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3. MerAligner: A Fully Parallel Sequence Aligner

Author

Georganas, E, Georganas, E, Buluc, A, Chapman, J, Oliker, L, Rokhsar, D, Yelick, K, Georganas, E, Georganas, E, Buluc, A, Chapman, J, Oliker, L, Rokhsar, D, and Yelick, K

Abstract

Aligning a set of query sequences to a set of target sequences is an important task in bioinformatics. In this work we present merAligner, a highly parallel sequence aligner that implements a seed-and-extend algorithm and employs parallelism in all of its components. MerAligner relies on a high performance distributed hash table (seed index) and uses onesided communication capabilities of the Unified Parallel C to facilitate a fine-grained parallelism. We leverage communication optimizations at the construction of the distributed hash table and software caching schemes to reduce communication during the aligning phase. Additionally, merAligner preprocesses the target sequences to extract properties enabling exact sequence matching with minimal communication. Finally, we efficiently parallelize the I/O intensive phases and implement an effective load balancing scheme. Results show that merAligner exhibits efficient scaling up to thousands of cores on a Cray XC30 supercomputer using real human and wheat genome data while significantly outperforming existing parallel alignment tools.

Published
2015

4. HipMer: An extreme-scale de novo genome assembler

Author

Georganas, E, Kern, Jackie1, Vetter, Jeffrey S, Georganas, E, Buluç, A, Chapman, J, Hofmeyr, S, Aluru, C, Egan, R, Oliker, L, Rokhsar, D, Yelick, K, Georganas, E, Kern, Jackie1, Vetter, Jeffrey S, Georganas, E, Buluç, A, Chapman, J, Hofmeyr, S, Aluru, C, Egan, R, Oliker, L, Rokhsar, D, and Yelick, K

Abstract

De novo whole genome assembly reconstructs genomic sequences from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMer, the first high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. First, we significantly improve scalability of parallel k-mer analysis for complex repetitive genomes that exhibit skewed frequency distributions. Next, we optimize the traversal of the de Bruijn graph of k-mers by employing a novel communication-avoiding parallel algorithm in a variety of use-case scenarios. Finally, we parallelize the Meraculous scaffolding modules by leveraging the one-sided communication capabilities of the Unified Parallel C while effectively mitigating load imbalance. Large-scale results on a Cray XC30 using grand-challenge genomes demonstrate efficient performance and scalability on thousands of cores. Overall, our pipeline accelerates Meraculous performance by orders of magnitude, enabling the complete assembly of the human genome in just 8.4 minutes on 15K cores of the Cray XC30, and creating unprecedented capability for extreme-scale genomic analysis.

Published
2015

5. MerAligner: A Fully Parallel Sequence Aligner

Author

Georganas, E, Georganas, E, Buluc, A, Chapman, J, Oliker, L, Rokhsar, D, Yelick, K, Georganas, E, Georganas, E, Buluc, A, Chapman, J, Oliker, L, Rokhsar, D, and Yelick, K

Abstract

Aligning a set of query sequences to a set of target sequences is an important task in bioinformatics. In this work we present merAligner, a highly parallel sequence aligner that implements a seed-and-extend algorithm and employs parallelism in all of its components. MerAligner relies on a high performance distributed hash table (seed index) and uses onesided communication capabilities of the Unified Parallel C to facilitate a fine-grained parallelism. We leverage communication optimizations at the construction of the distributed hash table and software caching schemes to reduce communication during the aligning phase. Additionally, merAligner preprocesses the target sequences to extract properties enabling exact sequence matching with minimal communication. Finally, we efficiently parallelize the I/O intensive phases and implement an effective load balancing scheme. Results show that merAligner exhibits efficient scaling up to thousands of cores on a Cray XC30 supercomputer using real human and wheat genome data while significantly outperforming existing parallel alignment tools.

Published
2015

6. HipMer: An extreme-scale de novo genome assembler

Author

Georganas, E, Kern, Jackie1, Vetter, Jeffrey S, Georganas, E, Buluç, A, Chapman, J, Hofmeyr, S, Aluru, C, Egan, R, Oliker, L, Rokhsar, D, Yelick, K, Georganas, E, Kern, Jackie1, Vetter, Jeffrey S, Georganas, E, Buluç, A, Chapman, J, Hofmeyr, S, Aluru, C, Egan, R, Oliker, L, Rokhsar, D, and Yelick, K

Abstract

De novo whole genome assembly reconstructs genomic sequences from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMer, the first high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. First, we significantly improve scalability of parallel k-mer analysis for complex repetitive genomes that exhibit skewed frequency distributions. Next, we optimize the traversal of the de Bruijn graph of k-mers by employing a novel communication-avoiding parallel algorithm in a variety of use-case scenarios. Finally, we parallelize the Meraculous scaffolding modules by leveraging the one-sided communication capabilities of the Unified Parallel C while effectively mitigating load imbalance. Large-scale results on a Cray XC30 using grand-challenge genomes demonstrate efficient performance and scalability on thousands of cores. Overall, our pipeline accelerates Meraculous performance by orders of magnitude, enabling the complete assembly of the human genome in just 8.4 minutes on 15K cores of the Cray XC30, and creating unprecedented capability for extreme-scale genomic analysis.

Published
2015

7. Parallel de Bruijn Graph Construction and Traversal for de Novo Genome Assembly

Author

Georganas, E, Damkroger, Trish1, Dongarra, Jack J, Georganas, E, Buluç, A, Chapman, J, Oliker, L, Rokhsar, D, Yelick, K, Georganas, E, Damkroger, Trish1, Dongarra, Jack J, Georganas, E, Buluç, A, Chapman, J, Oliker, L, Rokhsar, D, and Yelick, K

Abstract

De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous fragments called reads. We study optimized parallelization of the most time-consuming phases of Meraculous, a state of-the-art production assembler. First, we present a new parallel algorithm for k-mer analysis, characterized by intensive communication and I/O requirements, and reduce the memory requirements by 6.93×. Second, we efficiently parallelize de Bruijn graph construction and traversal, which necessitates a distributed hash table and is a key component of most de novo assemblers. We provide a novel algorithm that leverages one-sided communication capabilities of the Unified Parallel C (UPC) to facilitate the requisite fine-grained parallelism and avoidance of data hazards, while analytically proving its scalability properties. Overall results show unprecedented performance and efficient scaling on up to 15,360 cores of a Cray XC30, on human genome as well as the challenging wheat genome, with performance improvement from days to seconds.

Published
2014

8. Parallel de Bruijn Graph Construction and Traversal for de Novo Genome Assembly

Author

Georganas, E, Damkroger, Trish1, Dongarra, Jack J, Georganas, E, Buluç, A, Chapman, J, Oliker, L, Rokhsar, D, Yelick, K, Georganas, E, Damkroger, Trish1, Dongarra, Jack J, Georganas, E, Buluç, A, Chapman, J, Oliker, L, Rokhsar, D, and Yelick, K

Abstract

De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous fragments called reads. We study optimized parallelization of the most time-consuming phases of Meraculous, a state of-the-art production assembler. First, we present a new parallel algorithm for k-mer analysis, characterized by intensive communication and I/O requirements, and reduce the memory requirements by 6.93×. Second, we efficiently parallelize de Bruijn graph construction and traversal, which necessitates a distributed hash table and is a key component of most de novo assemblers. We provide a novel algorithm that leverages one-sided communication capabilities of the Unified Parallel C (UPC) to facilitate the requisite fine-grained parallelism and avoidance of data hazards, while analytically proving its scalability properties. Overall results show unprecedented performance and efficient scaling on up to 15,360 cores of a Cray XC30, on human genome as well as the challenging wheat genome, with performance improvement from days to seconds.

Published
2014

9. Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species

Author

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. -C, Corbeil, J., Fabbro, C. D., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. -W, Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., MacCallum, I., MacManes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. -M, Yuan, J., Zhang, G., Zhang, H., Zhou, S., Korf, I. F., Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. -C, Corbeil, J., Fabbro, C. D., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. -W, Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., MacCallum, I., MacManes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. -M, Yuan, J., Zhang, G., Zhang, H., Zhou, S., and Korf, I. F.

Abstract

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., QC 20170307

Published
2013
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10. The genome of Naegleria gruberi illuminates early eukaryotic versatility.

Author

Fritz-Laylin, Lillian K., Prochnik, Simon E., Ginger, Michael L., Dacks, Joel B., Carpenter, Meredith L., Field, Mark C., Kuo, Alan, Paredez, Alex, Chapman, Jarrod, Pham, Jonathan, Shu, Shengqiang, Neupane, Rochak, Cipriano, Michael, Mancuso, Joel, Tu, Hank, Salamov, Asaf, Lindquist, Erika, Shapiro, Harris, Lucas, Susan, Grigoriev, Igor V., Cande, W. Z., Fulton, C., Rokhsar, D. S., Dawson, Scott C., Fritz-Laylin, Lillian K., Prochnik, Simon E., Ginger, Michael L., Dacks, Joel B., Carpenter, Meredith L., Field, Mark C., Kuo, Alan, Paredez, Alex, Chapman, Jarrod, Pham, Jonathan, Shu, Shengqiang, Neupane, Rochak, Cipriano, Michael, Mancuso, Joel, Tu, Hank, Salamov, Asaf, Lindquist, Erika, Shapiro, Harris, Lucas, Susan, Grigoriev, Igor V., Cande, W. Z., Fulton, C., Rokhsar, D. S., and Dawson, Scott C.

Abstract

Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.

Published
2010

11. The genome of Naegleria gruberi illuminates early eukaryotic versatility.

Author

Fritz-Laylin, Lillian K., Prochnik, Simon E., Ginger, Michael L., Dacks, Joel B., Carpenter, Meredith L., Field, Mark C., Kuo, Alan, Paredez, Alex, Chapman, Jarrod, Pham, Jonathan, Shu, Shengqiang, Neupane, Rochak, Cipriano, Michael, Mancuso, Joel, Tu, Hank, Salamov, Asaf, Lindquist, Erika, Shapiro, Harris, Lucas, Susan, Grigoriev, Igor V., Cande, W. Z., Fulton, C., Rokhsar, D. S., Dawson, Scott C., Fritz-Laylin, Lillian K., Prochnik, Simon E., Ginger, Michael L., Dacks, Joel B., Carpenter, Meredith L., Field, Mark C., Kuo, Alan, Paredez, Alex, Chapman, Jarrod, Pham, Jonathan, Shu, Shengqiang, Neupane, Rochak, Cipriano, Michael, Mancuso, Joel, Tu, Hank, Salamov, Asaf, Lindquist, Erika, Shapiro, Harris, Lucas, Susan, Grigoriev, Igor V., Cande, W. Z., Fulton, C., Rokhsar, D. S., and Dawson, Scott C.

Abstract

Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.

Published
2010

12. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, Grigoriev Iv, Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, and Grigoriev Iv

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008
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13. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, Grigoriev Iv, Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, and Grigoriev Iv

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008
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14. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., Taylor, A. R., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L. S., Rokhsar, D. S., Weissenbach, J., Armbrust, E. V., Green, B. R., Van de Peer, Y., Grigoriev, I. V., Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., Taylor, A. R., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L. S., Rokhsar, D. S., Weissenbach, J., Armbrust, E. V., Green, B. R., Van de Peer, Y., and Grigoriev, I. V.

Published
2008

15. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, Grigoriev Iv, Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, and Grigoriev Iv

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008
Full Text
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16. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., Taylor, A. R., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L. S., Rokhsar, D. S., Weissenbach, J., Armbrust, E. V., Green, B. R., Van de Peer, Y., Grigoriev, I. V., Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., Taylor, A. R., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L. S., Rokhsar, D. S., Weissenbach, J., Armbrust, E. V., Green, B. R., Van de Peer, Y., and Grigoriev, I. V.

Published
2008

17. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, Grigoriev Iv, Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, and Grigoriev Iv

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008
Full Text
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18. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).

Author

Tuskan, G A, Difazio, S, Jansson, Stefan, Bohlmann, J, Grigoriev, I, Hellsten, U, Putnam, N, Ralph, S, Rombauts, S, Salamov, A, Schein, J, Sterck, L, Aerts, A, Bhalerao, Rupali R, Bhalerao, Rishikesh P, Blaudez, D, Boerjan, W, Brun, A, Brunner, A, Busov, V, Campbell, M, Carlson, J, Chalot, M, Chapman, J, Chen, G-L, Cooper, D, Coutinho, P M, Couturier, J, Covert, S, Cronk, Q, Cunningham, R, Davis, J, Degroeve, S, Déjardin, A, Depamphilis, C, Detter, J, Dirks, B, Dubchak, I, Duplessis, S, Ehlting, J, Ellis, B, Gendler, K, Goodstein, D, Gribskov, M, Grimwood, J, Groover, A, Gunter, L, Hamberger, B, Heinze, B, Helariutta, Y, Henrissat, B, Holligan, D, Holt, R, Huang, W, Islam-Faridi, N, Jones, S, Jones-Rhoades, M, Jorgensen, R, Joshi, C, Kangasjärvi, J, Karlsson, Jan, Kelleher, C, Kirkpatrick, R, Kirst, M, Kohler, A, Kalluri, U, Larimer, F, Leebens-Mack, J, Leplé, J-C, Locascio, P, Lou, Y, Lucas, S, Martin, F, Montanini, B, Napoli, C, Nelson, D R, Nelson, C, Nieminen, K, Nilsson, Ove, Pereda, V, Peter, G, Philippe, R, Pilate, G, Poliakov, A, Razumovskaya, J, Richardson, P, Rinaldi, C, Ritland, K, Rouzé, P, Ryaboy, D, Schmutz, J, Schrader, J, Segerman, Bo, Shin, H, Siddiqui, A, Sterky, Fredrik, Terry, A, Tsai, C-J, Uberbacher, E, Unneberg, P, Vahala, J, Wall, K, Wessler, S, Yang, G, Yin, T, Douglas, C, Marra, M, Sandberg, Göran, Van de Peer, Y, Rokhsar, D, Tuskan, G A, Difazio, S, Jansson, Stefan, Bohlmann, J, Grigoriev, I, Hellsten, U, Putnam, N, Ralph, S, Rombauts, S, Salamov, A, Schein, J, Sterck, L, Aerts, A, Bhalerao, Rupali R, Bhalerao, Rishikesh P, Blaudez, D, Boerjan, W, Brun, A, Brunner, A, Busov, V, Campbell, M, Carlson, J, Chalot, M, Chapman, J, Chen, G-L, Cooper, D, Coutinho, P M, Couturier, J, Covert, S, Cronk, Q, Cunningham, R, Davis, J, Degroeve, S, Déjardin, A, Depamphilis, C, Detter, J, Dirks, B, Dubchak, I, Duplessis, S, Ehlting, J, Ellis, B, Gendler, K, Goodstein, D, Gribskov, M, Grimwood, J, Groover, A, Gunter, L, Hamberger, B, Heinze, B, Helariutta, Y, Henrissat, B, Holligan, D, Holt, R, Huang, W, Islam-Faridi, N, Jones, S, Jones-Rhoades, M, Jorgensen, R, Joshi, C, Kangasjärvi, J, Karlsson, Jan, Kelleher, C, Kirkpatrick, R, Kirst, M, Kohler, A, Kalluri, U, Larimer, F, Leebens-Mack, J, Leplé, J-C, Locascio, P, Lou, Y, Lucas, S, Martin, F, Montanini, B, Napoli, C, Nelson, D R, Nelson, C, Nieminen, K, Nilsson, Ove, Pereda, V, Peter, G, Philippe, R, Pilate, G, Poliakov, A, Razumovskaya, J, Richardson, P, Rinaldi, C, Ritland, K, Rouzé, P, Ryaboy, D, Schmutz, J, Schrader, J, Segerman, Bo, Shin, H, Siddiqui, A, Sterky, Fredrik, Terry, A, Tsai, C-J, Uberbacher, E, Unneberg, P, Vahala, J, Wall, K, Wessler, S, Yang, G, Yin, T, Douglas, C, Marra, M, Sandberg, Göran, Van de Peer, Y, and Rokhsar, D

Abstract

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Published
2006
Full Text
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19. Comparative genomics of the lactic acid bacteria

Author

Makarova, K., Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., Shakhova, V., Grigoriev, I., Lou, Y., Rokhsar, D., Lucas, S., Huang, K., Goodstein, D. M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J.-H., Diaz-Muniz, I., Dosti, B., V, Smeianov, Wechter, W., Barabote, R., Lorca, G., Altermann, E., Barrangou, R., Ganesan, B., Xie, Y., Rawsthorne, H., Tamir, D., Parker, C., Breidt, F., Broadbent, J., Hutkins, R., O'Sullivan, D., Steele, J., Unlu, G., Saier, M., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., Mills, D., Makarova, K., Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., Shakhova, V., Grigoriev, I., Lou, Y., Rokhsar, D., Lucas, S., Huang, K., Goodstein, D. M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J.-H., Diaz-Muniz, I., Dosti, B., V, Smeianov, Wechter, W., Barabote, R., Lorca, G., Altermann, E., Barrangou, R., Ganesan, B., Xie, Y., Rawsthorne, H., Tamir, D., Parker, C., Breidt, F., Broadbent, J., Hutkins, R., O'Sullivan, D., Steele, J., Unlu, G., Saier, M., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., and Mills, D.

Abstract

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.

Published
2006

20. Comparative genomics of the lactic acid bacteria

Author

Makarova, K., Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., Shakhova, V., Grigoriev, I., Lou, Y., Rokhsar, D., Lucas, S., Huang, K., Goodstein, D. M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J.-H., Diaz-Muniz, I., Dosti, B., V, Smeianov, Wechter, W., Barabote, R., Lorca, G., Altermann, E., Barrangou, R., Ganesan, B., Xie, Y., Rawsthorne, H., Tamir, D., Parker, C., Breidt, F., Broadbent, J., Hutkins, R., O'Sullivan, D., Steele, J., Unlu, G., Saier, M., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., Mills, D., Makarova, K., Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., Shakhova, V., Grigoriev, I., Lou, Y., Rokhsar, D., Lucas, S., Huang, K., Goodstein, D. M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J.-H., Diaz-Muniz, I., Dosti, B., V, Smeianov, Wechter, W., Barabote, R., Lorca, G., Altermann, E., Barrangou, R., Ganesan, B., Xie, Y., Rawsthorne, H., Tamir, D., Parker, C., Breidt, F., Broadbent, J., Hutkins, R., O'Sullivan, D., Steele, J., Unlu, G., Saier, M., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., and Mills, D.

Abstract

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.

Published
2006

21. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism

Author

Ambrust, E.V., Ambrust, E.V., Berges, J., Bowler, C., Green, B., Martinez, D., Putnam, N., Zhou, S., Allen, A., Apt, K., Bechner, M., Brzezinski, M., Chaal, B., Chiovitti, A., Davis, A., Goodstein, D., Hadi, M., Hellsten, U., Hildebrand, M., Jenkins, B., Jurka, J., Kapitonov, V., Kroger, N., Lau, W., Lane, T., Larimer, F., Lippmeier, J., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. Schnitzler, Palenik, B., Pazour, G., Richardson, P., Rynearson, T., Saito, M., Schwartz, D., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F., Rokhsar, D., Wilkerson, F.P., Rokhsar, D.S., Ambrust, E.V., Ambrust, E.V., Berges, J., Bowler, C., Green, B., Martinez, D., Putnam, N., Zhou, S., Allen, A., Apt, K., Bechner, M., Brzezinski, M., Chaal, B., Chiovitti, A., Davis, A., Goodstein, D., Hadi, M., Hellsten, U., Hildebrand, M., Jenkins, B., Jurka, J., Kapitonov, V., Kroger, N., Lau, W., Lane, T., Larimer, F., Lippmeier, J., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. Schnitzler, Palenik, B., Pazour, G., Richardson, P., Rynearson, T., Saito, M., Schwartz, D., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F., Rokhsar, D., Wilkerson, F.P., and Rokhsar, D.S.

Published
2004

22. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism

Author

Armbrust, E. V., Berges, J. A., Bowler, C., Green, B. R., Martinez, D., Putnam, N. H., Zhou, S., Allen, A. E., Apt, K. E., Bechner, M., Brzezinski, M. A., Chaal, B. K., Chiovitti, A., Davis, A. K., Demarest, M. S., Detter, J. C., Glavina, T., Goodstein, D., Hadi, M. Z., Hellsten, U., Hildebrand, M., Jenkins, B. D., Jurka, J., Kapitonov, V. V., Kroeger, N., Lau, W. W., Lane, T. W., Larimer, F. W., Lippmeier, J. C., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. S., Palenik, B., Pazour, G. J., Richardson, P. M., Rynearson, T. A., Saito, M. A., Schwartz, D. C., Thamatrakoln, K., Valentin, Klaus-Ulrich, Vardi, A., Wilkerson, F. P., Rokhsar, D. S., Armbrust, E. V., Berges, J. A., Bowler, C., Green, B. R., Martinez, D., Putnam, N. H., Zhou, S., Allen, A. E., Apt, K. E., Bechner, M., Brzezinski, M. A., Chaal, B. K., Chiovitti, A., Davis, A. K., Demarest, M. S., Detter, J. C., Glavina, T., Goodstein, D., Hadi, M. Z., Hellsten, U., Hildebrand, M., Jenkins, B. D., Jurka, J., Kapitonov, V. V., Kroeger, N., Lau, W. W., Lane, T. W., Larimer, F. W., Lippmeier, J. C., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. S., Palenik, B., Pazour, G. J., Richardson, P. M., Rynearson, T. A., Saito, M. A., Schwartz, D. C., Thamatrakoln, K., Valentin, Klaus-Ulrich, Vardi, A., Wilkerson, F. P., and Rokhsar, D. S.

Published
2004

23. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism

Author

Ambrust, E.V., Ambrust, E.V., Berges, J., Bowler, C., Green, B., Martinez, D., Putnam, N., Zhou, S., Allen, A., Apt, K., Bechner, M., Brzezinski, M., Chaal, B., Chiovitti, A., Davis, A., Goodstein, D., Hadi, M., Hellsten, U., Hildebrand, M., Jenkins, B., Jurka, J., Kapitonov, V., Kroger, N., Lau, W., Lane, T., Larimer, F., Lippmeier, J., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. Schnitzler, Palenik, B., Pazour, G., Richardson, P., Rynearson, T., Saito, M., Schwartz, D., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F., Rokhsar, D., Wilkerson, F.P., Rokhsar, D.S., Ambrust, E.V., Ambrust, E.V., Berges, J., Bowler, C., Green, B., Martinez, D., Putnam, N., Zhou, S., Allen, A., Apt, K., Bechner, M., Brzezinski, M., Chaal, B., Chiovitti, A., Davis, A., Goodstein, D., Hadi, M., Hellsten, U., Hildebrand, M., Jenkins, B., Jurka, J., Kapitonov, V., Kroger, N., Lau, W., Lane, T., Larimer, F., Lippmeier, J., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. Schnitzler, Palenik, B., Pazour, G., Richardson, P., Rynearson, T., Saito, M., Schwartz, D., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F., Rokhsar, D., Wilkerson, F.P., and Rokhsar, D.S.

Published
2004

24. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism

Author

Armbrust, E. V., Berges, J. A., Bowler, C., Green, B. R., Martinez, D., Putnam, N. H., Zhou, S., Allen, A. E., Apt, K. E., Bechner, M., Brzezinski, M. A., Chaal, B. K., Chiovitti, A., Davis, A. K., Demarest, M. S., Detter, J. C., Glavina, T., Goodstein, D., Hadi, M. Z., Hellsten, U., Hildebrand, M., Jenkins, B. D., Jurka, J., Kapitonov, V. V., Kroeger, N., Lau, W. W., Lane, T. W., Larimer, F. W., Lippmeier, J. C., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. S., Palenik, B., Pazour, G. J., Richardson, P. M., Rynearson, T. A., Saito, M. A., Schwartz, D. C., Thamatrakoln, K., Valentin, Klaus-Ulrich, Vardi, A., Wilkerson, F. P., Rokhsar, D. S., Armbrust, E. V., Berges, J. A., Bowler, C., Green, B. R., Martinez, D., Putnam, N. H., Zhou, S., Allen, A. E., Apt, K. E., Bechner, M., Brzezinski, M. A., Chaal, B. K., Chiovitti, A., Davis, A. K., Demarest, M. S., Detter, J. C., Glavina, T., Goodstein, D., Hadi, M. Z., Hellsten, U., Hildebrand, M., Jenkins, B. D., Jurka, J., Kapitonov, V. V., Kroeger, N., Lau, W. W., Lane, T. W., Larimer, F. W., Lippmeier, J. C., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. S., Palenik, B., Pazour, G. J., Richardson, P. M., Rynearson, T. A., Saito, M. A., Schwartz, D. C., Thamatrakoln, K., Valentin, Klaus-Ulrich, Vardi, A., Wilkerson, F. P., and Rokhsar, D. S.

Published
2004

25. The genomic landscape of molecular responses to natural drought stress in Panicum hallii

Author

Lovell J., Jenkins J., Lowry D., Mamidi S., Sreedasyam A., Weng X., Barry K., Bonnette J., Campitelli B., Daum C., Gordon S., Gould B., Khasanova A., Lipzen A., MacQueen A., Palacio-Mejía J., Plott C., Shakirov E., Shu S., Yoshinaga Y., Zane M., Kudrna D., Talag J., Rokhsar D., Grimwood J., Schmutz J., Juenger T., Lovell J., Jenkins J., Lowry D., Mamidi S., Sreedasyam A., Weng X., Barry K., Bonnette J., Campitelli B., Daum C., Gordon S., Gould B., Khasanova A., Lipzen A., MacQueen A., Palacio-Mejía J., Plott C., Shakirov E., Shu S., Yoshinaga Y., Zane M., Kudrna D., Talag J., Rokhsar D., Grimwood J., Schmutz J., and Juenger T.

Abstract

© 2018, The Author(s). Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.

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