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  • Genome-wide association study in Eucalyptus grandis for resistance to Leptocybe invasa 
    Mhoswa, Lorraine (University of Pretoria, 2022-03)
    Eucalyptus species are commercially grown for their desirable growth, wood properties as well as a potential source for biofuel production making it a highly valuable commodity in the forest industry. However, this species ...
  • Genome-wide characterization and expression profiling of the Auxin Response Factors (ARF) gene family in Eucalyptus grandis 
    Yu, Hong; Soler, Marcal; Mila, Isabelle; Clemente, Helene San; Savelli, Bruno; Dunand, Christophe; Paiva, Jorge A.P.; Myburg, Alexander Andrew; Bouzayen, Mondher; Grima-Pettenati, Jacqueline; Cassan-Wang, Hua (Public Library of Science, 2014-09-30)
    Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF) are important actors of the auxin signalling pathway, regulating ...
  • Genome-wide diversity assessment for genetic resource management of Eucalyptus dunnii, E. grandis, E. nitens and E. urophylla 
    Henning, Johannes Stephanus (University of Pretoria, 2021)
    The genus Eucalyptus with its over 900 species is a dominant genus of the Australian flora, many provide the foundation for closed forest habitats on the continent. In addition to its ecological significance, this genus ...
  • Genome-wide diversity, population structure and signatures of inbreeding in the African buffalo in Mozambique 
    Colangelo, Paolo; Di Civita, Marika; Bento, Carlos; Franchini, Paolo; Meyer, Axel; Orel, Nadiya; Neves, Luis; Mulandane, Fernando C.; Almeida, Joao S.; Senczuk, Gabriele; Pilla, Fabio; Sabatelli, Simone (Springer, 2024)
    The African buffalo, Syncerus caffer, is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat acting as an ecosystem engineer. Over the last few centuries, African ...
  • Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes 
    Seyed Rahmani, Razgar; Shi, Tao; Zhang, Dongzhi; Gou, Xiaoping; Yi, Jin; Miclotte, Giles; Marchal, Kathleen; Li, Jia (BMC, 2021-06)
    BACKGROUND: Brassinosteroid (BR) signaling regulates plant growth and development in concert with other signaling pathways. Although many genes have been identified that play a role in BR signaling, the biological and ...
  • Genome-wide identification of breed-informative single-nucleotide polymorphisms in three South African indigenous cattle breeds 
    Zwane, Avhashoni Agnes; Maiwashe, A.; Makgahlela, M.L.; Choudhury, A.; Taylor, J.F.; Van Marle-Koster, Este (South African Society for Animal Science, 2016-09-20)
    Access to genotyping assays enables the identification of informative markers that discriminate between cattle breeds. Identification of these markers can assist in breed assignment, improvement and conservation. The ...
  • Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection 
    Kwenda, Stanford; Birch, P.R.J. (Paul); Moleleki, Lucy Novungayo (BioMed Central, 2016-08-11)
    BACKGROUND : Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the ...
  • Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers 
    Gong, Tingting; Jaratlerdsiri, Weerachai; Jiang, Jue; Willet, Cali; Chew, Tracy; Patrick, Sean Mark; Lyons, Ruth J.; Haynes, Anne‑Maree; Pasqualim, Gabriela; Brum, Ilma Simoni; Stricker, Phillip D.; Mutambirwa, Shingai B.A.; Sadsad, Rosemarie; Papenfuss, Anthony T.; Bornman, Maria S. (Riana); Chan, Eva K.F.; Hayes, Vanessa M. (BMC, 2022-08-31)
    BACKGROUND : African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub- Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded ...
  • Genome-wide macrosynteny among Fusarium species in the Gibberella fujikuroi complex revealed by amplified fragment length polymorphisms 
    De Vos, Lieschen; Steenkamp, Emma Theodora; Martin, Simon H.; Santana, Quentin C.; Fourie, Gerda; Van der Merwe, Nicolaas Albertus (Albie); Wingfield, Michael J.; Wingfield, Brenda D. (Public Library of Science, 2014-12)
    The Gibberella fujikuroi complex includes many Fusarium species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information ...
  • Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem 
    Hussey, Steven Grant; Mizrachi, Eshchar; Groover, Andrew; Berger, David Kenneth; Myburg, Alexander Andrew (BioMed Central, 2015-05-10)
    BACKGROUND : Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene ...
  • Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber 
    Zhang, Zhonghua; Mao, Linyong; Chen, Huiming; Bu, Fengjiao; Li, Guangcun; Sun, Jinjing; Li, Shua; Sun, Honghe; Jiao, Chen; Blakely, Rachel; Pan, Junsong; Cai, Run; Luo, Ruibang; Van de Peer, Yves; Jacobsen, Evert; Fei, Zhangjun; Huang, Sanwen (American Society of Plant Biologists, 2015)
    Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution ...
  • Genome-wide marker discovery in three South African indigenous cattle breeds (Afrikaner Drakensberger and Nguni) using next generation sequencing 
    Zwane, Avhashoni Agnes (University of Pretoria, 2017)
    Afrikaner, Drakensberger, and Nguni are the South African (SA) landraces that played major roles in the social, cultural and economic history of SA. These breeds are valuable genetic resources for beef production and limited ...
  • Genome-wide scan of single nucleotide polymorphisms for parentage analyses in South African indigenous beef breeds 
    Sanarana, Yandisiwe Patience (University of Pretoria, 2022)
    Genotyping panels using single nucleotide polymorphism (SNP) markers have superseded the use of microsatellites for parentage testing and other applications. High-density SNP arrays enable accurate parentage assignment but ...
  • Genome-wide SNP discovery in indigenous cattle breeds of South Africa 
    Zwane, Avhashoni Agnes; Schnabel, Robert D.; Hoff, Jesse; Choudhury, Ananyo; Makgahlela, Mahlako Linah; Maiwashe, Azwihangwisi; Van Marle-Koster, Este; Taylor, Jeremy F. (Frontiers Media, 2019-03-29)
    Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated ...
  • A genome-wide SNP genotyping resource for tropical pine tree species 
    Jackson, Colin; Christie, Nanette; Reynolds, Sharon Melissa; Marais, Gerhard C.; Tii-kuzu, Yokateme; Caballero, Madison; Kampman, Tamanique; Visser, Erik A.; Naidoo, Sanushka; Kain, Dominic; Whetten, Ross W.; Isik, Fikret; Wegrzyn, Jill; Hodge, Gary R.; Acosta, Juan J.; Myburg, Alexander Andrew (Wiley, 2022-02)
    We performed gene and genome targeted SNP discovery towards the development of a genome-wide, multispecies genotyping array for tropical pines. Pooled RNA-seq data from shoots of seedlings from five tropical pine species ...
  • Genome-wide transcriptome analysis of cassava challenged with Ugandan cassava brown streak virus (UCBSV) 
    Amuge, Teddy (University of Pretoria, 2019)
    Cassava is staple to millions in Africa, yet cassava brown streak disease (CBSD) greatly threatens cassava production. This study reports the mechanism of cassava’s resistance to CBSD using Ugandan cassava brown streak ...
  • Genomes of early-diverging streptophyte algae shed light on plant terrestrialization 
    Wang, Sibo; Li, Linzhou; Li, Haoyuan; Sahu, Sunil Kumar; Wang, Hongli; Xu, Yan; Xian, Wenfei; Song, Bo; Liang, Hongping; Cheng, Shifeng; Chang, Yue; Song, Yue; Cebi, Zehra; Wittek, Sebastian; Reder, Tanja; Peterson, Morten; Yang, Huanming; Wang, Jian; Melkonian, Barbara; Van de Peer, Yves; Xu, Xun; Wong, Gane Ka-Shu; Melkonian, Michael; Liu, Huan; Liu, Xin (Nature Research, 2020-02)
    Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of ...
  • Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy 
    Li, Ming-He; Liu, Ke-Wei; Li, Zhen; Lu, Hsiang-Chia; Ye, Qin-Liang; Zhang, Diyang; Wang, Jie-Yu; Li, Yu-Feng; Zhong, Zhi-Ming; Liu, Xuedie; Yu, Xia; Liu, Ding-Kun; Tu, Xiong-De; Liu, Bin; Hao, Yang; Liao, Xing-Yu; Jiang, Yu-Ting; Sun, Wei-Hong; Chen, Jinliao; Chen, Yan-Qiong; Ai, Ye; Zhai, Jun-Wen; Wu, Sha-Sha; Zhou, Zhuang; Hsiao, Yu-Yun; Wu, Wan-Lin; Chen, You-Yi; Lin, Yu-Fu; Hsu, Jui-Ling; Li, Chia-Ying; Wang, Zhi-Wen; Zhao, Xiang; Zhong, Wen-Ying; Ma, Xiao-Kai; Ma, Liang; Huang, Jie; Chen, Gui-Zhen; Huang, Ming-Zhong; Huang, Laiqiang; Peng, Dong-Hui; Luo, Yi-Bo; Zou, Shuang-Quan; Chen, Shi-Pin; Lan, Siren; Tsai, Wen-Chieh; Van de Peer, Yves; Liu, Zhong-Jian (Nature Research, 2022-05-21)
    To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis ...
  • Genomes shed light on the evolution of Begonia, a mega-diverse genus 
    Li, Lingfei; Chen, Xiaoli; Fang, Dongming; Dong, Shanshan; Guo, Xing; Li, Na; Campos-Dominguez, Lucia; Wang, Wenguang; Liu, Yang; Lang, Xiaoan; Peng, Yang; Tian, Daike; Thomas, Daniel C.; Mu, Weixue; Liu, Min; Wu, Chenyu; Yang, Ting; Zhang, Suzhou; Yang, Leilei; Yang, Jianfen; Liu, Zhong-Jian; Zhang, Liangsheng; Zhang, Xingtan; Chen, Fei; Jiao, Yuannian; Guo, Yalong; Hughes, Mark; Wang, Wei; Liu, Xiaofei; Zhong, Chunmei; Li, Airong; Sahu, Sunil Kumar; Yang, Huanming; Wu, Ernest; Sharbrough, Joel; Lisby, Michael; Liu, Xin; Xu, Xun; Soltis, Douglas E.; Van de Peer, Yves; Kidner, Catherine; Zhang, Shouzhou; Liu, Huan (Wiley, 2022-04)
    Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, ...
  • Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth 
    Lu, Qiang; Shao, Fenjuan; Macmillan, Colleen; Wilson, Iain W.; Van der Merwe, Karen; Hussey, Steven Grant; Myburg, Alexander Andrew; Dong, Xiaomei; Qiu, Deyou (Wiley Open Access, 2018-01)
    Lateral Organ Boundaries Domain (LBD) proteins are plant-specific transcription factors playing crucial roles in growth and development. However, the function of LBD proteins in Eucalyptus grandis remains largely unexplored. ...