Dataset Information

Understanding Aquaporin Transport System in Eelgrass (Zostera marina L.), an Aquatic Plant Species.

ABSTRACT: Aquaporins (AQPs) are a class of integral membrane proteins involved in the transport of water and many other small solutes. The AQPs have been extensively studied in many land species obtaining water and nutrients from the soil, but their distribution and evolution have never been investigated in aquatic plant species, where solute assimilation is mostly through the leaves. In this regard, identification of AQPs in the genome of Zostera marina L. (eelgrass), an aquatic ecological model species could reveal important differences underlying solute uptake between land and aquatic species. In the present study, genome-wide analysis led to the identification of 25 AQPs belonging to four subfamilies, plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic proteins (NIPs), small basic intrinsic proteins (SIPs) in eelgrass. As in other monocots, the XIP subfamily was found to be absent from the eelgrass genome. Further classification of subfamilies revealed a unique distribution pattern, namely the loss of the NIP2 (NIP-III) subgroup, which is known for silicon (Si) transport activity and ubiquitously present in monocot species. This finding has great importance, since the eelgrass population stability in natural niche is reported to be associated with Si concentrations in water. In addition, analysis of available RNA-seq data showed evidence of expression in 24 out of the 25 AQPs across four different tissues such as root, vegetative tissue, male flower and female flower. In contrast to land plants, higher expression of PIPs was observed in shoot compared to root tissues. This is likely explained by the unique plant architecture of eelgrass where most of the nutrients and water are absorbed by shoot rather than root tissues. Similarly, higher expression of the TIP1 and TIP5 families was observed specifically in male flowers suggesting a role in pollen maturation. This genome-wide analysis of AQP distribution, evolution and expression dynamics can find relevance in understanding the adaptation of aquatic and land species to their respective environments.

SUBMITTER: Shivaraj SM

PROVIDER: S-EPMC5541012 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Understanding Aquaporin Transport System in Eelgrass (<i>Zostera marina</i> L.), an Aquatic Plant Species.

Shivaraj S M SM Deshmukh Rupesh R Bhat Javaid A JA Sonah Humira H Bélanger Richard R RR

Frontiers in plant science 20170803

Aquaporins (AQPs) are a class of integral membrane proteins involved in the transport of water and many other small solutes. The AQPs have been extensively studied in many land species obtaining water and nutrients from the soil, but their distribution and evolution have never been investigated in aquatic plant species, where solute assimilation is mostly through the leaves. In this regard, identification of AQPs in the genome of <i>Zostera marina</i> L. (eelgrass), an aquatic ecological model s ...[more]

PMID: 28824671

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Project description:Seagrass habitats provide important ecosystem services, including their ability to take up and store substantial amounts of organic carbon, known as 'blue carbon.' However, the paucity of geospatial and carbon storage information along the Pacific Coast of Canada hinders the inclusion of blue carbon storage data in conservation planning and policy development in coastal habitats. We assessed the carbon storage and accumulation rates in three eelgrass (Zostera marina) meadows in southern Clayoquot Sound on the Pacific Coast of British Columbia. The intertidal and subtidal portions of each meadow were mapped and sampled to estimate eelgrass density, biomass, and carbon, and sediment cores were analyzed to estimate sediment carbon storage and accumulation rates. Aboveground biomass measurements were consistent with estimates for Z. marina in other regions, with average aboveground carbon biomass estimates of 16.78 g C m-2 and 16.25 g C m-2 in the intertidal and subtidal areas, respectively. However, the estimated aboveground to belowground biomass ratio was an order of magnitude higher than for seagrass species in temperate/tropical areas, largely because belowground biomass was up to 10 times lower than for other Z. marina meadows, averaging 6.17 g C m-2 and 5.03 g C m-2 in the intertidal and subtidal zones, respectively. Sediment carbon concentrations did not exceed 1.30%Corg, and carbon accumulation rates ranged from 2.90-39.61 g Corg m-2 yr-1, decreasing with depth and averaging 10.8 ± 5.2 g Corg m-2 yr-1. While sediment carbon stocks were generally higher in the eelgrass meadows relative to non-vegetated reference sites, carbons stocks averaged 1343 ± 482 g Corg m-2, substantially less than global averages. These carbon results confirm that eelgrass does contribute to carbon storage in Clayoquot Sound but at lower rates than identified for more tropical seagrasses. By improving the quantification of site-specific carbon dynamics, eelgrass' role in climate change mitigation and conservation planning can be assessed.

Project description:Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

Dataset Information

Understanding Aquaporin Transport System in Eelgrass (Zostera marina L.), an Aquatic Plant Species.

Publications

Understanding Aquaporin Transport System in Eelgrass (<i>Zostera marina</i> L.), an Aquatic Plant Species.

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