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Genomics and evolution

Section edited by David Alvarez-Ponce and Z Jeffrey Chen 

This section considers studies in the evolution of plants as well as comparative genomics in relation to plant biology.

Page 1 of 7

  1. Intergenomic gene transfer (IGT) between nuclear and organellar genomes is a common phenomenon during plant evolution. Gossypium is a useful model to evaluate the genomic consequences of IGT for both diploid and ...

    Authors: Nan Zhao, Corrinne E. Grover, Zhiwen Chen, Jonathan F. Wendel and Jinping Hua

    Citation: BMC Plant Biology 2019 19:492

    Content type: Research article

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  2. Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in the regulation of plant architecture and flowering time. The functions of PEBP genes have been studied in many plant species. However, little is ...

    Authors: Hanqi Jin, Xuemin Tang, Mengge Xing, Hong Zhu, Jiongming Sui, Chunmei Cai and Shuai Li

    Citation: BMC Plant Biology 2019 19:484

    Content type: Research article

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  3. Linoleic acid is an important polyunsaturated fatty acid, required for all eukaryotes. Microsomal delta-12 (Δ12) oleate desaturase (FAD2) is a key enzyme for linoleic acid biosynthesis. Desert shrub Artemisia sph...

    Authors: Xiumei Miao, Lijing Zhang, Xiaowei Hu, Shuzhen Nan, Xiaolong Chen and Hua Fu

    Citation: BMC Plant Biology 2019 19:481

    Content type: Research article

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  4. Meiosis of newly formed allopolyploids frequently encounter perturbations induced by the merging of divergent and hybridizable genomes. However, to date, the meiotic properties of allopolyploids with dysploid ...

    Authors: Qinzheng Zhao, Yunzhu Wang, Yunfei Bi, Yufei Zhai, Xiaqing Yu, Chunyan Cheng, Panqiao Wang, Ji Li, Qunfeng Lou and Jinfeng Chen

    Citation: BMC Plant Biology 2019 19:471

    Content type: Research article

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  5. Transposable elements (TEs) comprise over 80% of the wheat genome and usually possess unique features for specific super-families and families. However, the role of TEs in wheat evolution and reshaping the whe...

    Authors: Katherine Domb, Danielle Keidar-Friedman and Khalil Kashkush

    Citation: BMC Plant Biology 2019 19:461

    Content type: Research article

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  6. Blueberry is of high economic value. Most blueberry varieties selected for the fresh market have an appealing light blue coating or “bloom” on the fruit due to the presence of a visible heavy epicuticular wax ...

    Authors: Xinpeng Qi, Elizabeth L. Ogden, Jose V. Die, Mark K. Ehlenfeldt, James J. Polashock, Omar Darwish, Nadim Alkharouf and L. Jeannine Rowland

    Citation: BMC Plant Biology 2019 19:460

    Content type: Research article

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  7. Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) s...

    Authors: In-Su Choi, Erika N. Schwarz, Tracey A. Ruhlman, Mohammad A. Khiyami, Jamal S. M. Sabir, Nahid H. Hajarah, Mernan J. Sabir, Samar O. Rabah and Robert K. Jansen

    Citation: BMC Plant Biology 2019 19:448

    Content type: Research article

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  8. Multiprotein bridging factor 1 s (MBF1s) are members of the transcriptional co-activator family that have involved in plant growth, development and stress responses. However, little is known about the Solanum lyc...

    Authors: Xu Zhang, Zhixuan Xu, Lichen Chen and Zhonghai Ren

    Citation: BMC Plant Biology 2019 19:437

    Content type: Research article

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  9. Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well studied.

    Authors: Xiao-Ru Ji, Yi-He Yu, Pei-Yi Ni, Guo-Hai Zhang and Da-Long Guo

    Citation: BMC Plant Biology 2019 19:433

    Content type: Research article

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  10. Cotton fiber length and strength are both key traits of fiber quality, and fiber strength (FS) is tightly correlated with secondary cell wall (SCW) biosynthesis. The three-amino-acid-loop-extension (TALE) supe...

    Authors: Qiang Ma, Nuohan Wang, Pengbo Hao, Huiru Sun, Congcong Wang, Liang Ma, Hantao Wang, Xianlong Zhang, Hengling Wei and Shuxun Yu

    Citation: BMC Plant Biology 2019 19:432

    Content type: Research article

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  11. Synonymous mutations do not change amino acids but do sometimes change the tRNAs (anticodons) that decode a particular codon. An isoaccepting codon is a synonymous codon that shares the same tRNA. If a mutated...

    Authors: Duan Chu and Lai Wei

    Citation: BMC Plant Biology 2019 19:422

    Content type: Research article

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  12. Genome wide association studies (GWAS) are a powerful tool for identifying quantitative trait loci (QTL) and causal single nucleotide polymorphisms (SNPs)/genes associated with various important traits in crop...

    Authors: Abiskar Gyawali, Vivek Shrestha, Katherine E. Guill, Sherry Flint-Garcia and Timothy M. Beissinger

    Citation: BMC Plant Biology 2019 19:412

    Content type: Research article

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  13. Taxus spp. produces the anticancer drug, taxol, and hence is planted as an industrial crop in China. APETALA2/ethylene response element binding proteins (AP2/EREBPs) are the key regulators of plant development, g...

    Authors: Meng Zhang, Ying Chen, Xiaofei Jin, Yuxin Cai, Yuanyuan Yuan, Chunhua Fu and Longjiang Yu

    Citation: BMC Plant Biology 2019 19:413

    Content type: Research article

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  14. Around the Cretaceous-Paleogene (K-Pg) boundary, an obvious global cooling occurred, which resulted in dramatic changes in terrestrial ecosystems and the evolutionary trends of numerous organisms. However, how...

    Authors: Yi-Ming Cui, Wei Wang, David K. Ferguson, Jian Yang and Yu-Fei Wang

    Citation: BMC Plant Biology 2019 19:402

    Content type: Research article

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  15. Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for ...

    Authors: Muhammad Umair Ahsan, Alice Hayward, Mobashwer Alam, Jayeni Hiti Bandaralage, Bruce Topp, Christine Anne Beveridge and Neena Mitter

    Citation: BMC Plant Biology 2019 19:382

    Content type: Research article

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  16. The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, i...

    Authors: Shu-Fen Li, Jia-Rong Li, Jin Wang, Ran Dong, Ke-Li Jia, Hong-Wei Zhu, Ning Li, Jin-Hong Yuan, Chuan-Liang Deng and Wu-Jun Gao

    Citation: BMC Plant Biology 2019 19:361

    Content type: Research article

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  17. The PHOSPHATE1 (PHO1) gene family plays diverse roles in inorganic phosphate (Pi) transfer and signal transduction, and plant development. However, the functions and diversification of soybean PHO1 family are poo...

    Authors: Yan Wang, Huihui Gao, Lingli He, Weiwei Zhu, Lixin Yan, Qingshan Chen and Chaoying He

    Citation: BMC Plant Biology 2019 19:353

    Content type: Research article

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  18. Flavonoid 3′-hydroxlase (F3’H) is an important enzyme in determining the B-ring hydroxylation pattern of flavonoids. In monocots, previous studies indicated the presence of two groups of F3’Hs with different e...

    Authors: Yong Jia, Bo Li, Yujuan Zhang, Xiaoqi Zhang, Yanhao Xu and Chengdao Li

    Citation: BMC Plant Biology 2019 19:347

    Content type: Research article

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  19. In the study, the trihelix family, also referred to as GT factors, is one of the transcription factor families. Trihelix genes play roles in the light response, seed maturation, leaf development, abiotic and biol...

    Authors: Zhaotang Ma, Moyang Liu, Wenjun Sun, Li Huang, Qi Wu, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Plant Biology 2019 19:344

    Content type: Research article

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  20. APETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target euAP2 genes are involved in the process of phase transformat...

    Authors: Tengyue Wang, Xiaoke Ping, Yanru Cao, Hongju Jian, Yumin Gao, Jia Wang, Yingchao Tan, Xinfu Xu, Kun Lu, Jiana Li and Liezhao Liu

    Citation: BMC Plant Biology 2019 19:336

    Content type: Research article

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  21. Zinc finger proteins (ZFPs) containing only a single zinc finger domain play important roles in the regulation of plant growth and development, as well as in biotic and abiotic stress responses. To date, the e...

    Authors: Peng He, Yan Yang, Zihua Wang, Peng Zhao, Yi Yuan, Li Zhang, Yueqin Ma, Chaoyou Pang, Jianing Yu and Guanghui Xiao

    Citation: BMC Plant Biology 2019 19:329

    Content type: Research article

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  22. The WOX (WUSCHEL-RELATED HOMEOBOX) gene family encodes a class of transcription factors that are unique to green plants, where they are involved in regulating the development of plant tissues and organs by determ...

    Authors: Peng He, Yuzhou Zhang, Hao Liu, Yi Yuan, Chan Wang, Jianing Yu and Guanghui Xiao

    Citation: BMC Plant Biology 2019 19:312

    Content type: Research article

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  23. DNA methylation is a crucial epigenetic modification, which is involved in many biological processes, including gene expression regulation, embryonic development, cell differentiation and genomic imprinting et...

    Authors: Liuling Pei, Lin Zhang, Jianying Li, Chao Shen, Ping Qiu, Lili Tu, Xianlong Zhang and Maojun Wang

    Citation: BMC Plant Biology 2019 19:307

    Content type: Research article

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  24. Polyploidy and hybridization are ubiquitous in Rubus L., a large and taxonomically challenging genus. Chinese Rubus are mainly concentrated into two major sections, the diploid Idaeobatus and the polyploid Malach...

    Authors: Yan Wang, Qing Chen, Tao Chen, Jing Zhang, Wen He, Lin Liu, Ya Luo, Bo Sun, Yong Zhang, Hao-ru Tang and Xiao-rong Wang

    Citation: BMC Plant Biology 2019 19:303

    Content type: Research article

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  25. SPL (SQUAMOSA promoter binding protein-like) is a class of plant-specific transcription factors that play important roles in many growth and developmental processes, including shoot and inflorescence branching...

    Authors: Moyang Liu, Wenjun Sun, Zhaotang Ma, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Plant Biology 2019 19:299

    Content type: Research article

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  26. Premature senescence of flag leaf severely affects wheat yield and quality. Chlorophyll (Chl) degradation is the most obvious symptom during leaf senescence and catalyzed by a series of enzymes. Pheophytin phe...

    Authors: Huiyan Wang, Shuguang Wang, Xiaoping Chang, Chenyang Hao, Daizhen Sun and Ruilian Jing

    Citation: BMC Plant Biology 2019 19:296

    Content type: Research article

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  27. Robust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms. Paris japonica (Melanthiaceae) ...

    Authors: Lifang Yang, Zhenyan Yang, Changkun Liu, Zhengshan He, Zhirong Zhang, Jing Yang, Haiyang Liu, Junbo Yang and Yunheng Ji

    Citation: BMC Plant Biology 2019 19:293

    Content type: Research article

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  28. Saussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine pl...

    Authors: Xu Zhang, Tao Deng, Michael J. Moore, Yunheng Ji, Nan Lin, Huajie Zhang, Aiping Meng, Hengchang Wang, Yanxia Sun and Hang Sun

    Citation: BMC Plant Biology 2019 19:290

    Content type: Research article

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  29. Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each ...

    Authors: Cuihua Gu, Li Ma, Zhiqiang Wu, Kai Chen and Yixiang Wang

    Citation: BMC Plant Biology 2019 19:281

    Content type: Research article

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  30. Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been charact...

    Authors: Shenquan Cao, Mengjie Guo, Chong Wang, Wenjing Xu, Tianyuan Shi, Guimin Tong, Cheng Zhen, Hao Cheng, Chuanping Yang, Nabil Ibrahim Elsheery and Yuxiang Cheng

    Citation: BMC Plant Biology 2019 19:276

    Content type: Research article

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  31. The Growth-regulating factor (GRF) family encodes plant-specific transcription factors which contain two conserved domains, QLQ and WRC. Members of this family play vital roles in plant development and stress res...

    Authors: Feng Chen, Yingzeng Yang, Xiaofeng Luo, Wenguan Zhou, Yujia Dai, Chuan Zheng, Weiguo Liu, Wenyu Yang and Kai Shu

    Citation: BMC Plant Biology 2019 19:269

    Content type: Research article

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  32. Brassica napus L. has little or no primary dormancy, but exhibits great variation in secondary dormancy. Secondary dormancy potential in oilseed rape can lead to the emergence of volunteer plants that cause genet...

    Authors: Lei Liu, Fuxia Liu, Jinfang Chu, Xin Yi, Wenqi Fan, Tang Tang, Guimin Chen, Qiuhuan Guo and Xiangxiang Zhao

    Citation: BMC Plant Biology 2019 19:264

    Content type: Research article

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  33. ZF-HD is a family of genes that play an important role in plant growth, development, some studies have found that after overexpression AtZHD1 in Arabidopsis thaliana, florescence advance, the seeds get bigger and...

    Authors: Moyang Liu, Xiaoxiang Wang, Wenjun Sun, Zhaotang Ma, Tianrun Zheng, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Plant Biology 2019 19:248

    Content type: Research article

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  34. MiRNAs (microRNA) are 18–24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expr...

    Authors: Sufang Zhang, Shanshan Yan, Jiali Zhao, Huanhuan Xiong, Peiqi An, Junhui Wang, Hanguo Zhang and Lei Zhang

    Citation: BMC Plant Biology 2019 19:247

    Content type: Research article

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  35. Studies have demonstrated that BBX (B-BOX) genes play crucial roles in regulatory networks controlling plant growth, developmental processes and stress response. Nevertheless, comprehensive study of BBX genes in ...

    Authors: Yunpeng Cao, Dandan Meng, Yahui Han, Tianzhe Chen, Chunyan Jiao, Yu Chen, Qing Jin and Yongping Cai

    Citation: BMC Plant Biology 2019 19:245

    Content type: Research article

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  36. Elymus L. is the largest genus in the tribe Triticeae Dumort., encompassing approximately 150 polyploid perennial species widely distributed in the temperate regions of the world. It is considered to be an import...

    Authors: Zongyu Zhang, Wengang Xie, Yongqiang Zhao, Junchao Zhang, Na Wang, Fabrice Ntakirutimana, Jiajun Yan and Yanrong Wang

    Citation: BMC Plant Biology 2019 19:235

    Content type: Research article

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  37. Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots....

    Authors: Liheng He, Ruimin Tang, Xiaowen Shi, Wenbing Wang, Qinghe Cao, Xiayu Liu, Ting Wang, Yan Sun, Hongmei Zhang, Runzhi Li and Xiaoyun Jia

    Citation: BMC Plant Biology 2019 19:232

    Content type: Research article

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  38. Interspecific hybridisation resulting in polyploidy is one of the major driving forces in plant evolution. Here, we present data from the molecular cytogenetic analysis of three cytotypes of Elytrigia ×mucronata ...

    Authors: Ladislava Paštová, Alexander Belyayev and Václav Mahelka

    Citation: BMC Plant Biology 2019 19:230

    Content type: Research article

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  39. Persimmon (Diospyros kaki) is the most economically cultivated species belonging to the genus Diospyros. However, little is known about the interspecific diversity and mechanism of domestication, partly due to th...

    Authors: Changfei Guan, Shuyuan Liu, Mengke Wang, Hao Ji, Xiaofeng Ruan, Renzi Wang and Yong Yang

    Citation: BMC Plant Biology 2019 19:227

    Content type: Research article

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  40. Repetitive DNA motifs – not coding genetic information and repeated millions to hundreds of times – make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the rep...

    Authors: Qing Liu, Xiaoyu Li, Xiangying Zhou, Mingzhi Li, Fengjiao Zhang, Trude Schwarzacher and John Seymour Heslop-Harrison

    Citation: BMC Plant Biology 2019 19:226

    Content type: Research article

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  41. MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes i...

    Authors: Chunmei He, Can Si, Jaime A. Teixeira da Silva, Mingzhi Li and Jun Duan

    Citation: BMC Plant Biology 2019 19:223

    Content type: Research article

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  42. Mature fruit cracking during the normal season in African Pride (AP) atemoya is a major problem in postharvest storage. Our current understanding of the molecular mechanism underlying fruit cracking is limited...

    Authors: Jingjing Chen, Yajie Duan, Yulin Hu, Weiming Li, Dequan Sun, Huigang Hu and Jianghui Xie

    Citation: BMC Plant Biology 2019 19:219

    Content type: Research article

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  43. Banana (Musa spp.) is one of the world’s most important fruits and its production is largely limited by diverse stress conditions. SROs (SIMILAR TO RCD-ONE) have important functions in abiotic stress resistance a...

    Authors: Lu Zhang, Dengbo Zhou, Huigang Hu, Weiming Li, Yulin Hu, Jianghui Xie, Shangzhi Huang and Wei Wang

    Citation: BMC Plant Biology 2019 19:211

    Content type: Research article

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  44. Rice blast disease is one of the most destructive fungal disease of rice worldwide. The avirulence (AVR) genes of Magnaporthe oryzae are recognized by the cognate resistance (R) genes of rice and trigger race-spe...

    Authors: Jinbin Li, Qun Wang, Chengyun Li, Yunqing Bi, Xue Fu and Raoquan Wang

    Citation: BMC Plant Biology 2019 19:204

    Content type: Research article

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  45. The objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (th...

    Authors: Li Ma, Li Zhou, Shaowen Quan, Hang Xu, Jieping Yang and Jianxin Niu

    Citation: BMC Plant Biology 2019 19:192

    Content type: Research article

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  46. BRASSINAZOLE-RESISTANT (BZR) family genes encode plant-specific transcription factors (TFs) that participate in brassinosteroid signal transduction. BZR TFs have vital roles in plant growth, including cell elo...

    Authors: Wei Wang, Ya-Qing Sun, Guo-Long Li and Shao-Ying Zhang

    Citation: BMC Plant Biology 2019 19:191

    Content type: Research article

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  47. Senescence affects the quality and yield of plants by regulating different traits of plants. A few members of S40 gene family, the barley HvS40 and the Arabidopsis AtS40–3, have been shown to play a role in leaf ...

    Authors: Xiangzi Zheng, Muhammad Jehanzeb, Habiba, Yuanyuan Zhang, Li Li and Ying Miao

    Citation: BMC Plant Biology 2019 19:174

    Content type: Research article

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  48. Angiosperm sex chromosomes, where present, are generally recently evolved. The key step in initiating the development of sex chromosomes from autosomes is the establishment of a sex-determining locus within a ...

    Authors: S. M. Pilkington, J. Tahir, E. Hilario, S. E. Gardiner, D. Chagné, A. Catanach, J. McCallum, L. Jesson, L. G. Fraser, M. A. McNeilage, C. Deng, R. N. Crowhurst, P. M. Datson and Q. Zhang

    Citation: BMC Plant Biology 2019 19:172

    Content type: Research article

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