The Genome of a Southern Hemisphere Seagrass Species (<i>Zostera muelleri</i>)

Lee, HueyTyng; Golicz, Agnieszka A.; Bayer, Philipp E.; Jiao, Yuannian; Tang, Haibao; Paterson, Andrew H.; Sablok, Gaurav; Krishnaraj, Rahul R.; Chan, Chon‐Kit Kenneth; Batley, Jacqueline; Kendrick, Gary A.; Larkum, Anthony W. D.; Ralph, Peter J.; Edwards, David

doi:10.1104/pp.16.00868

Cited by 72 publications

(76 citation statements)

References 65 publications

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“…The OphVe-ZosMar element was identified in a large scaffold (accession # 30 Furthermore, neither the OphVe-ZosMar element nor it's flanking sequences 3 could be identified in the published genome assembly of Zoster muelleri [7], a related 4 seagrass species. Assuming that the OphVe-ZosMar element is genuinely 5 incorporated into the Z.marina genome (i.e.…”

mentioning

confidence: 99%

Identification of the first endogenous Ophiovirus sequence

Marsile-Medun

Debat

Gifford

2017

Preprint

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Endogenous viral elements (EVEs) are sequences in eukaryotic genomes that are derived from the ancestral integration of viral sequences into germline cells.Ophioviruses (family Ophioviridae) are a recently established family of viruses that infects plants. In this report, we describe the first example of an EVE derived from an ophiovirus, in the genome of eelgrass (Zostera marina). These findings extend the host range of ophioviruses to include seagrasses of the family Zosteraceae.

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mentioning

confidence: 99%

Identification of the first endogenous Ophiovirus sequence

Marsile-Medun

Debat

Gifford

2017

Preprint

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“…In-depth analysis of Zostera muelleri Transcriptomics Database (Hayward et al, in prep), revealed transcripts encoding proteins with high similarities to the domains of PEPC and CA proteins already identified in the seagrass Zostera marina (Olsen et al 2016). It is interesting to note that the genome of Z. muelleri, which was not available at the time of this study, has been published since (Lee et al 2016). The functional domains of three of these sequences, coding for PEPC1 (KMZ56135), PEPC2 (KMZ58048) and -CA (KMZ56166) respectively, were used as a template to design sequence-specific primers for RT-qPCR using the software, Primer3 0.4.0 (Koressaar and Remm 2007;Untergasser et al 2012) with default settings.…”

Section: Primer Designmentioning

confidence: 91%

Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri

et al. 2017

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Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C mechanism of carbon assimilation, and (ii) decreased the expression levels of phosphoenolpyruvate carboxylase and carbonic anhydrase. These molecular-physiological results suggest that regulation of the photophysiology of Z. muelleri might involve a close integration between the C and C, or other CO concentrating mechanisms metabolic pathways. Overall, this study highlights that the photophysiological response of Z. muelleri to changing oxygen in water is capable of rapid acclimation and the dynamic modulation of pathways should be considered when assessing seagrass primary production.

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“…Outlier loci identified by two or more methods were considered "candidate outliers" and their functional roles evaluated by subjecting 1000 base pairs upstream and downstream of each of the identified outlier SNPs to BLASTx searches, with the non-redundant protein sequence database and an E-value cut off of 10 -5 (Altschul et al 1997) using Blast2Go (Conesa et al 2005). In addition to BLASTing against the general NCBI database, these searches were also carried out against the Zosteraceae family in general, specifically, Zostera marina (Olsen et al 2016) and Z. muelleri (Lee et al 2016). Gene Ontology (GO) mapping, Interproscan and annotation were performed with Blast2Go default parameters.…”

Section: Outlier Loci Identification and Functional Annotationmentioning

confidence: 99%

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

Phair

Toonen

Knapp

et al. 2019

Preprint

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The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ~9600km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

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The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri)

Cited by 72 publications

References 65 publications

Identification of the first endogenous Ophiovirus sequence

Identification of the first endogenous Ophiovirus sequence

Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

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