Literature DB >> 25349325

Insights into conifer giga-genomes.

Amanda R De La Torre1, Inanc Birol1, Jean Bousquet1, Pär K Ingvarsson1, Stefan Jansson1, Steven J M Jones1, Christopher I Keeling1, John MacKay1, Ove Nilsson1, Kermit Ritland1, Nathaniel Street1, Alvin Yanchuk1, Philipp Zerbe1, Jörg Bohlmann2.   

Abstract

Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.
© 2014 American Society of Plant Biologists. All Rights Reserved.

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Year:  2014        PMID: 25349325      PMCID: PMC4256843          DOI: 10.1104/pp.114.248708

Source DB:  PubMed          Journal:  Plant Physiol        ISSN: 0032-0889            Impact factor:   8.340


  67 in total

1.  AUGUSTUS: a web server for gene finding in eukaryotes.

Authors:  Mario Stanke; Rasmus Steinkamp; Stephan Waack; Burkhard Morgenstern
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce.

Authors:  Igor A Yakovlev; Carl Gunnar Fossdal; Øystein Johnsen
Journal:  New Phytol       Date:  2010-06-17       Impact factor: 10.151

Review 3.  Genomic selection in plant breeding: from theory to practice.

Authors:  Jean-Luc Jannink; Aaron J Lorenz; Hiroyoshi Iwata
Journal:  Brief Funct Genomics       Date:  2010-02-15       Impact factor: 4.241

4.  Convergent evolution of syringyl lignin biosynthesis via distinct pathways in the lycophyte Selaginella and flowering plants.

Authors:  Jing-Ke Weng; Takuya Akiyama; Nicholas D Bonawitz; Xu Li; John Ralph; Clint Chapple
Journal:  Plant Cell       Date:  2010-04-06       Impact factor: 11.277

Review 5.  Hemicelluloses.

Authors:  Henrik Vibe Scheller; Peter Ulvskov
Journal:  Annu Rev Plant Biol       Date:  2010       Impact factor: 26.379

6.  Identification and functional characterization of monofunctional ent-copalyl diphosphate and ent-kaurene synthases in white spruce reveal different patterns for diterpene synthase evolution for primary and secondary metabolism in gymnosperms.

Authors:  Christopher I Keeling; Harpreet K Dullat; Mack Yuen; Steven G Ralph; Sharon Jancsik; Jörg Bohlmann
Journal:  Plant Physiol       Date:  2009-12-31       Impact factor: 8.340

7.  The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.

Authors:  Allen Kovach; Jill L Wegrzyn; Genis Parra; Carson Holt; George E Bruening; Carol A Loopstra; James Hartigan; Mark Yandell; Charles H Langley; Ian Korf; David B Neale
Journal:  BMC Genomics       Date:  2010-07-07       Impact factor: 3.969

8.  Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine.

Authors:  Zenaida V Magbanua; Seval Ozkan; Benjamin D Bartlett; Philippe Chouvarine; Christopher A Saski; Aaron Liston; Richard C Cronn; C Dana Nelson; Daniel G Peterson
Journal:  PLoS One       Date:  2011-01-21       Impact factor: 3.240

9.  Gene finding in novel genomes.

Authors:  Ian Korf
Journal:  BMC Bioinformatics       Date:  2004-05-14       Impact factor: 3.169

10.  Sequencing and assembly of the 22-gb loblolly pine genome.

Authors:  Aleksey Zimin; Kristian A Stevens; Marc W Crepeau; Ann Holtz-Morris; Maxim Koriabine; Guillaume Marçais; Daniela Puiu; Michael Roberts; Jill L Wegrzyn; Pieter J de Jong; David B Neale; Steven L Salzberg; James A Yorke; Charles H Langley
Journal:  Genetics       Date:  2014-03       Impact factor: 4.562

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  44 in total

1.  The gymnosperm cytochrome P450 CYP750B1 catalyzes stereospecific monoterpene hydroxylation of (+)-sabinene in thujone biosynthesis in western redcedar.

Authors:  Andreas Gesell; Markus Blaukopf; Lina Madilao; Macaire M S Yuen; Stephen G Withers; Jim Mattsson; John H Russell; Jörg Bohlmann
Journal:  Plant Physiol       Date:  2015-03-31       Impact factor: 8.340

2.  A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism.

Authors:  Teresa Laitinen; Kris Morreel; Nicolas Delhomme; Adrien Gauthier; Bastian Schiffthaler; Kaloian Nickolov; Günter Brader; Kean-Jin Lim; Teemu H Teeri; Nathaniel R Street; Wout Boerjan; Anna Kärkönen
Journal:  Plant Physiol       Date:  2017-05-18       Impact factor: 8.340

3.  Genomic insights into the genotype-environment mismatch and conservation units of a Qinghai-Tibet Plateau endemic cypress under climate change.

Authors:  Heng Yang; Jialiang Li; Richard Ian Milne; Wenjing Tao; Yi Wang; Jibin Miao; Wentao Wang; Tsam Ju; Sonam Tso; Jian Luo; Kangshan Mao
Journal:  Evol Appl       Date:  2022-06-10       Impact factor: 4.929

4.  Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products.

Authors:  Katrin Geisler; Niels Berg Jensen; Macaire M S Yuen; Lina Madilao; Jörg Bohlmann
Journal:  Plant Physiol       Date:  2016-03-02       Impact factor: 8.340

5.  Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families.

Authors:  Amanda R De La Torre; Yao-Cheng Lin; Yves Van de Peer; Pär K Ingvarsson
Journal:  Genome Biol Evol       Date:  2015-03-05       Impact factor: 3.416

6.  Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

Authors:  Lauren Coombe; René L Warren; Shaun D Jackman; Chen Yang; Benjamin P Vandervalk; Richard A Moore; Stephen Pleasance; Robin J Coope; Joerg Bohlmann; Robert A Holt; Steven J M Jones; Inanc Birol
Journal:  PLoS One       Date:  2016-09-15       Impact factor: 3.240

7.  Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing.

Authors:  Pedro Seoane-Zonjic; Rafael A Cañas; Rocío Bautista; Josefa Gómez-Maldonado; Isabel Arrillaga; Noé Fernández-Pozo; M Gonzalo Claros; Francisco M Cánovas; Concepción Ávila
Journal:  BMC Genomics       Date:  2016-02-27       Impact factor: 3.969

8.  Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir (Pseudotsuga menziesii).

Authors:  Jan-Peter George; Silvio Schueler; Michael Grabner; Sandra Karanitsch-Ackerl; Konrad Mayer; Michael Stierschneider; Lambert Weissenbacher; Marcela van Loo
Journal:  Ecol Evol       Date:  2021-05-17       Impact factor: 2.912

9.  Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats.

Authors:  Rafael A Cañas; Isabel Feito; José Francisco Fuente-Maqueda; Concepción Ávila; Juan Majada; Francisco M Cánovas
Journal:  BMC Genomics       Date:  2015-11-06       Impact factor: 3.969

10.  An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers.

Authors:  Xuan Lin; Nurul Faridi; Claudio Casola
Journal:  Genome Biol Evol       Date:  2016-05-02       Impact factor: 3.416

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