Actinidia Chinensis)

Total Page:16

File Type:pdf, Size:1020Kb

Actinidia Chinensis) c Indian Academy of Sciences RESEARCH NOTE Genomewide analysis of NBS-encoding genes in kiwi fruit (Actinidia chinensis) YINGJUN LI, YAN ZHONG, KAIHUI HUANG and ZONG-MING CHENG∗ College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China [Li Y., Zhong Y., Huang K. and Cheng Z.-M. 2016 Genomewide analysis of NBS-encoding genes in kiwi fruit (Actinidia chinensis). J. Genet. 95, 997–1001] Introduction (Huang et al. 2013). Although NBS-encoding genes were just identified by Huang et al. (2013) no evolutionary his- In plants, there are many layers of defense system against tory of NBS-encoding genes was detected. In this study, we pathogens in the environment. The first is structural bar- identified NBS-encoding genes in kiwi fruit genome and then rier and second is pathogen-associated molecular pattern divided them into families based on three criteria. Duplica- (PAMP) recognition receptors. The third is resistance genes tion time, phylogenetic relationship and selection pressure (R genes) against specific pathogens, which work in the trig- were also examined to obtain insight into evolutionary pat- gering effector immunity (ETI) that produces a hypersensi- terns of NBS-encoding genes. As a result, a total of 96 NBS- tive response (HR) (Jones and Dangl 2006). R genes confer encoding genes were identified, include 74 NBS–LRR genes. resistance to a diverse range of pathogens, including bacte- The recent duplication mainly contributed to the existing ria, fungi, oomycetes, viruses, insects and nematodes (Martin NBS-encoding genes. Further, purifying selection played an et al. 2003). important role in evolution process of NBS-encoding genes. Kiwi fruit (Actinidia chinensis) is a commercially valu- The analysis will help us deeply understand the evolution of able and nutritionally important fruit, which is well known as NBS-encoding genes in Actinidia. ‘the king of fruits’ for remarkably high vitamin C content. However, pathogen infections have lowered the yield and quality of kiwi fruit (Ferrante and Scortichini 2010; Biondi Methods and materials et al. 2013; Li et al. 2013). Therefore, better understanding Identification of NBS-encodings and gene family classification of resistance (R) genes in kiwi fruit could provide the strategy of kiwi fruit for improving resistance to pathogens. The class of NBS– LRR resistance genes, which encode nucleotide-binding sites Kiwi fruit (A. chinensis) assembly and annotation were (NBS) and leucine-rich repeat (LRR) domains, is one of the downloaded from kiwi fruit genome database (http://bioinfo. largest R genes families (McHale et al. 2006). bti.cornell.edu/cgi-bin/kiwi/download.cgi). The amino acid NBS-encoding genes are categorized as NBS-only genes sequence of NB-ARC domain was downloaded from Pfam and NBS–LRR genes. Based on an N-terminal domain of database (http://pfam.xfam.org/) by using Pfam ID (PF00931), toll and interleukin-1 receptors (TIR) NBS-encoding genes which was employed as a query in BLASTP searches, with are divided into two subclasses, TIR type genes and non- the threshold expectation set to one, for searching candidate TIR type genes. Some nonTIR NBS-encoding genes have NBS-encoding genes in kiwi fruit. Further, all hits were ver- a coil–coil motif in N-terminus (Dangl and Jones 2001), ified for the presence of NB-ARC domain by Pfam ver. 28.0 therefore, they are subdivided into CC-NBS genes (CNs), (http://pfam.xfam.org/). All NBS-encoding genes were fur- X-NBS genes (XNs), CC-NBS–LRR genes (CNLs) and ther analysed to detect the LRR, TIR and RPW8 domain X-NBS–LRR genes (XNLs). by Pfam ver. 28.0 and SMART analysis. The CC domain Recently, the genome of a heterozygous kiwi fruit cultivar was predicted by COILS server (http://www.ch.embnet.org/ ‘Hongyang’ (A. chinensis) was sequenced (616.1 Mb), which software/COILS_form.html) with a threshold of 0.9 (Lupas provides an opportunity for the study of NBS-encoding genes et al. 1991). There were three criteria to classify gene family. Both the coverage (aligned sequence/gene lengths) and iden- tity between sequences were not less than 70%. The stricter ∗ For correspondence. E-mail: [email protected]. criteria were not less than 80 and 90%. Keywords. R genes; NBS-encoding genes; NBS–LRR genes; Actinidia chinensis. Journal of Genetics, DOI 10.1007/s12041-016-0700-8, Vol. 95, No. 4, December 2016 997 Yingjun Li et al. Sequence alignment and phylogenetic analysis Table 1. Number of identified NBS-encoding genes in kiwi fruit. The NB-ARC domain sequences of 96 NBS-encoding genes Predicted protein domain Letter code A. chinensis were aligned by using MUSCLE program in MEGA 5.0 (Tamura et al. 2011). The phylogenetic tree was constructed NBS-encoding genes 96 based on the neighbour-joining (NJ) method with the default NBS–LRR type 74 options and 1000 bootstraps by ClustalW 2.0 (Larkin et al. TIR-NBS–LRR TNL 9 nonTIR-NBS–LRR non-TNL 65 2007). CC-NBS–LRR CNL 17 X-NBS–LRR XNL 48 Calculation of Ks and Ka/Ks NBS 22 TIR-NBS TN 2 The ratios of nonsynonymous substitution (Ka) to synony- nonTIR-NBS non-TN 20 mous substitution (Ks) were computed in the gene fami- CC-NBS CN 3 lies and divided according to the criterion of the coverage X-NBS XN 17 and the identity between sequences not less than 70%. The Whole genome genes 39040 Proportion of NBS-encoding genes 0.246% nucleotide coding sequences (CDSs) in each gene family Proportion of NBS–LRR genes 0.190% were aligned by ClustalW 2.0 and the values of Ka, Ks and Proportion of TIR-NBS–LRR genes 0.023% Ka/Ks were calculated by MEGA ver. 5.0. Proportion of nonTIR-NBS–LRR genes 0.166% Average exon of all genes 4.63 Average exon of TIR-NBS–LRR 3.33 Test for positive pressures Average exon of nonTIR-NBS–LRR 2.34 The phylogenetic analysis by maximum likehood 4 (PAML4) Average exon of CC-NBS–LRR 2.24 Average exon of NBS-encoding genes 2.35 package was used to test selection pressures on NBS- Average exon of NBS–LRR genes 2.46 encoding genes in gene families with three or more mem- bers using the site model and branch model (Yang 2007). For the site model, one single dN/dS ratio (model = 0) and models M7 (beta) and M8 (beta-ω) (NS site = 7, 8) were of it, which may be the reason that the number of NBS- set to identify the positive selection sites. Moreover, the LR encoding genes was larger in papaya and cucumber genomes test between model M7 and M8 was performed by the criti- (Huang et al. 2009). cal criterion of chi-square 5.991 (P < 0.05, df = 2) and 9.210 The average number of exons of NBS-encoding genes and (P < 0.01, df = 2), respectively. For the branch model, one NBS–LRR genes were 2.35 and 2.46, respectively which single dN/dS ratio (model = 0) and models 0 (NS site = 0) were less than the average number of whole-genome pre- were used to detect the dN/dS in gene families. dicted genes (4.63) (table 1). The phenomenon was also observed in other species, such as Arabidopsis, rice, poplar Results and discussion and strawberry. Identification of NBS-encodings in kiwi fruit Recent duplications of NBS-encoding genes were detected in the kiwi fruit genome We compared our results with the NBS-encoding genes identified in Huang et al.’s (2013), two sequences (Achn Gene duplication provides new genes for different mecha- 047351 and Achn 064331) were found as the same gene, and nisms of evolution and creates genetic novelty in organisms Achn 088471 was also detected encoding NB-ARC domain, (Magadum et al. 2013). We divided 96 NBS-encoding genes which were not in Huang’s results. As a result, 96 NBS- into gene families with three criteria to detect the duplica- encoding genes were identified containing 74 NBS–LRR tion events. For the criterion of 70%, 50% of NBS-encoding genes (table 1), which were more than that in papaya (36) genes (48) were classified into 13 multigene families, which (Ming et al. 2008), and cucumber (52) (Wan et al. 2013), suggested that half of the NBS-encoding genes could be but less in strawberry (144) (Zhong et al. 2015), and Ara- detected under duplication events. Moreover, the average bidopsis (147) (Meyers et al. 2003). Further, the propor- number of each family was significantly greater than that in tions of NBS–LRR genes in whole genome genes in papaya Arabidopsis (t-test, P < 0.01), and smaller than that in straw- (0.145%), cucumber (0.0821%), strawberry (0.439%) and berry (t-test, P < 0.01). To detect more recent duplication, we Arabidopsis (0.544%), were 0.76-, 0.33-, 1.78- and 2.86- applied the criteria of 80%. As a result, there are 40 NBS- fold to that of kiwi fruit (0.246%), which indicated that encoding genes (41.67%) belonging to 13 multigene families the number of NBS–LRR genes did not evolve proportion- and the proportion of NBS-encoding genes was significantly ally with the genome. Further, a relatively fewer number of larger than that of Arabidopsis (t-test, P < 0.01). When the third NBS–LRR disease-resistant genes in kiwi fruit, ‘Hongyang’ criterion of 90% was applied, the proportion of multigenes may be related to its disease susceptibility. In addition, kiwi (21.88%) in all NBS-encoding genes reduced significantly fruit genome underwent the recent whole-genome duplica- (t-test, P < 0.01).
Recommended publications
  • A High-Quality Actinidia Chinensis (Kiwifruit) Genome Haolin Wu1,Taoma1,Minghuikang1,Fandiai1, Junlin Zhang1, Guanyong Dong2 and Jianquan Liu1,3
    Wu et al. Horticulture Research (2019) 6:117 Horticulture Research https://doi.org/10.1038/s41438-019-0202-y www.nature.com/hortres ARTICLE Open Access A high-quality Actinidia chinensis (kiwifruit) genome Haolin Wu1,TaoMa1,MinghuiKang1,FandiAi1, Junlin Zhang1, Guanyong Dong2 and Jianquan Liu1,3 Abstract Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Two versions of the A. chinensis genomes have been previously assembled, based mainly on relatively short reads. Here, we report an improved chromosome-level reference genome of A. chinensis (v3.0), based mainly on PacBio long reads and Hi-C data. The high-quality assembled genome is 653 Mb long, with 0.76% heterozygosity. At least 43% of the genome consists of repetitive sequences, and the most abundant long terminal repeats were further identified and account for 23.38% of our novel genome. It has clear improvements in contiguity, accuracy, and gene annotation over the two previous versions and contains 40,464 annotated protein-coding genes, of which 94.41% are functionally annotated. Moreover, further analyses of genetic collinearity revealed that the kiwifruit genome has undergone two whole-genome duplications: one affecting all Ericales families near the K-T extinction event and a recent genus-specific duplication. The reference genome presented here will be highly useful for further molecular elucidation of diverse traits and for the breeding of this horticultural crop, as well as evolutionary studies with related taxa. Introduction require improvement because of difficulties in assembling “ ” 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Kiwifruit (known as the king of fruits because of its the short reads into long contigs and scaffolds.
    [Show full text]
  • ACTINIDIACEAE 1. ACTINIDIA Lindley, Nat. Syst. Bot., Ed. 2, 439
    ACTINIDIACEAE 猕猴桃科 mi hou tao ke Li Jianqiang (李建强)1, Li Xinwei (李新伟)1; Djaja Djendoel Soejarto2 Trees, shrubs, or woody vines. Leaves alternate, simple, shortly or long petiolate, not stipulate. Flowers bisexual or unisexual or plants polygamous or functionally dioecious, usually fascicled, cymose, or paniculate. Sepals (2 or 3 or)5, imbricate, rarely valvate. Petals (4 or)5, sometimes more, imbricate. Stamens 10 to numerous, distinct or adnate to base of petals, hypogynous; anthers 2- celled, versatile, dehiscing by apical pores or longitudinally. Ovary superior, disk absent, locules and carpels 3–5 or more; placentation axile; ovules anatropous with a single integument, 10 or more per locule; styles as many as carpels, distinct or connate (then only one style), generally persistent. Fruit a berry or leathery capsule. Seeds not arillate, with usually large embryos and abundant endosperm. Three genera and ca. 357 species: Asia and the Americas; three genera (one endemic) and 66 species (52 endemic) in China. Economically, kiwifruit (Actinidia chinensis var. deliciosa) is an important fruit, which originated in central China and is especially common along the Yangtze River (well known as yang-tao). Now, it is widely cultivated throughout the world. For additional information see the paper by X. W. Li, J. Q. Li, and D. D. Soejarto (Acta Phytotax. Sin. 45: 633–660. 2007). Liang Chou-fen, Chen Yong-chang & Wang Yu-sheng. 1984. Actinidiaceae (excluding Sladenia). In: Feng Kuo-mei, ed., Fl. Reipubl. Popularis Sin. 49(2): 195–301, 309–334. 1a. Trees or shrubs; flowers bisexual or plants functionally dioecious .................................................................................. 3. Saurauia 1b.
    [Show full text]
  • De Novo Transcriptome Sequencing in Kiwifruit (Actinidia Chinensis Var
    agronomy Article De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources Juan Alfonso Salazar 1,* , Cristian Vergara-Pulgar 2,3, Claudia Jorquera 4, Patricio Zapata 4 , David Ruiz 1, Pedro Martínez-Gómez 1 , Rodrigo Infante 4 and Claudio Meneses 2,3 1 Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, E-30100 Murcia, Espinardo, Spain; [email protected] (D.R.); [email protected] (P.M.-G.) 2 Centro de Biotecnología Vegetal, Facultad Ciencias Biológicas, Universidad Andrés Bello, República 217, Santiago 8370146, Chile; [email protected] (C.V.-P.); [email protected] (C.M.) 3 FONDAP Center for Genome Regulation, República 217, Santiago 8370371, Chile 4 Departamento de Producción Agrícola, Universidad de Chile, Santiago 8820000, Chile; [email protected] (C.J.); [email protected] (P.Z.); [email protected] (R.I.) * Correspondence: [email protected] Abstract: Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently, only a small body of transcriptomic and proteomic Citation: Salazar, J.A.; data are available for A. chinensis var. deliciosa. In this low molecular knowledge context, the Vergara-Pulgar, C.; Jorquera, C.; main goal of this study is to construct a tissue-specific de novo transcriptome assembly, generating Zapata, P.; Ruiz, D.; Martínez-Gómez, differential expression analysis among these specific tissues, to obtain new useful transcriptomic P.; Infante, R.; Meneses, C.
    [Show full text]
  • A New Crop for California: Kiwifruit
    Studies show that kiwifruit can be successfully canned, but that frozen, sliced kiwifruits are closest to freshfruit in appearance and flavor. James A. Beutel Frank H. Winter Spencer C. Manners Martin W. Miller he kiwifruit (Actinidia chinensis Considerable kiwifruit acreage was California could produce 3,000 to T Planch), a native of south central not covered by this survey. It is presently 4,000 tons of fruit by 1980, compared to China, grows on a large, woody, decidu- estimated that more than 1,200 acres the 6,000 tons now being produced in ous vine. In 1906 it was introduced into have already been planted in small com- New Zealand. Full-bearing, 10-year-old New Zealand under the name of “Chinese mercial lots of 2 to 25 acres from Chico kiwifruit vineyards produce 4 to 7 tons gooseberry,” and during the next quarter south to San Diego; however, about per acre. century New Zealand nurserymen 100 acres are bearing (4 years and older). Kiwifruit vines are planted in rows selected large-fruited seedlings, which The 1975 kiwifruit production was only 15 feet apart. Vines are spaced 18 to became commercial varieties. When New 120 tons, but acreage already planted in 20 feet apart in the rows and are trained Zealand first began to export the fruits commercially in 1953, the name was changed to “kiwi,” because the fruits A new crop for superficially resemble New Zealand’s native bird, the kiwi. In 1935 the U.S. Plant Introduction California: Station at Chico, California, received plants of a large-fruited variety from a New Zealand grower of Chinese goose- berries.
    [Show full text]
  • Kiwifruit, a Botany, Chemical and Sensory Approach a Review
    Advances in Plants & Agriculture Research Review Article Open Access Kiwifruit, a botany, chemical and sensory approach a review Abstract Volume 8 Issue 6 - 2018 The kiwi is a fruit with a great agricultural, botanical, and economic interest. Teresa Pinto, Alice Vilela Originally from China, this species is currently widespread in practically all the Department of Biology and Environment, University of Trás-os- world, due to the high nutritional value of the fruits, excellent organoleptic qualities Montes and Alto Douro, Portugal besides therapeutic benefits in the health. The most common kiwifruit species grown commercially is Actinidia deliciosa even though many varieties of this fruit are Correspondence: T Pinto, University of Trás-os-Montes and produced by other cultivars or by another kind of plants, such as Actinidia chinensis Alto Douro, Biology and Environment Department, Centre and the Actinidia kolomikta or the Actinidia argute. Although there are many varieties for the Research and Technology of Agro-Environmental and in this species, the A. deliciosa Hayward cultivar is the most popular variety marketed Biological Sciences (CITAB), 5001 801 Vila Real, Portugal, commercially. Kiwifruits contain aromatic compounds able to attract consumers due Email to their palatability. The esters, ethyl butanoate and methyl benzoate and the aldehyde E-2-hexenal, were shown to increase “characteristic kiwifruit aroma and flavor”. All Received: July 04, 2018 | Published: November 17, 2018 these characteristics are appreciated by the kiwi-consumers. Several preservation techniques have now been used to augment kiwi shelf life, including cold storage, chemical dipping, modified atmosphere packaging and edible coatings, making it possible for the consumers to enjoin the fruit all the year.
    [Show full text]
  • Draft Genome of the Kiwifruit Actinidia Chinensis
    ARTICLE Received 29 May 2013 | Accepted 19 Sep 2013 | Published 18 Oct 2013 DOI: 10.1038/ncomms3640 OPEN Draft genome of the kiwifruit Actinidia chinensis Shengxiong Huang1,2, Jian Ding3, Dejing Deng4, Wei Tang2, Honghe Sun5, Dongyuan Liu4, Lei Zhang6, Xiangli Niu1, Xia Zhang2, Meng Meng2, Jinde Yu2, Jia Liu1, Yi Han1, Wei Shi1, Danfeng Zhang1, Shuqing Cao1, Zhaojun Wei1, Yongliang Cui3, Yanhua Xia4, Huaping Zeng4, Kan Bao5, Lin Lin2, Ya Min2, Hua Zhang1, Min Miao1,2, Xiaofeng Tang1,2, Yunye Zhu1, Yuan Sui1, Guangwei Li1, Hanju Sun1, Junyang Yue1, Jiaqi Sun2, Fangfang Liu2, Liangqiang Zhou3, Lin Lei3, Xiaoqin Zheng3, Ming Liu4, Long Huang4, Jun Song4, Chunhua Xu4, Jiewei Li7, Kaiyu Ye7, Silin Zhong5,8, Bao-Rong Lu9, Guanghua He10, Fangming Xiao11, Hui-Li Wang1, Hongkun Zheng4, Zhangjun Fei5,12 & Yongsheng Liu1,2 The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Here we report the draft genome sequence of a heterozygous kiwifruit, assembled from B140-fold next-generation sequencing data. The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (g) shared by core eudicots and two more recent whole-genome duplication events. Both recent duplication events occurred after the divergence of kiwifruit from tomato and potato and have contributed to the neofunctionalization of genes involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism. As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage.
    [Show full text]
  • Plant Collecting on Wudang Shan
    Plant on Shan Collecting Wudang , Peter Del Tredici, Paul Meyer, Hao Riming, Mao Cailiang, " Kevin Conrad, and R. William Thomas . American and Chinese botanists describe the locales and vegetation encountered during a few key days of their expedition to China’s Northern Hubei Province. From September 4 to October 11, 1994, repre- north as Wudang Shan. He did, however, visit sentatives from four botanical gardens in the the town of Fang Xian, about fifty kilometers to United States, together with botanists from the southwest. * The first systematic study of the Nanjing Botanical Garden, participated the flora of Wudang Shan was done in 1980 by a in a collecting expedition on Wudang Shan team of botanists from Wuhan University, who (shan=mountain) in Northern Hubei Province, made extensive herbarium collections. In the China. The American participants were from spring of 1983, the British plant collector Roy member institutions of the North American- Lancaster visited the region with a group of China Plant Exploration Consortium (NACPEC),), tourists, making him the first Western botanist a group established in 1991 to facilitate the ex- to explore the mountain (Lancaster, 1983, 1989).). change of both plant germplasm and scientific Wudang Shan is famous throughout China as information between Chinese and North an important center of Ming Dynasty Taoism. American botanical institutions. Over five hundred years ago, about three hun- Paul Meyer, director of the Morris Arbore- dred thousand workers were employed on the tum, led the expedition. He was joined by Kevin mountain building some forty-six temples, Conrad from the U.S. National Arboretum, seventy-two shrines, thirty-nine bridges, and Peter Del Tredici from the Arnold Arboretum, twelve pavilions, many of which are still stand- and Bill Thomas from Longwood Gardens.
    [Show full text]
  • JOURNAL of the AMERICAN HORTICULTURAL SOCIETY, INC, A.Pril 1966 AMERICAN HORTICULTURAL SOCIETY
    'I'IIE A.:M:ERICAN ~GAZINE JOURNAL OF THE AMERICAN HORTICULTURAL SOCIETY, INC, A.pril 1966 AMERICAN HORTICULTURAL SOCIETY 1600 BLADENSBURG ROAD, NORTHEAST / WASHINGTON, D. c. 20002 For United Horticulture *** to accumu.late, inn-ease, and disseminate horticultuml information Editorial Committee Directors FRANCIS DE VOS, Chainnan Terms ExpiTing 1966 J. HAROLD CLARKE JOHN L . CREECH Washington f 'REDERIC P. LEE W. H . HODGE Maryland CARLTON P. LEES FREDERIC P. LEE Massachusetts RUSSELL J. SEIBERT CONRAD B. LINK Pennsylvania DONALD'VATSON FREDER ICK G. MEYER Hawaii "VII.BUR H. YOUNGMAN T erms Expi?'ing 1967 MRS. ROBERT L. EMERY, J R. Louisiana Officers A. C. HILDRETH Colorado PRESIDENT DAVID LEACH JOHN H . WALKER Pennsylvania A lexandria, Virginia CHARLES G. MEYER New Yo rk MRS. STANLEY ROWE F IRST VI CE- PRESIDENT Ohio FRED C. GALLE Terms ExjJiring 1968 Pine Mountain, Geo?-gia FRANCIS DE VOS Maryland SECOND VICE-PRESIDENT MRS. ELSA U. K NO LL TOM D. THROCKMORTON California Des Moines, Io wa VICTOR RIES Ohio STEWART D . VVI NN ACTING SECRETARY-TREASURER GRACE P. WILSON ROBERT WINTZ Bladensburg, Maryland Illinois The A merican Horticultural Magazine is the official publication of the American Horticultural Society and is issued four times a year during the quarters commencing with January, April, J!lly and October. It is devoted to the dissemination of knowledge in the science and art of growmg ornamental plants, fruits, vegetables, and related subjects. Original papers increasing the historical, varietal, and cultural knowledges of plant mate~ials of economic and aesthetic importance are welcomed and will be published as early as pOSSible.
    [Show full text]
  • An Actinidia Chinensis (Kiwifruit) Efp Browser and Network Analysis of Transcription Factors
    An Actinidia chinensis (kiwifruit) eFP browser and network analysis of transcription factors Lara Brian Plant and Food Research Ltd: New Zealand Institute for Plant and Food Research Ltd Ben Warren Plant and Food Research Ltd: New Zealand Institute for Plant and Food Research Ltd Peter McAtee Plant and Food Research Ltd: New Zealand Institute for Plant and Food Research Ltd Jessica Rodrigues Plant and Food Research Ltd: New Zealand Institute for Plant and Food Research Ltd Niels Nieuwenhuizen Plant and Food Research Ltd: New Zealand Institute for Plant and Food Research Ltd Karine M. David School of biological sciences: The University of Auckland Annette Richardson Plant and Food Research Ltd: New Zealand Institute for Plant and Food Research Ltd Andrew C. Allan Plant and Food Research Ltd: New Zealand Institute for Plant and Food Research Ltd Erika Varkonyi-Gasic Plant and Food Research Ltd: New Zealand Institute for Plant and Food Research Ltd Robert J Schaffer ( [email protected] ) Plant and Food Research Ltd https://orcid.org/0000-0003-1272-667X Research article Keywords: Actinidia, eFP Browser, Transcription factors Posted Date: November 10th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-101514/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/21 Version of Record: A version of this preprint was published on February 27th, 2021. See the published version at https://doi.org/10.1186/s12870-021-02894-x. Page 2/21 Abstract Background Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes.
    [Show full text]
  • Agrobiodiversity Hotspots in India: Conservation and Benefit Sharing Volume II
    Agrobiodiversity Hotspots in India: Conservation and Benefit Sharing Volume II M.P. Nayar, A.K. Singh, K.Narayanan Nair Protection of Plant Varieties and Farmers’ Rights Authority Government of India New Delhi Agrobiodiversity Hotspots in India: Conservation and Benefit Sharing Volume II © PPV & FR Authority, 2009 Final Report of the Task Force 06/2007 constituted by the PPV & FRA, vide OM No. PPV & FRA/6-22/07/1312, dated October, 08, 2007 to identify the Agrobiodiversity hotspots in India for purposes of the 'National Gene Fund' usage. Published by: PPV & FR Authority, NASC Complex, D.P.S. Marg, New Delhi-110012 ISBN-978-81-908786-0-9 ISBN-978-81-908786-2-3 Citation: Nayar M.P., Singh A.K. and Nair, K.N. 2009. Agrobiodiversity Hotspots in India : Conservation and Benefit Sharing, Vol. II, i-xii+ total pages 309 Photo credits: Dr. D. C. Bhandari, Dr. D. K. Hore, Dr. K. Narayanan Nair, Dr. M. P. Nayar, Dr. M. Sabu, Dr. M. Sanjappa, Dr. S. K. Sharma, Dr. D. K. Singh. Dr. S. R. Yadav, Dr. S. Maiti. Reviewing Scientists: Dr. Bhag Mal, Honorary Fellow, Bioversity International- India, New Delhi Dr. R. S. Rana, Former Director, National Bureau of Plant Genetic Resources, New Delhi Cover page photographs (clockwise from top left) : l Pepper (Piper longum)- endemic to Malabar Agrobiodiversity Region l Karonda (Carissa carandas)- an important minor fruit l The blue Star Lily (Nymphea nouchali)- widely found in water bodies l Brinjal (Lycopersicon esculentum)- local variety grown in NE India l Farmers harvesting Bach (Acorus calamus)-an important medicinal plant.
    [Show full text]
  • Cold Hardiness Within the Genus Actinidia
    HORTSCIENCE 30(2):329–332. 1995. intermittent mist (Roche, 1983). Cuttings were transplanted and grown in a plastic green- house until May 1991. In winter, all cuttings Cold Hardiness within the Genus were replanted into 5-liter pots containing 3 leaf-mold : 1 peat : 1 sand (by volume) and cut Actinidia back to 20 cm above ground level. In May 1991, vines were transferred to an outdoor site Joëlle Chat for natural cold acclimation until they were Institut National de la Recherche Agronomique, Station de Recherches tested. The pots were watered daily and fertil- ized from May to July 1991 with 15N–15P– Fruitières, B.P. 81, 33883 Villenave D’Ornon Cedex, France 15K for a total application rate of 30 g/pot. Additional index words. Actinidia arguta, Actinidia deliciosa, Actinidia kolomikta, Actinidia Freezing tests. Two tests were carried out polygama, artificial freezing test, freezing tolerance, kiwifruit with a 3-day interval on 19 and 22 Feb. 1992. The first test involved A. deliciosa, the second Abstract. Two-year-old Actinidia vines, grown on their own roots, were subjected to involved the other species. All vines were artificial freezing tests in midwinter to determine their relative hardiness. Plant survival, subjected to the same temperature regime. growth recovery, and stem necrosis were used for estimating freezing injury. Actinidia One clone of a female A. arguta and ‘Hayward’ deliciosa (A. Chev.) C.F. Liang & A.R. Ferguson var. deliciosa vines, which included were used as reference genotypes in each test. ‘Abbott’, ‘Bruno’, ‘Greensill’, ‘Hayward’, and ‘Jones’ kiwifruit, were all severely dam- In addition, two vines per genotype, not sub- aged by exposure to a temperature of –18C for 4 hours.
    [Show full text]
  • Invasive Hardy Kiwi
    AN EMERGING INVASIVE IN THE NORTHEASTERN UNITED STATES INVASIVE HARDY KIWI BOWERBERRY, TARA VINE, CHINESE GOOSEBERRY Actinidia arguta Compiled by Berkshire Environmental Action Team (BEAT) with Elizabeth Orenstein, Monica Conlin, and Lisa Levine TO ORDER COPIES OF THIS GUIDE contact BEAT at [email protected] or (413) 230-7321 This publication is supported, in part, with funding from the Northeastern IPM Center (NortheastIPM.org) and the USDA National Institute of Food and Agriculture. The Northeastern Integrated Pest Management Center fosters the development and adoption of IPM, a science-based approach to managing pests in ways that generate economic, environmental, and human health benefits. The Center works in partnership with stakeholders from agricultural, urban, and rural settings to identify and address regional priorities for research, education, and outreach. BEAT would like to thank Jane Winn, Elizabeth Orenstein, Monica Conlin, and Lisa Levine for their work on this project. © Berkshire Environmental Action Team Printed by QualPrint; 50; 2/2019 AN EMERGING INVASIVE IN THE NORTHEASTERN UNITED STATES INVASIVE HARDY KIWI BOWERBERRY, TARA VINE, CHINESE GOOSEBERRY Actinidia arguta WHAT IS HARDY KIWI? The genus Actinidia is well known for producing the delicious green fruit common to fruit salads. There are approximately 80 species of Actinidia in the world, with some grown for their berries and others prized for their ornamental vines. The most popular varieties are commercial kiwi, Actinidia deliciosa, the green kiwi, and Actinidia chinensis, yellow kiwi (Hoover, 2015 and Tiyayon, 2001). While Actinidia originates in eastern Asia, the kiwifruit's common name comes from New Zealand's flightless bird. Farmers of that country commercialized the fruit in the 1950s trying to make it synonymous with the South Pacific.
    [Show full text]