentioning

confidence: 94%

The Mediator Complex in Plants: Structure, Phylogeny, and Expression Profiling of Representative Genes in a Dicot (Arabidopsis) and a Monocot (Rice) during Reproduction and Abiotic Stress

et al. 2011

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The Mediator (Med) complex relays regulatory information from DNA-bound transcription factors to the RNA polymerase II in eukaryotes. This macromolecular unit is composed of three core subcomplexes in addition to a separable kinase module. In this study, conservation of Meds has been investigated in 16 plant species representing seven diverse groups across the plant kingdom. Using Hidden Markov Model-based conserved motif searches, we have identified all the known yeast/metazoan Med components in one or more plant groups, including the Med26 subunits, which have not been reported so far for any plant species. We also detected orthologs for the Arabidopsis (Arabidopsis thaliana) Med32, -33, -34, -35, -36, and -37 in all the plant groups, and in silico analysis identified the Med32 and Med33 subunits as apparent orthologs of yeast/metazoan Med2/ 29 and Med5/24, respectively. Consequently, the plant Med complex appears to be composed of one or more members of 34 subunits, as opposed to 25 and 30 members in yeast and metazoans, respectively. Despite low similarity in primary Med sequences between the plants and their fungal/metazoan partners, secondary structure modeling of these proteins revealed a remarkable similarity between them, supporting the conservation of Med organization across kingdoms. Phylogenetic analysis between plant, human, and yeast revealed single clade relatedness for 29 Med genes families in plants, plant Meds being closer to human than to yeast counterparts. Expression profiling of rice (Oryza sativa) and Arabidopsis Med genes reveals that Meds not only act as a basal regulator of gene expression but may also have specific roles in plant development and under abiotic stress conditions.

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“…We now know that the lineage of Arabidopsis has experienced two genome duplications as divergence from a common ancestor shared with cotton (Ming et al, 2008;Tang et al, 2008a), accounting for the majority of Arabidopsis gene duplications (Bowers et al, 2003). In this same time period, cotton has independently experienced a paleoduplication (Rong et al, 2005) and the well-known polyploid formation.…”

Section: Introductionmentioning

confidence: 99%