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Plant genomics

Section edited by David Lightfoot and Keiichi Mochida

This section covers all aspects of the genome structure and function of plants, including crop species.

Page 1 of 32

  2. Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, t...

    Authors: Wen-Kai Hui, Fei-Yan Zhao, Jing-Yan Wang, Xiao-Yang Chen, Jue-Wei Li, Yu Zhong, Hong-Yun Li, Jun-Xing Zheng, Liang-Zhen Zhang, Qing-Min Que, Ai-Min Wu and Wei Gong

    Citation: BMC Genomics 2020 21:81

    Content type: Research article

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  3. Paspalum notatum exhibits both sexual and apomictic cytotypes and, thus, is considered a good model for studies of apomixis because it facilitates comparative approaches. In this work, transcriptome sequencing wa...

    Authors: Fernanda A. de Oliveira, Bianca B. Z. Vigna, Carla C. da Silva, Alessandra P. Fávero, Frederico P. de Matta, Ana L. S. Azevedo and Anete P. de Souza

    Citation: BMC Genomics 2020 21:78

    Content type: Research article

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  4. Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. ...

    Authors: Yating Zhang, Dong An, Changsheng Li, Zhixuan Zhao and Wenqin Wang

    Citation: BMC Genomics 2020 21:76

    Content type: Research article

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  5. Calcium-dependent protein kinase (CPK) is one of the main Ca2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of th...

    Authors: Man Zhang, Yanhui Liu, Qing He, Mengnan Chai, Youmei Huang, Fangqian Chen, Xiaomei Wang, Yeqiang Liu, Hanyang Cai and Yuan Qin

    Citation: BMC Genomics 2020 21:72

    Content type: Research article

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  6. Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification...

    Authors: Lanjie Zhao, Youjun Lü, Wei Chen, Jinbo Yao, Yan Li, Qiulin Li, Jingwen Pan, Shengtao Fang, Jie Sun and Yongshan Zhang

    Citation: BMC Genomics 2020 21:69

    Content type: Research article

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  7. Alternative splicing (AS) may generate multiple mRNA splicing isoforms from a single mRNA precursor using different splicing sites, leading to enhanced diversity of transcripts and proteins. AS has been implic...

    Authors: Yeyun Li, Xiaozeng Mi, Shiqi Zhao, Junyan Zhu, Rui Guo, Xiaobo Xia, Lu Liu, Shengrui Liu and Chaoling Wei

    Citation: BMC Genomics 2020 21:65

    Content type: Research article

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  8. The APETALA2/ethylene responsive factor (AP2/ERF) superfamily members are transcription factors that regulate diverse developmental processes and stress responses in plants. They have been identified in many p...

    Authors: Shuting Zhang, Chen Zhu, Yumeng Lyu, Yan Chen, Zihao Zhang, Zhongxiong Lai and Yuling Lin

    Citation: BMC Genomics 2020 21:62

    Content type: Research article

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  9. Structural variations (SVs) have been reported to play an important role in genetic diversity and trait regulation. Many computer algorithms detecting SVs have recently been developed, but the use of multiple ...

    Authors: Yueyuan Liu, Mingyue Zhang, Jieying Sun, Wenjing Chang, Manyi Sun, Shaoling Zhang and Jun Wu

    Citation: BMC Genomics 2020 21:61

    Content type: Research article

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  10. Ca2+ played as a ubiquitous secondary messenger involved in plant growth, development, and responses to various environmental stimuli. Calcium-dependent protein kinases (CDPK) were important Ca2+ sensors, which c...

    Authors: Feng Wen, Feng Ye, Zhulong Xiao, Liang Liao, Tongjian Li, Mingliang Jia, Xinsheng Liu and Xiaozhu Wu

    Citation: BMC Genomics 2020 21:53

    Content type: Research article

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  11. Pennisetum giganteum, an abundant, fast-growing perennial C4 grass that belongs to the genus Pennisetum, family Poaceae, has been developed as a source of biomass for mushroom cultivation and production, as a sou...

    Authors: Qingyuan Li, Conglin Xiang, Lin Xu, Jinghua Cui, Shao Fu, Baolin Chen, Shoukun Yang, Pan Wang, Yanfeng Xie, Ming Wei and Zhanchang Wang

    Citation: BMC Genomics 2020 21:52

    Content type: Research article

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  12. Clinopodium gracile (Benth.) Matsum (C. gracile) is an annual herb with pharmacological properties effective in the treatment of various diseases, including hepatic carcinoma. Triterpenoid saponins are crucial bi...

    Authors: Chunmiao Shan, Chenkai Wang, Shengxiang Zhang, Yuanyuan Shi, Kelong Ma, Qingshan Yang and Jiawen Wu

    Citation: BMC Genomics 2020 21:49

    Content type: Research article

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  13. Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they e...

    Authors: Antonios Kioukis, Vassiliki A. Michalopoulou, Laura Briers, Stergios Pirintsos, David J. Studholme, Pavlos Pavlidis and Panagiotis F. Sarris

    Citation: BMC Genomics 2020 21:48

    Content type: Research article

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  14. Genomic prediction (GP) is used in animal and plant breeding to help identify the best genotypes for selection. One of the most important measures of the effectiveness and reliability of GP in plant breeding i...

    Authors: Vanda Milheiro Lourenço, Joseph Ochieng Ogutu and Hans-Peter Piepho

    Citation: BMC Genomics 2020 21:43

    Content type: Methodology Article

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  16. Light is the main source of energy and, as such, is one of the most important environmental factors for plant growth, morphogenesis, and other physiological responses. MicroRNAs (miRNAs) are endogenous non-cod...

    Authors: Fei Dong, Chuanzeng Wang, Yuhui Dong, Shuqin Hao, Lixia Wang, Xiudong Sun and Shiqi Liu

    Citation: BMC Genomics 2020 21:37

    Content type: Research article

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  17. The general combining ability (GCA) of parents in hybrid rice affects not only heterotic level of grain yield and other important agronomic traits, but also performance of grain quality traits of F2 bulk populati...

    Authors: Moaz S. Eltahawy, Nour Ali, Imdad U. Zaid, Dalu Li, Dina Abdulmajid, Lal Bux, Hui Wang and Delin Hong

    Citation: BMC Genomics 2020 21:31

    Content type: Research article

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  18. Fusarium circinatum, the causal agent of pitch canker disease, poses a serious threat to several Pinus species affecting plantations and nurseries. Although Pinus pinaster has shown moderate resistance to F. circ...

    Authors: Laura Hernandez-Escribano, Erik A. Visser, Eugenia Iturritxa, Rosa Raposo and Sanushka Naidoo

    Citation: BMC Genomics 2020 21:28

    Content type: Research article

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  20. Potato virus Y (PVY) is a major pathogen of potatoes with major impact on global agricultural production. Resistance to PVY can be achieved by engineering potatoes to express a recessive, resistant allele of e...

    Authors: Pablo A. Gutierrez Sanchez, Lavanya Babujee, Helena Jaramillo Mesa, Erica Arcibal, Megan Gannon, Dennis Halterman, Molly Jahn, Jiming Jiang and Aurélie M. Rakotondrafara

    Citation: BMC Genomics 2020 21:18

    Content type: Research article

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  21. Cotton grows in altering environments that are often unfavorable or stressful for its growth and development. Consequently, the plant must cope with abiotic stresses such as soil salinity, drought, and excessi...

    Authors: Yanchao Xu, Richard Odongo Magwanga, Xiu Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Zhongli Zhou, Kunbo Wang and Fang Liu

    Citation: BMC Genomics 2020 21:15

    Content type: Research article

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  22. Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has n...

    Authors: Qi Yang, Xiaocui Niu, Xiaona Tian, Xiujuan Zhang, Jingyu Cong, Ruigang Wang, Guosheng Zhang and Guojing Li

    Citation: BMC Genomics 2020 21:12

    Content type: Research article

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  24. In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, e...

    Authors: Glenn T. Howe, Keith Jayawickrama, Scott E. Kolpak, Jennifer Kling, Matt Trappe, Valerie Hipkins, Terrance Ye, Stephanie Guida, Richard Cronn, Samuel A. Cushman and Susan McEvoy

    Citation: BMC Genomics 2020 21:9

    Content type: Research article

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  25. Pineapple is the most important crop with CAM photosynthesis, but its molecular biology is underexplored. MADS-box genes are crucial transcription factors involving in plant development and several biological ...

    Authors: Xiaodan Zhang, Mahpara Fatima, Ping Zhou, Qing Ma and Ray Ming

    Citation: BMC Genomics 2020 21:8

    Content type: Research article

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  26. Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system fo...

    Authors: Yukun Chen, Xiaoping Xu, Zhuanxia Liu, Zihao Zhang, Xu XuHan, Yuling Lin and Zhongxion Lai

    Citation: BMC Genomics 2020 21:4

    Content type: Research article

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  27. Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing ...

    Authors: Ying Li, Chunxia Zhang, Kebin Yang, Jingjing Shi, Yulong Ding and Zhimin Gao

    Citation: BMC Genomics 2019 20:1035

    Content type: Research article

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  28. Grape buds exhibit non-uniform, or delayed, break in early spring in subtropical regions because the accumulation of chilling is insufficient. Hydrogen cyanamide (H2CN2, HC) can partially replace chilling to effe...

    Authors: Dong Liang, Xiaojing Huang, Yanqiu Shen, Tian Shen, Huifen Zhang, Lijin Lin, Jin Wang, Qunxian Deng, Xiulan Lyu and Hui Xia

    Citation: BMC Genomics 2019 20:1034

    Content type: Research article

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  29. MYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth and development. Recent studies have revealed that some MYCs are involved in the ...

    Authors: Jian-fang Bai, Yu-kun Wang, Li-ping Guo, Xiao-ming Guo, Hao-yu Guo, Shao-hua Yuan, Wen-jing Duan, Zihan Liu, Chang-ping Zhao, Feng-ting Zhang and Li-ping Zhang

    Citation: BMC Genomics 2019 20:1032

    Content type: Research article

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  30. Non-key traits (NKTs) in radiata pine (Pinus radiata D. Don) refer to traits other than growth, wood density and stiffness, but still of interest to breeders. Branch-cluster frequency, stem straightness, external...

    Authors: Yongjun Li, Jaroslav Klápště, Emily Telfer, Phillip Wilcox, Natalie Graham, Lucy Macdonald and Heidi S. Dungey

    Citation: BMC Genomics 2019 20:1026

    Content type: Research article

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  31. Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still...

    Authors: Shenghui Zhou, Jinpeng Zhang, Haiming Han, Jing Zhang, Huihui Ma, Zhi Zhang, Yuqing Lu, Weihua Liu, Xinming Yang, Xiuquan Li and Lihui Li

    Citation: BMC Genomics 2019 20:1025

    Content type: Research article

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  32. Agricultural insects are one of the major threats to crop yield. It is a known fact that pesticide application is an extensive approach to eliminate insect pests, and has severe adverse effects on environment ...

    Authors: Sajid Muhammad, Jingai Tan, Pingchuan Deng, Tingting Li, Haohua He, Jianmin Bian and Liang Wu

    Citation: BMC Genomics 2019 20:1009

    Content type: Research article

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  34. Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential...

    Authors: Vera Thole, Jean-Etienne Bassard, Ricardo Ramírez-González, Martin Trick, Bijan Ghasemi Afshar, Dario Breitel, Lionel Hill, Alexandre Foito, Louise Shepherd, Sabine Freitag, Cláudia Nunes dos Santos, Regina Menezes, Pilar Bañados, Michael Naesby, Liangsheng Wang, Artem Sorokin…

    Citation: BMC Genomics 2019 20:995

    Content type: Research article

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  35. F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S prote...

    Authors: Shulin Zhang, Zailong Tian, Haipeng Li, Yutao Guo, Yanqi Zhang, Jeremy A. Roberts, Xuebin Zhang and Yuchen Miao

    Citation: BMC Genomics 2019 20:993

    Content type: Research article

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  36. Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variati...

    Authors: Priya Darshini Gurung, Atul Kumar Upadhyay, Pardeep Kumar Bhardwaj, Ramanathan Sowdhamini and Uma Ramakrishnan

    Citation: BMC Genomics 2019 20:989

    Content type: Research article

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  37. As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, w...

    Authors: Minmin Li, Ying Liu, Yahan Tao, Chongjing Xu, Xin Li, Xiaoming Zhang, Yingpeng Han, Xue Yang, Jingzhe Sun, Wenbin Li, Dongmei Li, Xue Zhao and Lin Zhao

    Citation: BMC Genomics 2019 20:987

    Content type: Research article

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  38. Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one ...

    Authors: Ruibin Wang, Jingfei Ma, Qian Zhang, Chunlai Wu, Hongyan Zhao, Yanan Wu, Guangxiao Yang and Guangyuan He

    Citation: BMC Genomics 2019 20:986

    Content type: Research article

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  39. The plant homeodomain (PHD) finger is a Cys4HisCys3-type zinc finger which promotes protein-protein interactions and binds to the cis-acting elements in the promoter regions of target genes. In Medicago truncatul...

    Authors: Wenli Quan, Xun Liu, Lihua Wang, Mingzhu Yin, Li Yang and Zhulong Chan

    Citation: BMC Genomics 2019 20:982

    Content type: Research article

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  40. Alginate is an important cell wall component and mannitol is a soluble storage carbon substance in the brown seaweed Saccharina japonica. Their contents vary with kelp developmental periods and harvesting time. A...

    Authors: Zhanru Shao, Pengyan Zhang, Chang Lu, Shaoxuan Li, Zhihang Chen, Xiuliang Wang and Delin Duan

    Citation: BMC Genomics 2019 20:975

    Content type: Research article

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  41. Bud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during ...

    Authors: Noémie Vimont, Mathieu Fouché, José Antonio Campoy, Meixuezi Tong, Mustapha Arkoun, Jean-Claude Yvin, Philip A. Wigge, Elisabeth Dirlewanger, Sandra Cortijo and Bénédicte Wenden

    Citation: BMC Genomics 2019 20:974

    Content type: Research article

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  42. Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fift...

    Authors: Amanda M. Vondras, Andrea Minio, Barbara Blanco-Ulate, Rosa Figueroa-Balderas, Michael A. Penn, Yongfeng Zhou, Danelle Seymour, Zirou Ye, Dingren Liang, Lucero K. Espinoza, Michael M. Anderson, M. Andrew Walker, Brandon Gaut and Dario Cantu

    Citation: BMC Genomics 2019 20:972

    Content type: Research article

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  43. Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is ma...

    Authors: Shimin Fu, Jonathan Shao, Avijit Roy, Ronald H. Brlansky, Changyong Zhou and John S. Hartung

    Citation: BMC Genomics 2019 20:969

    Content type: Research article

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  44. Tetraploid Thinopyrum elongatum (2n = 4x = 28) is a promising source of useful genes, including those related to adaptability and resistance to diverse biotic (Fusarium head blight, rust, powdery mildew, and yell...

    Authors: Daiyan Li, Juwei Zhang, Haijiao Liu, Binwen Tan, Wei Zhu, Lili Xu, Yi Wang, Jian Zeng, Xing Fan, Lina Sha, Haiqin Zhang, Jian Ma, Guoyue Chen, Yonghong Zhou and Houyang Kang

    Citation: BMC Genomics 2019 20:963

    Content type: Research article

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  45. The advent of third-generation sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promising for enhancing the quality of fragmented draft assemblies constructed from next-g...

    Authors: Mao Qin, Shigang Wu, Alun Li, Fengli Zhao, Hu Feng, Lulu Ding and Jue Ruan

    Citation: BMC Genomics 2019 20:955

    Content type: Software

    Published on:

  46. Somatic mutations occurring within meristems of vegetative propagation material have had a major role in increasing the genetic diversity of the domesticated grapevine (Vitis vinifera subsp. vinifera). The most w...

    Authors: Vanessa Ferreira, José Tomás Matus, Olinda Pinto-Carnide, David Carrasco, Rosa Arroyo-García and Isaura Castro

    Citation: BMC Genomics 2019 20:952

    Content type: Research article

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  47. Fusarium head blight (FHB) resistance in the durum wheat breeding gene pool is rarely reported. Triticum turgidum ssp. carthlicum line Blackbird is a tetraploid relative of durum wheat that offers partial FHB res...

    Authors: Ehsan Sari, Adrian L. Cabral, Brittany Polley, Yifang Tan, Emma Hsueh, David J. Konkin, Ron E. Knox, Yuefeng Ruan and Pierre R. Fobert

    Citation: BMC Genomics 2019 20:925

    Content type: Research article

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  48. GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, indu...

    Authors: Yao Chen, Panpan Zhu, Shaoyuan Wu, Yan Lu, Jian Sun, Qinghe Cao, Zongyun Li and Tao Xu

    Citation: BMC Genomics 2019 20:911

    Content type: Research article

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  49. Meloidogyne chitwoodi commonly known as Columbia root-knot nematode or CRKN is one of the most devastating pests of potato in the Pacific Northwest of the United States of America. In addition to the roots, it in...

    Authors: Sapinder Bali, Kelly Vining, Cynthia Gleason, Hassan Majtahedi, Charles R. Brown and Vidyasagar Sathuvalli

    Citation: BMC Genomics 2019 20:907

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:30

  50. The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is t...

    Authors: Rashmi Jain, Jerry Jenkins, Shengqiang Shu, Mawsheng Chern, Joel A. Martin, Dario Copetti, Phat Q. Duong, Nikki T. Pham, David A. Kudrna, Jayson Talag, Wendy S. Schackwitz, Anna M. Lipzen, David Dilworth, Diane Bauer, Jane Grimwood, Catherine R. Nelson…

    Citation: BMC Genomics 2019 20:905

    Content type: Research article

    Published on:

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