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1. Changes in soil organic carbon and nitrogen capacities of Salix cheilophila Schneid along a revegetation chronosequence in semi-arid degraded sandy land of the Gonghe Basin, Tibet Plateau

Author

Y. Yu and Z. Q. Jia

Subjects
Geology, QE1-996.5, Stratigraphy, QE640-699
Abstract

The Gonghe Basin is a sandified and desertified region of China, but the distribution of soil organic carbon (SOC) and total nitrogen (TN) along the cultivation chronosequence across this ecologically fragile region is not well understood. This study was carried out to understand the effects of restoration with Salix cheilophila for different periods of time (6, 11, 16, 21 years) to test whether it enhanced C and N storage. Soil samples, in four replications from seven depth increments (0–10, 10–20, 20–30, 30–50, 50–100, 100–150 and 150–200 cm), were collected in each stand. Soil bulk density, SOC, TN, aboveground biomass and root biomass were measured. Results indicated that changes occurred in both the upper and deeper soil layers with an increase in revegetation time. The 0–200 cm soil showed that the 6-year stand gained 3.89 Mg C ha−1 and 1.00 Mg N ha−1, which accounted for 40.82% of the original SOC and 11.06% of the TN of the 0-year stand. The 11-year stand gained 7.82 Mg C ha−1 and 1.98 Mg N ha−1 in the 0–200 cm soil layers, accounting for 58.06% of the SOC and 19.80% of the TN of the 0-year stand. The 16-year stand gained 11.32 Mg C ha−1 and 3.30 Mg N ha−1 in the 0–200 cm soil layers, accounting for 66.71% of the SOC and 21.98% of the TN of the 0-year stand. The 21-year stand gained 13.05 Mg C ha−1 and 5.45 Mg N ha−1 from the same soil depth, accounting for 69.79% of the SOC and 40.47% of the TN compared with the 0-year stand. The extent of these changes depended on soil depth and plantation age. The results demonstrated that, as stand age increased, the storage of SOC and TN increased. These results further indicated that restoration with S. cheilophila has positive impacts on the Gonghe Basin and has increased the capacity of SOC sequestration and N storage. The shrub's role as carbon sink is compatible with system management and persistence. The findings are significant for assessing C and N sequestration accurately in semi-arid degraded high, cold sandy regions in the future.

Published
2014
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2. First Wide Field-of-view X-Ray Observations by a Lobster-eye Focusing Telescope in Orbit

Author

C. Zhang, Z. X. Ling, X. J. Sun, S. L. Sun, Y. Liu, Z. D. Li, Y. L. Xue, Y. F. Chen, Y. F. Dai, Z. Q. Jia, H. Y. Liu, X. F. Zhang, Y. H. Zhang, S. N. Zhang, F. S. Chen, Z. W. Cheng, W. Fu, Y. X. Han, H. Li, J. F. Li, Y. Li, P. R. Liu, X. H. Ma, Y. J. Tang, C. B. Wang, R. J. Xie, A. L. Yan, Q. Zhang, B. W. Jiang, G. Jin, L. H. Li, X. B. Qiu, D. T. Su, J. N. Sun, Z. Xu, S. K. Zhang, Z. Zhang, N. Zhang, X. Z. Bi, Z. M. Cai, J. W. He, H. Q. Liu, X. C. Zhu, H. Q. Cheng, C. Z. Cui, D. W. Fan, H. B. Hu, M. H. Huang, C. C. Jin, D. Y. Li, H. W. Pan, W. X. Wang, Y. F. Xu, X. Yang, B. Zhang, M. Zhang, W. D. Zhang, D. H. Zhao, M. Bai, Z. Ji, Y. R. Liu, F. L. Ma, J. Su, J. Z. Tong, Y. S. Wang, Z. J. Zhao, C. Feldman, P. O’Brien, J. P. Osborne, R. Willingale, V. Burwitz, G. Hartner, A. Langmeier, T. Müller, S. Rukdee, T. Schmidt, E. Kuulkers, and W. Yuan

Subjects
High Energy Astrophysical Phenomena (astro-ph.HE), Space and Planetary Science, FOS: Physical sciences, Astronomy and Astrophysics, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics, Instrumentation and Methods for Astrophysics (astro-ph.IM)
Abstract

As a novel X-ray focusing technology, lobster eye micro-pore optics (MPO) feature both a wide observing field of view and true imaging capability, promising sky monitoring with significantly improved sensitivity and spatial resolution in soft X-rays. Since first proposed by Angel (1979), the optics have been extensively studied, developed and trialed over the past decades. In this Letter, we report on the first-light results from a flight experiment of the Lobster Eye Imager for Astronomy ($LEIA$), a pathfinder of the wide-field X-ray telescope of the Einstein Probe mission. The piggyback imager, launched in July 2022, has a mostly un-vignetted field of view of $18.6^\circ \times 18.6^\circ $. Its spatial resolution is in the range of 4$-$7 arcmin in FWHM and the focal spot effective area is 2$-$3 cm$^2$, both showing only mild fluctuations across the field of view. We present images of the Galactic center region, Sco X-1 and the diffuse Cygnus Loop nebular taken in snapshot observations over 0.5$-$4 keV. These are truly wide-field X-ray images of celestial bodies observed, for the first time, by a focusing imaging telescope. Initial analyses of the in-flight data show excellent agreement between the observed images and the on-ground calibration and simulations. The instrument and its characterization are briefly described, as well as the flight experiment. The results provide a solid basis for the development of the present and proposed wide-field X-ray missions using lobster eye MPO., Comment: 11 pages, 4 figures. Accepted for publication in Astrophysical Journal Letter

Published
2022

3. Changes in soil organic carbon and nitrogen capacities of Salix cheilophila Schneid along a revegetation chronosequence in semi-arid degraded sandy land of the Gonghe Basin, Tibet Plateau

Author

Z. Q. Jia and Yang Yu

Subjects
Biomass (ecology), Soil test, Stratigraphy, Chronosequence, lcsh:QE1-996.5, Paleontology, Soil Science, Carbon sink, Geology, Soil science, Soil carbon, Bulk density, lcsh:Geology, Geophysics, Agronomy, lcsh:Stratigraphy, Geochemistry and Petrology, Soil horizon, Environmental science, Revegetation, Earth-Surface Processes, lcsh:QE640-699
Abstract

The Gonghe Basin is a sandified and desertified region of China, but the distribution of soil organic carbon (SOC) and total nitrogen (TN) along the cultivation chronosequence across this ecologically fragile region is not well understood. This study was carried out to understand the effects of restoration with Salix cheilophila for different periods of time (6, 11, 16, 21 years) to test whether it enhanced C and N storage. Soil samples, in four replications from seven depth increments (0–10, 10–20, 20–30, 30–50, 50–100, 100–150 and 150–200 cm), were collected in each stand. Soil bulk density, SOC, TN, aboveground biomass and root biomass were measured. Results indicated that changes occurred in both the upper and deeper soil layers with an increase in revegetation time. The 0–200 cm soil showed that the 6-year stand gained 3.89 Mg C ha−1 and 1.00 Mg N ha−1, which accounted for 40.82% of the original SOC and 11.06% of the TN of the 0-year stand. The 11-year stand gained 7.82 Mg C ha−1 and 1.98 Mg N ha−1 in the 0–200 cm soil layers, accounting for 58.06% of the SOC and 19.80% of the TN of the 0-year stand. The 16-year stand gained 11.32 Mg C ha−1 and 3.30 Mg N ha−1 in the 0–200 cm soil layers, accounting for 66.71% of the SOC and 21.98% of the TN of the 0-year stand. The 21-year stand gained 13.05 Mg C ha−1 and 5.45 Mg N ha−1 from the same soil depth, accounting for 69.79% of the SOC and 40.47% of the TN compared with the 0-year stand. The extent of these changes depended on soil depth and plantation age. The results demonstrated that, as stand age increased, the storage of SOC and TN increased. These results further indicated that restoration with S. cheilophila has positive impacts on the Gonghe Basin and has increased the capacity of SOC sequestration and N storage. The shrub's role as carbon sink is compatible with system management and persistence. The findings are significant for assessing C and N sequestration accurately in semi-arid degraded high, cold sandy regions in the future.

Published
2014

4. Application of the hybrid laser ultrasonic method in rail inspection

Author

J H Sun, Z Q Jia, R Guo, J F Song, S Liu, J Ma, and Y Zhao

Subjects
Materials science, Mechanics of Materials, law, Mechanical Engineering, Acoustics, Rail inspection, Materials Chemistry, Metals and Alloys, Ultrasonic sensor, Composite material, Laser, law.invention
Published
2014

5. Natural history of fetal rat cardiomyocytes transplanted into adult rat myocardial scar tissue

Author

R K, Li, D A, Mickle, R D, Weisel, M K, Mohabeer, J, Zhang, V, Rao, G, Li, F, Merante, and Z Q, Jia

Subjects
Rats, Sprague-Dawley, Cicatrix, Fetal Heart, Cell Transplantation, Fetal Tissue Transplantation, Pregnancy, Animals, Female, Rats
Abstract

Fetal rat cardiomyocytes transplanted into left ventricular scar tissue of the adult rat heart limit scar expansion and improve heart function. This study determined morphologic changes of transplanted fetal rat cardiomyocytes in myocardial scar tissue.The left ventricles of 500-g Sprague-Dawley rats were cryodamaged. At 4 weeks after myocardial injury, a transmural scar (54+/-11 mm2) (mean+/-1 SDak) formed at the apex (n=6). Cardiomyocytes freshly isolated from 18-day-gestation Sprague-Dawley rat hearts were transfected with plasmid containing the beta-galactosidase and then injected into the 4-week-old scar tissue. Cell culture medium was injected into the scar tissue of control animals. At 4 weeks posttransplantation, the cardiomyocytes had formed cardiac tissue (20.7+/-6.9 mm2, n=14), which stained positively for beta-galactosidase activity in the scar (90.4+/-25 mm2, n=14). The transplanted cardiomyocytes formed sarcomeres and were linked by junctions composed of desmosomes and fascia adherens. Lymphocyte infiltration occurred despite use of cyclosporin A. No myocardial tissue was found in the scar tissue of the control animals (n=14). More arterioles and venules were found (P.01) in the cardiomyocyte grafts (1.2+/-0.6 vessel/0.8 mm2; n=14) than in the control scar tissue (0.1+/-0.1 vessels/0.8 mm2; n=14). At 20 weeks post-transplantation, the transplant tissue size (6+/-6 mm2; n=7) was smaller (P=.007) than 4-week old transplant, and the scar (162+/-46 mm2; n=7) was larger (P=.005) than 4-week-old scar. Lymphocyte infiltration was still present among the remaining transplanted cells.This study demonstrated that cardiac tissue formed by transplanted fetal cardiomyocytes in the myocardial scar tissue decreased in size with time probably secondary to rejection.

Published
1997

6. Transplanted cardiomyocytes survive in scar tissue and improve heart function

Author

G. Li, R-K Li, Molly K. Mohabeer, Richard D. Weisel, Donald A.G. Mickle, Z-Q Jia, Vivek Rao, and Frank Merante

Subjects
Transplantation, Pathology, medicine.medical_specialty, business.industry, Cell Transplantation, Heart Ventricles, Myocardium, Scar tissue, Graft Survival, Heart, Myocardial Contraction, Rats, Cicatrix, Text mining, Heart Injuries, Fetal Tissue Transplantation, medicine, Animals, Surgery, business, Function (biology)
Published
1997

7. The effects of artery occlusion on temperature homogeneity during hyperthermia in rabbit kidneys in vivo

Author

John W. Hunt, Z. Q. Jia, A.E. Worthington, and Richard P. Hill

Subjects
Hyperthermia, Cancer Research, Pathology, medicine.medical_specialty, Time Factors, Physiology, Ischemia, Kidney, Vascular occlusion, Renal Circulation, Renal Artery, Physiology (medical), medicine.artery, Occlusion, Medicine, Animals, Artery occlusion, Aorta, Abdominal, Renal artery, Ligation, business.industry, Histocytochemistry, Temperature, Hyperthermia, Induced, medicine.disease, Arterial occlusion, medicine.anatomical_structure, Female, Rabbits, medicine.symptom, business, Nuclear medicine
Abstract

To investigate the role of arterial occlusion on temperature homogeneity during hyperthermia for deep seated tissue, a renal hyperthermia animal model has been established using New Zealand white rabbits. The effects of ultrasound-induced renal hyperthermia, with or without continuous and intermittent renal artery occlusion, were compared and analysed. Both continuous and intermittent occlusion showed certain protection of surrounding tissue and demonstrated improved temperature homogeneity and heating efficiency. The benefits of continuous vs. intermittent occlusion are compared and discussed as well.

Published
1997

10. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Changbao, Shuang, Yang, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Wencai, Sanwen, Yongchen, Zhang, Zhonghua, Jianchang, Guo, Yanmei, Xiaoxuan, Ying, Chuanyou, Zhukuan, Zuo, Jianru, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Bao, Hongshuang, Zhenjun, Fuyou, Chen, Bingtang, Han, Bin, Feng, Fan, Danlin, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, McCombie, W. Richard, Lippman, Zachary B., Chia, Jer-Ming, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigo, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Junhong, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, Dixit, Rekha, Singh, Manju, Archana, Pal, Jitendra Kumar, Pandit, Awadhesh, Pradeep Kumar, Mahato, Ajay Kumar, Dogra, Vivek, Gaikwad, Kishor, Sharma, Tilak Raj, Mohapatra, Trilochan, Nagendra Kumar, Causse, Mathilde, Rothan, Christophe, Schiex, Noirot, Celine, Bellec, Arnaud, Klopp, Delalande, Corinne, Berges, Helene, Mariette, Jerome, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latche, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Osorio, Fernandez del Carmen, Asuncion, Monforte, Antonio, Granell, Fernandez-Munoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Keygene N. V. Marco G. M., Feron, Richard M. C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Sangmi, Koo, Dal-Hoe, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Joecker, Anika, Warfsmann, Jens, Goebel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Eliog. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Byung Dong, Park, Minkyu, Seungill, Yeom, Seon-In, Yong-Hwan, Yang-Do, Guangcun, Jianwei, Yongsheng, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuniga, Sheila, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Goicoechea, Jose Luis, Yeisoo, Kudrna, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Gurazada, Aishwarya Bala, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Arun K., Khurana, Paramjit, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Barbazuk, W. Brad, Jingping, Hui, Tae-Ho, Yupeng, Dong, Paterson, Andrew H., Xiyin, Tang, Haibao, Barone, Amalia, Chiusano, Maria Luisa, Ercolano, Maria Raffaella, D'Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Chunmei, Shi, Ruihua, Douglas, Xing, Yanbo, Keqin, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, D'Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Lankhorst, Rene M. Klein, Beasley, Helen, McLaren, Karen, Nicholson, Riddle, Claire, Gianese, Giulio, Tomato Genome Consortium, S., Sato, S., Tabata, H., Hirakawa, E., Asamizu, K., Shirasawa, S., Isobe, T., Kaneko, Y., Nakamura, D., Shibata, K., Aoki, M., Egholm, J., Knight, R., Bogden, C. B., Li, Y., Shuang, X., Xu, S. K., Pan, S. F., Cheng, X., Liu, Y. Y., Ren, J., Wang, A., Albiero, F. D., Pero, S., Todesco, J. V., Eck, R. M., Buel, A., Bombarely, J. R., Gosselin, M. Y., Huang, J. A., Leto, N., Menda, S., Strickler, L. Y., Mao, S., Gao, I. Y., Tecle, T., York, Y., Zheng, J. T., Vrebalov, J., Lee, S. L., Zhong, L. A., Mueller, W. J., Stiekema, P., Ribeca, T., Alioto, W. C., Yang, S. W., Huang, Y. C., Du, Z. H., Zhang, J. C., Gao, Y. M., Guo, X. X., Wang, Y., Li, J., He, C. Y., Li, Z. K., Cheng, J. R., Zuo, J. F., Ren, J. H., Zhao, L. H., Yan, H. L., Jiang, B., Wang, H. S., Li, Z. J., Li, F. Y., Fu, B. T., Chen, B., Han, Q., Feng, D. L., Fan, Y., Wang, H. Q., Ling, Y. B., A., D., Ware, W. R., Mccombie, Z. B., Lippman, J. M., Chia, K., Jiang, S., Pasternak, L., Gelley, M., Kramer, L. K., Anderson, S. B., Chang, S. M., Royer, L. A., Shearer, S. M., Stack, J. K., C., Y. M., Xu, N., Eannetta, A. J., Mata, R., Mcquinn, S. D., Tanksley, F., Camara, R., Guigo, S., Rombaut, J., Fawcett, Y. V., De, D., Zamir, C. B., Liang, M., Spannagl, H., Gundlach, R., Bruggmann, K., Mayer, Z. Q., Jia, J. H., Zhang, Z. B., A., G. J., Bishop, S., Butcher, R., Lopez Cobollo, D., Buchan, I., Filippi, J., Abbott, R., Dixit, M., Singh, A., Singh, J. K., Pal, A., Pandit, P. K., Singh, A. K., Mahato, V., Dogra, K., Gaikwad, T. R., Sharma, T., Mohapatra, N. K., Singh, M., Causse, C., Rothan, T., Schiex, C., Noirot, A., Bellec, C., Klopp, C., Delalande, H., Berge, J., Mariette, P., Frasse, S., Vautrin, M., Zouine, A., Latche, C., Rousseau, F., Regad, J. C., Pech, M., Philippot, M., Bouzayen, P., Pericard, S., Osorio, A. F., Del, A., Monforte, A., Granell, R., Fernandez Munoz, M., Conte, G., Lichtenstein, F., Carrari, G. D., Belli, F., Fuligni, C., Peano, S., Grandillo, P., Termolino, M., Pietrella, E., Fantini, G., Falcone, A., Fiore, G., Giuliano, L., Lopez, P., Facella, G., Perrotta, L., Daddiego, G., Bryan, M., Orozco, X., Pastor, D., Torrent, K. N. V., R. M. C., J. v., Oeveren, P. d., Heer, L., Daponte, S., Jacobs Oomen, M., Cariaso, M., Prin, M. J., T., A., Janssen, M. J., J., S. H., Jo, J., Kim, S. Y., Kwon, S., Kim, D. H., Koo, S., Lee, C. G., Hur, C., Clouser, A., Rico, A., Hallab, C., Gebhardt, K., Klee, A., Jocker, J., Warfsmann, U., Gobel, S., Kawamura, K., Yano, J. D., Sherman, H., Fukuoka, S., Negoro, S., Bhutty, P., Chowdhury, D., Chattopadhyay, E., Datema, S., Smit, E. W., M., J. v., De, J. C., Van, S. A., Peter, M. J., Van, M. H. C., P. J. W., T., Hesselink, R. C., H., G. Y., Jiang, M., Droege, D., Choi, B. C., Kang, B. D., Kim, M., Park, S. I., Yeom, Y. H., Lee, Y. D., Choi, G. C., Li, J. W., Gao, Y. S., Liu, S. X., Huang, V., Fernandez Pedrosa, C., Collado, S., Zuniga, G. P., Wang, R., Cade, R. A., Dietrich, J., Roger, S., Knapp, Z. J., Fei, R. A., White, T. W., Thannhauser, J. J., Giovannoni, M. A., Botella, L., Gilbert, R., Gonzalez, J. L., Goicoechea, Y., Yu, D., Kudrna, K., Collura, M., Wissotski, R., Wing, H., Schoof, B. C., Meyer, A. B., Gurazada, P. J., Green, S., Mathur, S., Vya, A. U., Solanke, R., Kumar, V., Gupta, A. K., Sharma, P., Khurana, J. P., Khurana, A. K., Tyagi, T., Dalmay, I., Mohorianu, B., Walt, S., Chamala, W. B., Barbazuk, J. P., Li, H., Guo, T. H., Lee, Y. P., Wang, D., Zhang, A. H., Paterson, X. Y., Wang, H. B., Tang, Barone, Amalia, Chiusano, MARIA LUISA, Ercolano, MARIA RAFFAELLA, D'Agostino, Nunzio, M. D., Filippo, A., Traini, W., Sanseverino, Frusciante, Luigi, G. B., Seymour, M., Elharam, Y., Fu, A., Hua, S., Kenton, J., Lewi, S. P., Lin, F., Najar, H. S., Lai, B. F., Qin, C. M., Qu, R. H., Shi, D., White, J., White, Y. B., Xing, K. Q., Yang, J., Yi, Z. Y., Yao, L. P., Zhou, B. A., Roe, A., Vezzi, M., D'Angelo, R., Zimbello, R., Schiavon, E., Caniato, C., Rigobello, D., Campagna, N., Vitulo, G., Valle, D. R., Nelson, E. D., Paoli, D., Szinay, H. H., De, Y. L., Bai, R. G. F., R. M. K., H., Beasley, K., Mclaren, C., Nicholson, C., Riddle, G., Gianese, Kazusa DNA Research Institute (KDRI), 454 Life Sciences, Amplicon Express Inc., Beijing Academy of Agriculture and Forestry Sciences, Chinese Academy of Sciences (CAS), Beijing Genomics Institute [Shenzhen] (BGI), BMR Genomics S.R.L., Partenaires INRAE, Boyce Thompson Inst Plant Res, Cornell University [New York], Centre for Biosystems Genomics, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain, China Agricultural University (CAU), Chinese Academy of Agricultural Sciences (CAAS), Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn, Chinese Academy of Sciences [Beijing] (CAS), Cold Spring Harbor, Cold Spring Harbor Laboratory, Colorado State University [Fort Collins] (CSU), National Taiwan University, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Unité de Biométrie et Intelligence Artificielle (UBIA), Centre National de Ressources Génomiques Végétales (CNRGV), This work was supported by: Argentina: INTA and CONICET. Belgium: Flemish Institute for Biotechnology and Ghent University. China: The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Ministry of Science and Technology (2006AA10A116, 2004CB720405, 2006CB101907, 2007DFB30080) Ministry of Agriculture (‘948’ Program: 2007-Z5), National Natural Science Foundation (36171319), Postdoctoral Science Foundation (20070420446). European Union: FP6 Integrated Project EU-SOL PL 016214. France: Institute National de la Recherche Agronomique and Agence Nationale de la Recherche. Germany: the Max Planck Society. India: Department of Biotechnology, Government of India, Indian Council of Agricultural Research. Italy: Ministry of Research (FIRB-SOL, FIRB-Parallelomics, ItaLyco and GenoPOM projects), Ministry of Agriculture (Agronanotech and Biomassval projects), FILAS foundation, ENEA, CNR-ENEA project L. 191/2009. Japan: Kazusa DNA Research Institute Foundation and National Institute of Vegetable and Tea Science. Korea: KRIBB Basic Research Fund and Crop Functional Genomics Research Center (CFGC), MEST. Netherlands: Centre for BioSystems Genomics, Netherlands Organization for Scientific Research. Spain: Fundación Genoma España, Cajamar, FEPEX, Fundación Séneca, ICIA, IFAPA, Fundación Manrique de Lara, Instituto Nacional de Bioinformatica. UK: BBSRC grant BB/C509731/1, DEFRA, SEERAD. USA: NSF (DBI-0116076, DBI-0421634, DBI-0606595, IOS-0923312, DBI-0820612, DBI-0605659, DEB-0316614, DBI 0849896 and MCB 1021718), USDA (2007-02773 and 2007-35300-19739), USDA-ARS. We acknowledge the Potato Genome Sequencing Consortium for sharing data before publication, potato RNA-Seq data was provided by C. R. Buell from the NSF-funded Potato Genome Sequence and Annotation project, tomato RNA-Seq data by the USDA-funded SolCAP project, N. Sinha and J. Maloof, the Amplicon Express team for BAC pooling services, construction of the Whole Genome Profiling (WGP) physical map was supported by EnzaZaden, RijkZwaan, Vilmorin & Cie, and Takii & Co. Keygene N.V. owns patents and patent applications covering its AFLP and Whole Genome Profiling technologies, AFLP and Keygene are registered trademarks of Keygene N.V. The following individuals are also acknowledged for their contribution to the work described: J. Park, B. Wang, C. Niu, D. Liu, F. Cojutti, S. Pescarolo, A. Zambon, G. Xiao, J. Chen, J. Shi, L. Zhang, L. Zeng, M. Caccamo, D. Bolser, D. Martin, M. Gonzalez, P. A. Bedinger, P. A. Covey, P. Pachori, R. R. Pousada, S. Hakim, S. Sims, V. Cahais, W. Long, X. Zhou, Y. Lu, W. Haso, C. Lai, S. Lepp, C. Peluso, H. Teramu, H. De Jong, R. Lizarralde, E. R. May and Z. Li. M. Zabeau is thanked for his support and encouragement and S. van den Brink for her secretarial support., Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Université de Bordeaux 1 (FRANCE), Université de Bordeaux 2 - Victor Segalen (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), and Universitat de Barcelona

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Laboratory of Virology, tomato, 01 natural sciences, Genome, Laboratorium voor Plantenveredeling, Arabidopsis, Genetic Variation, Genome, Plant, Genomics, Lycopersicon esculentum, Molecular Sequence Data, Phylogeny, RNA, Plant, Sequence Analysis, DNA, Solanum tuberosum, Soybeans, Synteny, Evolution, Molecular, Solanum lycopersicum, Génétique des plantes, Tomàquets, Wild tomato, Genome Sequencing, Lycopersicon-esculentum, gene, diversification : arabidopsis, patterns, ortholog, history, sorghum, potato, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Solanum chilense, biology, EPS-4, BioSolar Cells, food and beverages, Solanum pimpinellifolium, BIOS Applied Metabolic Systems, Neofunctionalization, Laboratory of Genetics, Sequence Analysis, diversification, Génomique, Transcriptomique et Protéomique, Evolution, Bioinformatics, Laboratorium voor Erfelijkheidsleer, Article, Genètica molecular, Laboratorium voor Virologie, 03 medical and health sciences, BIOS Applied Bioinformatics, Tomatoes, Botany, Bioinformatica, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genomes, Laboratorium voor Nematologie, lycopersicon-esculentum, 030304 developmental biology, fungi, Molecular, Plant, DNA, Genètica evolutiva, 15. Life on land, biology.organism_classification, Tomato genome, Plant Breeding, arabidopsis, Genòmica, RNA, Solanum, Laboratory of Nematology, Plant sciences, 010606 plant biology & botany
Abstract

[EN] Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness., This work was supported by: Argentina: INTA and CONICET. Belgium: Flemish Institute for Biotechnology and Ghent University. China: The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences; Ministry of Science and Technology (2006AA10A116, 2004CB720405, 2006CB101907, 2007DFB30080) Ministry of Agriculture ('948' Program: 2007-Z5); National Natural Science Foundation (36171319); Postdoctoral Science Foundation (20070420446). European Union: FP6 Integrated Project EU-SOL PL 016214. France: Institute National de la Recherche Agronomique and Agence Nationale de la Recherche. Germany: the Max Planck Society. India: Department of Biotechnology, Government of India; Indian Council of Agricultural Research. Italy: Ministry of Research (FIRB-SOL, FIRB-Parallelomics, ItaLyco and GenoPOM projects); Ministry of Agriculture (Agronanotech and Biomassval projects); FILAS foundation; ENEA; CNR-ENEA project L. 191/2009. Japan: Kazusa DNA Research Institute Foundation and National Institute of Vegetable and Tea Science. Korea: KRIBB Basic Research Fund and Crop Functional Genomics Research Center (CFGC), MEST. Netherlands: Centre for BioSystemsGenomics, Netherlands Organization for Scientific Research. Spain: Fundacion Genoma Espana; Cajamar; FEPEX; Fundacion Seneca; ICIA; IFAPA; Fundacion Manrique de Lara; Instituto Nacional de Bioinformatica. UK: BBSRC grant BB/C509731/1; DEFRA; SEERAD. USA: NSF (DBI-0116076; DBI-0421634; DBI-0606595; IOS-0923312; DBI-0820612; DBI-0605659; DEB-0316614; DBI 0849896 and MCB 1021718); USDA (2007-02773 and 2007-35300-19739); USDA-ARS. We acknowledge the Potato Genome Sequencing Consortium for sharing data before publication; potato RNA-Seq data was provided by C. R. Buell from the NSF-funded Potato Genome Sequence and Annotation project; tomato RNA-Seq data by the USDA-funded SolCAP project, N. Sinha and J. Maloof; the Amplicon Express team for BAC pooling services; construction of the Whole Genome Profiling (WGP) physical map was supported by EnzaZaden, RijkZwaan, Vilmorin&Cie, and Takii & Co. Keygene N. V. owns patents and patent applications covering its AFLP and Whole Genome Profiling technologies; AFLP and Keygene are registered trademarks of Keygene N. V.

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