Literature DB >> 27443314

The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses.

Peter A Davey1, Mathieu Pernice1, Gaurav Sablok1, Anthony Larkum1, Huey Tyng Lee2, Agnieszka Golicz2, David Edwards2, Rudy Dolferus3, Peter Ralph4.   

Abstract

Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.

Keywords:  Angiosperms; Marine plants; Molecular profiling; Next generation sequencing; Omics; Seagrass

Mesh:

Year:  2016        PMID: 27443314     DOI: 10.1007/s10142-016-0501-4

Source DB:  PubMed          Journal:  Funct Integr Genomics        ISSN: 1438-793X            Impact factor:   3.410


  86 in total

1.  Five microsatellite loci in eelgrass Zostera marina and a test of cross-species amplification in Z. noltii and Z. japonica.

Authors:  T B Reusch
Journal:  Mol Ecol       Date:  2000-03       Impact factor: 6.185

2.  Genome-wide identification of rice class I metallothionein gene: tissue expression patterns and induction in response to heavy metal stress.

Authors:  Neelam Gautam; Pankaj Kumar Verma; Shikha Verma; Rudra Deo Tripathi; Prabodh Kumar Trivedi; Bijan Adhikari; Debasis Chakrabarty
Journal:  Funct Integr Genomics       Date:  2012-10-10       Impact factor: 3.410

3.  Development of microsatellite primers of the largest seagrass, Enhalus acoroides (Hydrocharitaceae).

Authors:  Hui Gao; Kai Jiang; Yan Geng; Xiao-Yong Chen
Journal:  Am J Bot       Date:  2012-02-16       Impact factor: 3.844

4.  Small RNA profiling of virus-infected grapevines: evidences for virus infection-associated and variety-specific miRNAs.

Authors:  Kashmir Singh; Aarthi Talla; Wenping Qiu
Journal:  Funct Integr Genomics       Date:  2012-08-19       Impact factor: 3.410

Review 5.  Single-cell C(4) photosynthesis versus the dual-cell (Kranz) paradigm.

Authors:  Gerald E Edwards; Vincent R Franceschi; Elena V Voznesenskaya
Journal:  Annu Rev Plant Biol       Date:  2004       Impact factor: 26.379

6.  The RNA-seq approach to discriminate gene expression profiles in response to melatonin on cucumber lateral root formation.

Authors:  Na Zhang; Hai-Jun Zhang; Bing Zhao; Qian-Qian Sun; Yun-Yun Cao; Ren Li; Xin-Xin Wu; Sarah Weeda; Li Li; Shuxin Ren; Russel J Reiter; Yang-Dong Guo
Journal:  J Pineal Res       Date:  2013-10-15       Impact factor: 13.007

7.  Purification of intact chloroplasts from marine plant Posidonia oceanica suitable for organelle proteomics.

Authors:  Amalia Piro; Ilia Anna Serra; Antonia Spadafora; Monica Cardilio; Linda Bianco; Gaetano Perrotta; Rui Santos; Silvia Mazzuca
Journal:  Proteomics       Date:  2015-12       Impact factor: 3.984

8.  In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning.

Authors:  Maria Greco; Adriana Chiappetta; Leonardo Bruno; Maria Beatrice Bitonti
Journal:  J Exp Bot       Date:  2011-11-04       Impact factor: 6.992

9.  Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network.

Authors:  Agnieszka A Golicz; Martin Schliep; Huey Tyng Lee; Anthony W D Larkum; Rudy Dolferus; Jacqueline Batley; Chon-Kit Kenneth Chan; Gaurav Sablok; Peter J Ralph; David Edwards
Journal:  J Exp Bot       Date:  2015-01-06       Impact factor: 6.992

10.  Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles.

Authors:  Emanuela Dattolo; Jenny Gu; Philipp E Bayer; Silvia Mazzuca; Ilia A Serra; Antonia Spadafora; Letizia Bernardo; Lucia Natali; Andrea Cavallini; Gabriele Procaccini
Journal:  Front Plant Sci       Date:  2013-06-17       Impact factor: 5.753

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  8 in total

1.  Molecular Mechanisms behind the Physiological Resistance to Intense Transient Warming in an Iconic Marine Plant.

Authors:  Lazaro Marín-Guirao; Laura Entrambasaguas; Emanuela Dattolo; Juan M Ruiz; Gabriele Procaccini
Journal:  Front Plant Sci       Date:  2017-06-29       Impact factor: 5.753

2.  Linking gene expression to productivity to unravel long- and short-term responses of seagrasses exposed to CO2 in volcanic vents.

Authors:  Irene Olivé; João Silva; Chiara Lauritano; Monya M Costa; Miriam Ruocco; Gabriele Procaccini; Rui Santos
Journal:  Sci Rep       Date:  2017-02-13       Impact factor: 4.379

3.  SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants.

Authors:  Gaurav Sablok; Regan J Hayward; Peter A Davey; Rosiane P Santos; Martin Schliep; Anthony Larkum; Mathieu Pernice; Rudy Dolferus; Peter J Ralph
Journal:  Sci Rep       Date:  2018-02-09       Impact factor: 4.379

4.  The Tropical Invasive Seagrass, Halophila stipulacea, Has a Superior Ability to Tolerate Dynamic Changes in Salinity Levels Compared to Its Freshwater Relative, Vallisneria americana.

Authors:  Michelle A Oscar; Simon Barak; Gidon Winters
Journal:  Front Plant Sci       Date:  2018-07-04       Impact factor: 5.753

5.  Tissue-specific transcriptome profiles identify functional differences key to understanding whole plant response to life in variable salinity.

Authors:  Mitchell W Booth; Martin F Breed; Gary A Kendrick; Philipp E Bayer; Anita A Severn-Ellis; Elizabeth A Sinclair
Journal:  Biol Open       Date:  2022-08-23       Impact factor: 2.643

6.  Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis.

Authors:  Zhijian Jiang; Manoj Kumar; Matthew P Padula; Mathieu Pernice; Tim Kahlke; Mikael Kim; Peter J Ralph
Journal:  Front Plant Sci       Date:  2017-08-15       Impact factor: 5.753

7.  Stress Memory in Seagrasses: First Insight Into the Effects of Thermal Priming and the Role of Epigenetic Modifications.

Authors:  Hung Manh Nguyen; Mikael Kim; Peter J Ralph; Lázaro Marín-Guirao; Mathieu Pernice; Gabriele Procaccini
Journal:  Front Plant Sci       Date:  2020-04-28       Impact factor: 5.753

Review 8.  The Cell Wall of Seagrasses: Fascinating, Peculiar and a Blank Canvas for Future Research.

Authors:  Lukas Pfeifer; Birgit Classen
Journal:  Front Plant Sci       Date:  2020-10-23       Impact factor: 5.753

  8 in total

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