DOCSLIB.ORG

Triticeae Resources in Ensembl Plants Pca Niecollection Online Special Dan M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Triticeae Resources in Ensembl Plants Pca Niecollection Online Special Dan M Triticeae Resources in Ensembl Plants Special Online Collection Dan M. Bolser, Arnaud Kerhornou, Brandon Walts and Paul Kersey* Ensembl Genomes, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK *Corresponding author: E-mail, [email protected]; Fax, +44 223 494 468. (Received September 22, 2014; Accepted November 12, 2014) Recent developments in DNA sequencing have enabled the Introduction large and complex genomes of many crop species to be determined for the first time, even those previously intract- The first cereal genome sequenced was rice in 2002 (Goff et al. able due to their polyploid nature. Indeed, over the course of 2002, Yu et al. 2002). More recently, progress has accelerated the last 2 years, the genome sequences of several commer- with the publication of the genome sequence of maize in 2009 cially important cereals, notably barley and bread wheat, (Schnable et al. 2009), barley in 2012 (International Barley have become available, as well as those of related wild spe- Sequencing Consortium 2012), progenitors of the bread cies. While still incomplete, comparison with other, more wheat A and D genomes in 2013 (Jia et al. 2013, Ling et al. completely assembled species suggests that coverage of 2013) and the draft bread wheat genome itself in 2014 genic regions is likely to be high. Ensembl Plants (http:// (Brenchley et al. 2012, International Wheat Genome – Database Paper plants.ensembl.org) is an integrative resource organizing, Sequencing Consortium 2014). These four cereals, barley, analyzing and visualizing genome-scale information for im- maize, rice and wheat, together account for 30% of global portant crop and model plants. Available data include ref- food production or 2.4 out of 3.8 billion tonnes annually. erence genome sequence, variant loci, gene models and It is important to note that the current reference genome functional annotation. For variant loci, individual and popu- assemblies vary considerably in their contiguity and in the detail lation genotypes, linkage information and, where available, of available functional annotation. The Triticeae genomes phenotypic information are shown. Comparative analyses were all sequenced primarily using short read sequencing are performed on DNA and protein sequence alignments. (mainly from the Illumina platform), and the completion of The resulting genome alignments and gene trees, represent- these assemblies remains a scientific challenge, due to ing the implied evolutionary history of the gene family, are their large size and repetitive nature. The improvement of made available for visualization and analysis. Driven by the sequencing technologies, particularly those capable of captur- case of bread wheat, specific extensions to the analysis pipe- ing long-range information, will be necessary to achieve lines and web interface have recently been developed to this goal. However, even in their existing condition, these re- support polyploid genomes. Data in Ensembl Plants is ac- sources are already sufficiently complete to be usefully repre- cessible through a genome browser incorporating various sented through data analysis and visualization platforms specialist interfaces for different data types, and through a designed for genomes with finished assemblies, such as variety of additional methods for programmatic access and Ensembl Plants. data mining. These interfaces are consistent with those Ensembl Plants (http://plants.ensembl.org) offers integrative offered through the Ensembl interface for the genomes of access to a wide range of genome-scale data from plant species non-plant species, including those of plant pathogens, pests (Kersey et al. 2014), using the Ensembl software infrastructure and pollinators, facilitating the study of the plant in its (Flicek et al. 2014). Currently, the site includes data from 38 environment. plant genomes, from algae to flowering plants. Genomes are selected for inclusion in the resource based on the availability of Keywords: Comparative genomics Functional genomics the complete genome sequence, their importance as model Editor-in-Chief’s Choice Genetic variation Genome browser Transcriptomics organisms (e.g. Arabidopsis thaliana, Brachypodium distach- Triticeae. yon), their importance in agriculture (e.g. potato, tomato, vari- Abbreviations: API, Application Programming Interface; EST, ous cereals and Brassicaceae) or because of their interest as expressed sequence tag; FTP, File Transfer Protocol; GO, gene evolutionary reference points (e.g the basal angiosperm, ontology; IEA, Inferred by Electronic Annotation; MIPS, Amborella trichopoda, the aquatic alga Chlamydomonas rein- Helmholtz Zentrum Mu¨nchen; POPSEQ, POPulation hardtii, the moss Physcomitrella patens and the vascular non- SEQuencing; QTL, quantitative trait locus; REST, seed spikemoss Selaginella moellendorffii). In total, the resource REpresentational State Transfer; RNA-Seq, RNA sequencing; contains the genomes of 19 true grasses, Musa accuminata SNP, single nucleotide polymorphism; SQL, structured query (banana), 12 dicots and six other species that provide evolu- language; TREP, Triticeae Repeat Sequence Database. tionary context for the plant lineage. Plant Cell Physiol. 56(1): e3(1–11) (2015) doi:10.1093/pcp/pcu183, Advance Access publication on 27 November 2014, available FREE online at www.pcp.oxfordjournals.org ! The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. D. M. Bolser et al. | Triticeae resources in Ensembl plants All species in the resource have data for genome sequence, databases optimized to support the efficient performance of annotations of protein-coding and non-coding genes, and common gene- and variant-centric queries, and can be accessed gene-centric comparative analysis. Additional data types through their own web-based and programmatic interfaces. within the resource include gene expression, sequence poly- morphism and whole-genome alignments, which are selectively Triticeae genomes in Ensembl Plants available for different species. In this sense, Ensembl Plants is Four Triticeae genomes are currently hosted in Ensembl Plants similar to comparable, species-, clade- or data type-specific re- (Table 1): Hordeum vulgare (barley), Triticum aestivum (bread sources such as WheatGenome.info (Lai et al. 2012), HapRice wheat, also known as common wheat) and the genomes of two (Yonemaru et al. 2014) or ATTED-II (Obayashi et al. 2014). of bread wheat’s diploid progenitors: Triticum urartu (the A- Ensembl Plants is released 4–5 times a year, in synchrony genome progenitor) and Aegilops tauschii (the D-genome pro- with releases of other genomes (from animals, fungi, protists genitor). In addition, a further three wheat transcriptomes were and bacteria) in the Ensembl system. The provision of common included by alignment (described below). interfaces allows access to genomic data from across the tree of Barley is the world’s fourth most important cereal crop and life in a consistent manner, including data from plant patho- an important model for ecological adaptation, having been gens, pests and pollinators. cultivated in all temperate regions from the Arctic Circle to the tropics. It was one of the first domesticated cereal grains, originating in the Fertile Crescent of south-west Asia/north- Database east Africa >10,000 years ago (Harlan and Zohary 1966). With a haploid genome size of approximately 5.3 Gbp in The Ensembl genome browser seven chromosomes, the barley genome is among the largest Interactive access to Ensembl Plants is provided through an yet sequenced. However, as a diploid, it is a natural model for advanced genome browser. The browser allows users to visual- the genetics and genomics of the polyploid members of the ize a graphical representation of a completely assembled Triticeae tribe, including wheat and rye. chromosome sequence or a contiguous sequence assembly The current barley genome assembly (cv. Morex) was pro- comprising only a small portion of a molecule at various duced by the International Barley Genome Sequencing levels of resolution. Functionally interesting ‘features’ are de- Consortium (2012). The assembly is highly fragmented, but picted on the sequence with defined locations. Features include comparison with related grass species suggested that coverage conceptual annotations such as genes and variant loci, se- of the gene space was good. The assembly was dubbed a ‘gene- quence patterns such as repeats, and experimental data such ome’, a near complete gene set integrated into a chromosome- as sequence features mapped onto the genome, which often scale assembly using physical and genetic information. provide direct support for the annotations (Fig. 1). Functional Sequence contigs that could not be assigned chromosomal information is provided through import of manual annotation positions in this way were binned by homology to low-coverage from the UniProt Knowledgebase (Uniprot Consortium 2014), shotgun sequence of flow-sorted chromosome arms (Mun˜oz- imputation from protein sequence using the classification tool Amatriaı´n et al. 2011). This method integrated 22% of the total InterProScan (Jones et al. 2014), or by projection from orthologs assembled
Load more

Recommended publications
  • Analysing Complex Triticeae Genomes – Concepts and Strategies Manuel Spannagl*, Mihaela M Martis, Matthias Pfeifer, Thomas Nussbaumer and Klaus FX Mayer*
    Spannagl et al. Plant Methods 2013, 9:35 http://www.plantmethods.com/content/9/1/35 PLANT METHODS REVIEW Open Access Analysing complex Triticeae genomes – concepts and strategies Manuel Spannagl*, Mihaela M Martis, Matthias Pfeifer, Thomas Nussbaumer and Klaus FX Mayer* Abstract The genomic sequences of many important Triticeae crop species are hard to assemble and analyse due to their large genome sizes, (in part) polyploid genomes and high repeat content. Recently, the draft genomes of barley and bread wheat were reported thanks to cost-efficient and fast NGS technologies. The genome of barley is estimated to be 5 Gb in size whereas the genome of bread wheat accounts for 17 Gb and harbours an allo-hexaploid genome. Direct assembly of the sequence reads and access to the gene content is hampered by the repeat content. As a consequence, novel strategies and data analysis concepts had to be developed to provide much-needed whole genome sequence surveys and access to the gene repertoires. Here we describe some analytical strategies that now enable structuring of massive NGS data generated and pave the way towards structured and ordered sequence data and gene order. Specifically we report on the GenomeZipper, a synteny driven approach to order and structure NGS survey sequences of grass genomes that lack a physical map. In addition, to access and analyse the gene repertoire of allo-hexaploid bread wheat from the raw sequence reads, a reference-guided approach was developed utilizing representative genes from rice, Brachypodium distachyon, sorghum and barley. Stringent sub-assembly on the reference genes prevented collapsing of homeologous wheat genes and allowed to estimate gene retention rate and determine gene family sizes.
    [Show full text]
  • Evolutionary Divergence and Biased Expression Ofnac Transcription
    plants Article Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat (Triticum aestivum L.) Jianhui Ma 1,†, Meng Yuan 1,†, Bo Sun 1, Daijing Zhang 1, Jie Zhang 2,3, Chunxi Li 1, Yun Shao 1, Wei Liu 2,* and Lina Jiang 1,* 1 College of Life Science, Henan Normal University, Xinxiang 453007, China; [email protected] (J.M.); [email protected] (M.Y.); [email protected] (B.S.); [email protected] (D.Z.); [email protected] (C.L.); [email protected] (Y.S.) 2 Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China; [email protected] 3 School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China * Correspondence: [email protected] (W.L.); [email protected] (L.J.) † These authors contributed equally to this work. Abstract: The NAC genes, a large plant-specific family of transcription factors, regulate a wide range of pathways involved in development and response to biotic and abiotic stress. In this study, the NAC transcription factors were identified in 27 green plants, and the results showed that NAC transcription factors in plants undergo an appearance stage from water to land and a number expansion stage from gymnosperm to angiosperm. Investigating the evolutionary process of the NAC transcription factors from diploid species to hexaploid wheat revealed that tandem replications during the polyploidiza- Citation: Ma, J.; Yuan, M.; Sun, B.; tion process is an important event for increasing the number of NAC transcription factors in wheat. Zhang, D.; Zhang, J.; Li, C.; Shao, Y.; Then, the molecular characteristics, phylogenetic relationships, and expression patterns of 462 NAC Liu, W.; Jiang, L.
    [Show full text]
  • WHEAT and WHEAT IMPROVEMENT Second Edition
    5910 * WHEAT AND WHEAT IMPROVEMENT Second Edition E. G. Heyne, editor Editorial Committee E. G. Heyne. chair Dale [\Ioss D. R. Knott Gregory Shaner Rosalind Morris Billy Tucker Managing F:ditors: S. H. Mickdson \V. R. Luellen Editor-in-Chief.iSA Puhlications: D. R. Buxton Editor-in-Chief CSS.·/ Puhlications: E. S. Horner Editor-in-ChiefSS5.i. Puhlications: J. J. Mortvedt Number 13 in the series AGRONOl\1Y American Society of Agronomy, Inc. Crop Science Sodety of America, Inc. Soil Science Society of America, Inc. Publishers Madison, Wisconsin. USA 1987 ·5 Origins and AnaJyses of Genes and Genomes in Wheat and Its Relatives Rosalind l\tlorns A. Evolution in the Genus Triticum and the Origin of Cultivated Wheat G. Kimber and E. R. Sears B. The Molecular Genetics of Wheat: Toward an Understanding of 16 Billion Base Pairs of DNA C. E. May and R. Appels C. Genetic and Biochemical Studies of Enzymes Gary E. Hart D. Genetic and Biochemical Studies of Nonenzymatic Endospenn Proteins Jerold A. Bietz . E: Chromosome Banding Methods. Standard Chromosome Band Nomenclature. and Applications in Cytogenetic Analysis Bikram S. Gill F. Aneuploid Analysis in Tetraploid Wheat L. R. Joppa G. Gene Location and Gene Mapping in Hexaploid Wheat R. A. McIntosh H. Linkage Map of Hexaploid Wheat R. A. McIntosh and Jane E. Cusick 151 Tlheat and Wheat Improvement Second Edition 5910* E. G. Heyne, editor 1987 50 Genetic and Biochemical Studies of Nonenzymatic Endosperm Proteins Jerold A. Bietz USDA-ARS Peoria, Illinois The endosperm ofcommon wheat (Triticum aestivum L.) contains a great number of nonenzymatic storage proteins that are the components of gluten, one of the most intricate naturally occurring protein complexes.
    [Show full text]
  • Genome-Wide Analysis of Wheat Calcium Atpases and Potential Role of Selected Acas and Ecas in Calcium Stress Roohi Aslam1, Lorraine E
    Aslam et al. BMC Plant Biology (2017) 17:174 DOI 10.1186/s12870-017-1112-5 RESEARCH ARTICLE Open Access Genome-wide analysis of wheat calcium ATPases and potential role of selected ACAs and ECAs in calcium stress Roohi Aslam1, Lorraine E. Williams2, Muhammad Faraz Bhatti1 and Nasar Virk1* Abstract Background: P2- type calcium ATPases (ACAs-auto inhibited calcium ATPases and ECAs-endoplasmic reticulum calcium ATPases) belong to the P- type ATPase family of active membrane transporters and are significantly involved in maintaining accurate levels of Ca2+,Mn2+ and Zn2+ in the cytosol as well as playing a very important role in stress signaling, stomatal opening and closing and pollen tube growth. Here we report the identification and possible role of some of these ATPases from wheat. Results: In this study, ACA and ECA sequences of six species (belonging to Poaceae) were retrieved from different databases and a phylogenetic tree was constructed. A high degree of evolutionary relatedness was observed among P2 sequences characterized in this study. Members of the respective groups from different plant species were observed to fall under the same clade. This pattern highlights the common ancestry of P2− type calcium ATPases. Furthermore, qRT-PCR was used to analyse the expression of selected ACAs and ECAs from Triticum aestivum (wheat) under calcium toxicity and calcium deficiency. The data indicated that expression of ECAsis enhanced under calcium stress, suggesting possible roles of these ATPases in calcium homeostasis in wheat. Similarly, the expression of ACAs was significantly different in plants grown under calcium stress as compared to plants grown under control conditions.
    [Show full text]
  • Genome-Wide Identification and Expression Profiling Analysis Of
    International Journal of Molecular Sciences Article Genome-Wide Identification and Expression Profiling Analysis of WOX Family Protein-Encoded Genes in Triticeae Species Lei Shi 1,2, Ke Wang 1, Lipu Du 1, Yuxia Song 2, Huihui Li 1,* and Xingguo Ye 1,3,* 1 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; [email protected] (L.S.); [email protected] (K.W.); [email protected] (L.D.) 2 Key Laboratory of Agricultural Biotechnology of Ningxia, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; [email protected] 3 National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China * Correspondence: [email protected] (H.L.); [email protected] (X.Y.) Abstract: The WOX family is a group of plant-specific transcription factors which regulate plant growth and development, cell division and differentiation. From the available genome sequence databases of nine Triticeae species, 199 putative WOX genes were identified. Most of the identified WOX genes were distributed on the chromosomes of homeologous groups 1 to 5 and originated via the orthologous evolution approach. Parts of WOX genes in Triticum aestivum were confirmed by the specific PCR markers using a set of Triticum. durum-T. aestivum genome D substitution lines. All of these identified WOX proteins could be grouped into three clades, similar to those in rice and Arabidopsis. WOX family members were conserved among these Triticeae plants; all of them contained the HOX DNA-binding homeodomain, and WUS clade members contained the characteristic WUS-box motif, while only WUS and WOX9 contained the EAR motif.
    [Show full text]
  • (Triticum Durum Desf) Variety “Utuba” Performance in Ethiopia
    Research Article Agri Res & Tech: Open Access J Volume 18 Issue 4 - November 2018 Copyright © All rights are reserved by Mekuria Temtme DOI: 10.19080/ARTOAJ.2018.18.556063 Durum wheat (Triticum durum Desf) Variety “Utuba” Performance in Ethiopia Mekuria Temtme*, Wasihun Legese, Shitaye Homa and Asenafi Gemechu Ethiopian Institute of Agricultural Research (EIAR), Ethiopia Submission: September 22, 2018, Published: November 02, 2018 *Corresponding author: Mekuria Temtme, Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit Research Center, P.O. Box 32, Addis Ababa, Ethiopia. Abstract Durum wheat (Triticum durum Desf.) is industrial and a staple food crop of Ethiopians. Produced in most parts of Ethiopia and has existed in Ethiopia for thousand years. Annually, it occupies 500 thousand hectares in the country. However, the national average yield of durum wheat is low 2.2 t ha-1. The use of unimproved local cultivars and biotic and a biotic stresses are partially attributed to the low yield of the crop. Thus, the experiment was designed to develop high yielding, disease resistant and desirable quality improved varieties of durum wheat suitable for diverse agro-ecologies, farming systems and purposes. Eighteen durum wheat genotypes including four standard checks were laid out in randomized complete block design using four replications for two years (2013 and 2014) at eight locations. The combined data analysis across locations and over the years indicated that candidate variety “Utuba” (IDON-MD-2009_off/53/2009) performed better than the four standard checks and other testKeywords: genotypes. Durum Consequently, wheat; Utuba; Utuba Yield; was Quality identified and released for large scale production.
    [Show full text]
  • Long Non-Coding Rnas in Wild Wheat Progenitors
    bioRxiv preprint doi: https://doi.org/10.1101/301804; this version posted April 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title Long non-coding RNAs in wild wheat progenitors Authors Alice Pieri1, Mario Enrico Pè1, Edoardo Bertolini1,2* Affiliations 1 Institute of Life Sciences, Scuola Superiore Sant’Anna. Piazza Martiri della Libertà 33, 56127 Pisa (Italy) 2 Present address: Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, Missouri 63132 (USA) *Corresponding author e-mail: [email protected] Running title Wild wheat long noncoding RNAs Key words Long noncoding RNAs, Triticum urartu, Aegilops tauschii, bread wheat, emmer wheat 1 bioRxiv preprint doi: https://doi.org/10.1101/301804; this version posted April 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Triticum urartu and Aegilops tauschii are the diploid progenitors of the hexaploid Triticum aestivum (AuAuBBDD), donors of the Au and D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives. Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515 T. urartu and 20,908 Ae. tauschii bona- fide lncRNA transcripts that show features similar to those of other plant and animal counterparts. Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs.
    [Show full text]
  • Perspectives from Reticulate Evolution Abstract Introduction
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 April 2021 Wheat speciation and adaptation: perspectives from reticulate evolution Authors Xuebo Zhao1,2, Xiangdong Fu1,2, Changbin Yin1,*, Fei Lu1,2,3,* Affiliations 1State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China. 2University of Chinese Academy of Sciences, Beijing, China. 3CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. Correspondence [email protected] (F.L.); [email protected] (C.Y.) Abstract Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.
    [Show full text]
  • Aetmyc1, the Candidate Gene Controlling the Red Coleoptile Trait in Aegilops Tauschii Coss
    molecules Article AetMYC1, the Candidate Gene Controlling the Red Coleoptile Trait in Aegilops tauschii Coss. Accession As77 Dong Cao 1,3,4,†, Guangji Ye 2,†, Yuan Zong 2, Bo Zhang 1,4, Wenjie Chen 1,4, Baolong Liu 1,4,* and Huaigang Zhang 1,4,* 1 Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, China; [email protected] (D.C.); [email protected] (B.Z.); [email protected] (W.C.) 2 State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai, Xining 800010, China; [email protected] (G.Y.); [email protected] (Y.Z.) 3 Northwest Institute of Plateau Biology, University of Chinese Academy of Sciences, Beijing 100049, China 4 Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China * Correspondence: [email protected] (B.L.); [email protected] (H.Z.); Tel.: +86-971-6143-610 (B.L.); +86-971-6143-630(H.Z.); Fax: +86-971-6143-282 (H.Z.) † These authors contributed equally to this paper. Received: 21 November 2017; Accepted: 15 December 2017; Published: 18 December 2017 Abstract: The red coleoptile trait can help monocotyledonous plants withstand stresses, and key genes responsible for the trait have been isolated from Triticum aestivum, Triticum urartu, and Triticum monococcum, but no corresponding research has been reported for Aegilops tauschii. In this research, transcriptome analysis was performed to isolate the candidate gene controlling the white coleoptile trait in Ae. tauschii. There were 5348 upregulated, differentially-expressed genes (DEGs) and 4761 downregulated DEGs in red coleoptile vs.
    [Show full text]
  • Gene Family from Triticeae Species
    International Journal of Molecular Sciences Article Characterization of the Heavy-Metal-Associated Isoprenylated Plant Protein (HIPP) Gene Family from Triticeae Species Heng Zhang 1, Xu Zhang 1, Jia Liu 1, Ying Niu 1, Yiming Chen 1, Yongli Hao 1, Jia Zhao 1,2, Li Sun 1, Haiyan Wang 1, Jin Xiao 1,* and Xiue Wang 1,* 1 State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China; [email protected] (H.Z.); [email protected] (X.Z.); [email protected] (J.L.); [email protected] (Y.N.); [email protected] (Y.C.); [email protected] (Y.H.); [email protected] (J.Z.); [email protected] (L.S.); [email protected] (H.W.) 2 College of Agriculture, South China Agriculture University, Guangzhou 510642, China * Correspondence: [email protected] (J.X.); [email protected] (X.W.); Tel.: +86-25-84395308 (X.W.) Received: 15 July 2020; Accepted: 25 August 2020; Published: 27 August 2020 Abstract: Heavy-metal-associated (HMA) isoprenylated plant proteins (HIPPs) only exist in vascular plants. They play important roles in responses to biotic/abiotic stresses, heavy-metal homeostasis, and detoxification. However, research on the distribution, diversification, and function of HIPPs in Triticeae species is limited. In this study, a total of 278 HIPPs were identified from a database from five Triticeae species, and 13 were cloned from Haynaldia villosa. These genes were classified into five groups by phylogenetic analysis. Most HIPPs had one HMA domain, while 51 from Clade I had two, and all HIPPs had good collinear relationships between species or subgenomes.
    [Show full text]
  • Draft Genome of the Wheat A-Genome Progenitor Triticum Urartu
    Draft genome of the wheat A-genome progenitor Triticum urartu Ling, Hong-Qing; Zhao, Shancen; Liu, Dongcheng; Wang, Junyi; Sun, Hua; Zhang, Chi; Fan, Huajie; Li, Dong; Dong, Lingli; Tao, Yong; Gao, Chuan; Wu, Huilan; Li, Yiwen; Cui, Yan; Guo, Xiaosen; Zheng, Shusong; Wang, Biao; Yu, Kang; Liang, Qinsi; Yang, Wenlong; Lou, Xueyuan; Chen, Jie; Feng, Mingji; Jian, Jianbo; Zhang, Xiaofei; Luo, Guangbin; Jiang, Ying; Liu, Junjie; Wang, Zhaobao; Sha, Yuhui; Zhang, Bairu; Wu, Huajun; Tang, Dingzhong; Shen, Qianhua; Xue, Pengya; Zou, Shenhao; Wang, Xiujie; Liu, Xin; Wang, Famin; Yang, Yanping; An, Xueli; Dong, Zhenying; Zhang, Kunpu; Zhang, Xiangqi; Luo, Ming-Cheng; Dvorak, Jan; Tong, Yiping; Wang, Jian; Yang, Huanming; Li, Zhensheng; Wang, Daowen; Zhang, Aimin; Wang, Jun Published in: Nature DOI: 10.1038/nature11997 Publication date: 2013 Document version Publisher's PDF, also known as Version of record Citation for published version (APA): Ling, H-Q., Zhao, S., Liu, D., Wang, J., Sun, H., Zhang, C., Fan, H., Li, D., Dong, L., Tao, Y., Gao, C., Wu, H., Li, Y., Cui, Y., Guo, X., Zheng, S., Wang, B., Yu, K., Liang, Q., ... Wang, J. (2013). Draft genome of the wheat A- genome progenitor Triticum urartu. Nature, 496(7443), 87-90. https://doi.org/10.1038/nature11997 Download date: 27. Sep. 2021 LETTER OPEN doi:10.1038/nature11997 Draft genome of the wheat A-genome progenitor Triticum urartu Hong-Qing Ling1*, Shancen Zhao2,3*, Dongcheng Liu1*, Junyi Wang1,2*, Hua Sun1*, Chi Zhang2*, Huajie Fan1,DongLi2, Lingli Dong1, Yong Tao2, Chuan Gao2, Huilan
    [Show full text]
  • Unleashing Floret Fertility in Wheat Through the Mutation of a Homeobox Gene
    Unleashing floret fertility in wheat through the mutation of a homeobox gene Shun Sakumaa,b,c,1, Guy Goland, Zifeng Guob, Taiichi Ogawaa,e, Akemi Tagiria, Kazuhiko Sugimotoa,f, Nadine Bernhardtg, Jonathan Brassacg, Martin Mascherh,i, Goetz Henselj, Shizen Ohnishik, Hironobu Jinnok, Yoko Yamashital, Idan Ayalond, Zvi Pelegd, Thorsten Schnurbuschb,m,1, and Takao Komatsudaa,f,1 aAgrogenomics Research Center, National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan; bIndependent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany; cFaculty of Agriculture, Tottori University, 680-8553 Tottori, Japan; dThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, 7610001 Rehovot, Israel; eInstitute of Agrobiological Sciences, National Agriculture and Food Research Organization, 305-8518 Tsukuba, Japan; fInstitute of Crop Science, National Agriculture and Food Research Organization, 305-8518 Tsukuba, Japan; gResearch Group Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany; hIndependent Research Group Domestication Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany; iGerman Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, 04103 Leipzig, Germany; jResearch Group Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany;
    [Show full text]