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Fanelli F, Montemurro M, Chieffi D, Cho GS, Franz CMAP, Dell'Aquila A, Rizzello CG, Fusco V. Novel Insights Into the Phylogeny and Biotechnological Potential of Weissella Species. Front Microbiol 2022; 13:914036. [PMID: 35814678 PMCID: PMC9257631 DOI: 10.3389/fmicb.2022.914036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/19/2022] [Indexed: 11/29/2022] Open
Abstract
In this study, the genomes of the Weissella (W.) beninensis, W. diestrammenae, W. fabalis, W. fabaria, W. ghanensis, and W. uvarum type strains were sequenced and analyzed. Moreover, the ability of these strains to metabolize 95 carbohydrates was investigated, and the genetic determinants of such capability were searched within the sequenced genomes. 16S rRNA gene and genome-based-phylogeny of all the Weissella species described to date allowed a reassessment of the Weissella genus species groups. As a result, six distinct species groups within the genus, namely, W. beninensis, W. kandleri, W. confusa, W. halotolerans, W. oryzae, and W. paramesenteroides species groups, could be described. Phenotypic analyses provided further knowledge about the ability of the W. beninensis, W. ghanensis, W. fabaria, W. fabalis, W. uvarum, and W. diestrammenae type strains to metabolize certain carbohydrates and confirmed the interspecific diversity of the analyzed strains. Moreover, in many cases, the carbohydrate metabolism pathway and phylogenomic species group clustering overlapped. The novel insights provided in our study significantly improved the knowledge about the Weissella genus and allowed us to identify features that define the role of the analyzed type strains in fermentative processes and their biotechnological potential.
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Affiliation(s)
- Francesca Fanelli
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Marco Montemurro
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Daniele Chieffi
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | | | - Anna Dell'Aquila
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | | | - Vincenzina Fusco
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
- *Correspondence: Vincenzina Fusco
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Carvalho LJ, Agustini MA, Anderson JV, Vieira EA, de Souza CR, Chen S, Schaal BA, Silva JP. Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root. BMC PLANT BIOLOGY 2016; 16:133. [PMID: 27286876 PMCID: PMC4902922 DOI: 10.1186/s12870-016-0826-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/31/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Cassava (Manihot esculenta Crantz) storage root provides a staple food source for millions of people worldwide. Increasing the carotenoid content in storage root of cassava could provide improved nutritional and health benefits. Because carotenoid accumulation has been associated with storage root color, this study characterized carotenoid profiles, and abundance of key transcripts associated with carotenoid biosynthesis, from 23 landraces of cassava storage root ranging in color from white-to-yellow-to-pink. This study provides important information to plant breeding programs aimed at improving cassava storage root nutritional quality. RESULTS Among the 23 landraces, five carotenoid types were detected in storage root with white color, while carotenoid types ranged from 1 to 21 in storage root with pink and yellow color. The majority of storage root in these landraces ranged in color from pale-to-intense yellow. In this color group, total β-carotene, containing all-E-, 9-Z-, and 13-Z-β-carotene isomers, was the major carotenoid type detected, varying from 26.13 to 76.72 %. Although no α-carotene was observed, variable amounts of a α-ring derived xanthophyll, lutein, was detected; with greater accumulation of α-ring xanthophylls than of β-ring xanthophyll. Lycopene was detected in a landrace (Cas51) with pink color storage root, but it was not detected in storage root with yellow color. Based on microarray and qRT-PCR analyses, abundance of transcripts coding for enzymes involved in carotenoid biosynthesis were consistent with carotenoid composition determined by contrasting HPLC-Diode Array profiles from storage root of landraces IAC12, Cas64, and Cas51. Abundance of transcripts encoding for proteins regulating plastid division were also consistent with the observed differences in total β-carotene accumulation. CONCLUSIONS Among the 23 cassava landraces with varying storage root color and diverse carotenoid types and profiles, landrace Cas51 (pink color storage root) had low LYCb transcript abundance, whereas landrace Cas64 (intense yellow storage root) had decreased HYb transcript abundance. These results may explain the increased amounts of lycopene and total β-carotene observed in landraces Cas51 and Cas64, respectively. Overall, total carotenoid content in cassava storage root of color class representatives were associated with spatial patterns of secondary growth, color, and abundance of transcripts linked to plastid division. Finally, a partial carotenoid biosynthesis pathway is proposed.
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Affiliation(s)
| | | | - James V Anderson
- USDA-ARS, Sunflower and Plant Biology Research Unit, Fargo, ND, USA
| | | | | | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agriculture, Hainan, China.
| | - Barbara A Schaal
- Department of Biology, Washington University in St. Louis, St Louis, MO, USA
| | - Joseane P Silva
- EMBRAPA Genetic Resources and Biotechnology, Brasília, DF, Brazil
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8
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Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, Møller BL, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJCB, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, Jørgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, López-Lavalle LAB, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K, Peng M. Cassava genome from a wild ancestor to cultivated varieties. Nat Commun 2014; 5:5110. [PMID: 25300236 PMCID: PMC4214410 DOI: 10.1038/ncomms6110] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022] Open
Abstract
Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
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Affiliation(s)
- Wenquan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Binxiao Feng
- 1] Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China [2] Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Jingfa Xiao
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Zhiqiang Xia
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Xincheng Zhou
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Pinghua Li
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Weixiong Zhang
- 1] Department of Computer Science and Engineering and Department of Genetics, Washington University, Saint Louis, Missouri 63130, USA [2] Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Ying Wang
- South China Botanical Garden, CAS, Guangzhou 510650, China
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Peng Zhang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS, Shanghai 200032, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Gong Xiao
- South China Botanical Garden, CAS, Guangzhou 510650, China
| | - Jingxing Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jun Yang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS, Shanghai 200032, China
| | - Songbi Chen
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Pablo D Rabinowicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Xin Chen
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Henan Ceballos
- International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Meiling Zou
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Luiz J C B Carvalho
- Brazilian Enterprise for Agricultural Research (EMBRAPA), Genetic Resources and Biotechnology, Brasilia 70770, Brazil
| | - Changying Zeng
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Jing Xia
- 1] Department of Computer Science and Engineering and Department of Genetics, Washington University, Saint Louis, Missouri 63130, USA [2] Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Shixiang Sun
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yuhua Fu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Haiyan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Cheng Lu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Mengbin Ruan
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China
| | - Zhicheng Wu
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China
| | - Hui Liu
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China
| | - Rubini Maya Kannangara
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Kirsten Jørgensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Rebecca Louise Neale
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Maya Bonde
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Nanna Heinz
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Wenli Zhu
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Shujuan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Yang Zhang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Kun Pan
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Mingfu Wen
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Ping-An Ma
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Zhengxu Li
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Meizhen Hu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Wenbin Liao
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Wenbin Hu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Shengkui Zhang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Jinli Pei
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Anping Guo
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Jianchun Guo
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Jiaming Zhang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Zhengwen Zhang
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Jianqiu Ye
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Wenjun Ou
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Yaqin Ma
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Xinyue Liu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Kevin Galens
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Sandra Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jie Huang
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Jingjing Xue
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Feifei An
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Qingqun Yao
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Xiaojing Lu
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Martin Fregene
- International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | | | - Jiajie Wu
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Frank M You
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Meili Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Guojiang Wu
- South China Botanical Garden, CAS, Guangzhou 510650, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Peng Ling
- Citrus Research and Education Center (CREC), University of Florida, Gainesville, Florida 32611, USA
| | - Yeyuan Chen
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Qinghuang Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Guodao Liu
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Bin Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Biogeography and Bioresources in Arid Land, Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China
| | - Kaimian Li
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Ming Peng
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
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