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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 8

  1. Plant genomes contain a large number of HAK/KUP/KT transporters, which play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant dev...

    Authors: Xiaomin Feng, Yongjun Wang, Nannan Zhang, Zilin Wu, Qiaoying Zeng, Jiayun Wu, Xiaobin Wu, Lei Wang, Jisen Zhang and Yongwen Qi

    Citation: BMC Plant Biology 2020 20:20

    Content type: Research article

    Published on:

  2. The BAHD acyltransferase superfamily exhibits various biological roles in plants, including regulating fruit quality, catalytic synthesizing of terpene, phenolics and esters, and improving stress resistance. Howe...

    Authors: Chunxin Liu, Xin Qiao, Qionghou Li, Weiwei Zeng, Shuwei Wei, Xin Wang, Yangyang Chen, Xiao Wu, Jun Wu, Hao Yin and Shaoling Zhang

    Citation: BMC Plant Biology 2020 20:14

    Content type: Research article

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  3. Pectin methylesterase (PME) is a hydrolytic enzyme that catalyzes the demethylesterification of homogalacturonans and controls pectin reconstruction, being essential in regulation of cell wall modification. Du...

    Authors: Cheng Xue, Si-Cong Guan, Jian-Qing Chen, Chen-Jin Wen, Jian-Fa Cai and Xu Chen

    Citation: BMC Plant Biology 2020 20:13

    Content type: Research article

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  4. Cytoplasmic male sterility (CMS) plays a crucial role in the utilization of heterosis and various types of CMS often have different abortion mechanisms. Therefore, it is important to understand the molecular m...

    Authors: Zihan Liu, Sha Li, Wei Li, Qi Liu, Lingli Zhang and Xiyue Song

    Citation: BMC Plant Biology 2020 20:10

    Content type: Research article

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  5. Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstruc...

    Authors: Jesse R. Walsh, Margaret R. Woodhouse, Carson M. Andorf and Taner Z. Sen

    Citation: BMC Plant Biology 2020 20:4

    Content type: Research article

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  6. Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections thro...

    Authors: Hélène Muranty, Caroline Denancé, Laurence Feugey, Jean-Luc Crépin, Yves Barbier, Stefano Tartarini, Matthew Ordidge, Michela Troggio, Marc Lateur, Hilde Nybom, Frantisek Paprstein, François Laurens and Charles-Eric Durel

    Citation: BMC Plant Biology 2020 20:2

    Content type: Research article

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  7. The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model p...

    Authors: Feng Chen, Qin Zhou, Lan Wu, Fei Li, Baojun Liu, Shuting Zhang, Jiaqi Zhang, Manzhu Bao and Guofeng Liu

    Citation: BMC Plant Biology 2019 19:600

    Content type: Research article

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  8. Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for ide...

    Authors: Nan Lu, Miaomiao Zhang, Yao Xiao, Donghua Han, Ying Liu, Yu Zhang, Fei Yi, Tianqing Zhu, Wenjun Ma, Erqin Fan, Guanzheng Qu and Junhui Wang

    Citation: BMC Plant Biology 2019 19:596

    Content type: Research article

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  9. Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, littl...

    Authors: Yiyang Liu, Jiao Zhu, Sheng Sun, Feng Cui, Yan Han, Zhenying Peng, Xuejie Zhang, Shubo Wan and Guowei Li

    Citation: BMC Plant Biology 2019 19:593

    Content type: Research article

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  10. Pueraria candollei var. mirifica, a Thai medicinal plant used traditionally as a rejuvenating herb, is known as a rich source of phytoestrogens, including isoflavonoids and the highly estrogenic miroestrol and de...

    Authors: Nithiwat Suntichaikamolkul, Kittitya Tantisuwanichkul, Pinidphon Prombutara, Khwanlada Kobtrakul, Julie Zumsteg, Siriporn Wannachart, Hubert Schaller, Mami Yamazaki, Kazuki Saito, Wanchai De-eknamkul, Sornkanok Vimolmangkang and Supaart Sirikantaramas

    Citation: BMC Plant Biology 2019 19:581

    Content type: Research article

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  11. Phenotypic diversity of floral organs plays an important role in plant systematic taxonomy and genetic variation studies. Previous research have focused on the direction of variation but disregarded its degree...

    Authors: Ting Zhou, Junjun Fan, Mingming Zhao, Donglin Zhang, Qianhui Li, Guibin Wang, Wangxiang Zhang and Fuliang Cao

    Citation: BMC Plant Biology 2019 19:574

    Content type: Methodology article

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  12. Gynodioecious species exist in two sexes – male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(...

    Authors: Manuela Krüger, Oushadee A. J. Abeyawardana, Miloslav Juříček, Claudia Krüger and Helena Štorchová

    Citation: BMC Plant Biology 2019 19:568

    Content type: Research article

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  13. Sucrose synthase (SUS) is widely considered a key enzyme participating in sucrose metabolism in higher plants and regarded as a biochemical marker for sink strength in crops. However, despite significant progr...

    Authors: Xiaoyang Xu, Yongheng Yang, Chunxiao Liu, Yuming Sun, Ting Zhang, Menglan Hou, Suzhen Huang and Haiyan Yuan

    Citation: BMC Plant Biology 2019 19:566

    Content type: Research article

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  14. Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Pa...

    Authors: Yunheng Ji, Lifang Yang, Mark W. Chase, Changkun Liu, Zhenyan Yang, Jin Yang, Jun-Bo Yang and Ting-Shuang Yi

    Citation: BMC Plant Biology 2019 19:543

    Content type: Research article

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  15. Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba ...

    Authors: Yaqiong Wu, Jing Guo, Tongli Wang, Fuliang Cao and Guibin Wang

    Citation: BMC Plant Biology 2019 19:527

    Content type: Research article

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  16. The WRKYs are a major family of plant transcription factors that play roles in the responses to biotic and abiotic stresses; however, a comprehensive study of the WRKY family in roses (Rosa sp.) has not previousl...

    Authors: Xintong Liu, Dandan Li, Shiya Zhang, Yaling Xu and Zhao Zhang

    Citation: BMC Plant Biology 2019 19:522

    Content type: Research article

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  17. Germplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of sampl...

    Authors: Jorge Franco-Duran, José Crossa, Jiafa Chen and Sarah Jane Hearne

    Citation: BMC Plant Biology 2019 19:520

    Content type: Research article

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  18. The structural reinforcement of cell walls by hydroxycinnamates has a significant role in defense against pests and pathogens, but it also interferes with forage digestibility and biofuel production. Elucidati...

    Authors: A. López-Malvar, A. Butrón, L. F. Samayoa, D. J. Figueroa-Garrido, R. A. Malvar and R. Santiago

    Citation: BMC Plant Biology 2019 19:519

    Content type: Research article

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  19. Ascorbate is a powerful antioxidant in plants and an essential micronutrient for humans. The GDP-L-galactose phosphorylase (GGP) gene encodes the rate-limiting enzyme of the L-galactose pathway—the dominant ascor...

    Authors: Ronan C. Broad, Julien P. Bonneau, Jesse T. Beasley, Sally Roden, Joshua G. Philips, Ute Baumann, Roger P. Hellens and Alexander A. T. Johnson

    Citation: BMC Plant Biology 2019 19:515

    Content type: Research article

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  20. The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especiall...

    Authors: Juan Wang, Yuan Li, Chunjuan Li, Caixia Yan, Xiaobo Zhao, Cuiling Yuan, Quanxi Sun, Chengren Shi and Shihua Shan

    Citation: BMC Plant Biology 2019 19:504

    Content type: Research article

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  21. Polygonum cuspidatum of the Polygonaceae family is a traditional medicinal plant with many bioactive compounds that play important roles in human health and stress responses. Research has attempted to identify bi...

    Authors: Xiaowei Wang, Zhijun Wu, Wenqi Bao, Hongyan Hu, Mo Chen, Tuanyao Chai and Hong Wang

    Citation: BMC Plant Biology 2019 19:498

    Content type: Research article

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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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

    Published on:

  45. 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

    Published on:

  46. 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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  47. 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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  48. 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

    Published on:

  49. 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

    Published on:

  50. 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

    Published on:

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