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Diversity, Distribution and Evolution of the Planktonic Diatom Family Chaetocerotaceae

Gaonkar, Chetan Chandrakant (2017). Diversity, Distribution and Evolution of the Planktonic Diatom Family Chaetocerotaceae. PhD thesis The Open University.

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Abstract

The number and abundance of diatom species in environmental samples are counted traditionally by means of light microscopy (LM). However, recognizing –let alone, counting- species is often challenging because of the existence of cryptic species and intraspecific phenotypic plasticity. Proper characterization requires isolation of cells, growing them into monoclonal cultures, and characterizing the cultures genetically and morphologically. However, not all species grow in culture, featureless ones are less likely to be isolated, and the procedure is laborious. High-throughput sequencing (HTS) metabarcoding bypasses morphology; DNA is collected from environmental samples, a particular marker sequenced, and the resulting sequences sorted into clusters or terminal clades assumed to represent species. Yet, reference barcodes of taxonomically validated species are needed to identify these clades. This exercise is the main aim of my thesis.

Since it is impossible to do this for all the diversity within a PhD thesis project, we selected Chaetocerotaceae, an abundant and diverse family of marine planktonic diatoms, containing two genera: Chaetoceros and Bacteriastrum. Its members uniquely share setae; thin siliceous tubes emerging from the valve corners, facilitating detection in samples. Strains were obtained from the Gulf of Naples (GoN), from Central Chile and Roscoff – at sites for which LTER time series data are available.

A total of 270 strains were obtained from these sites, and their 18S- and partial 28S rDNA sequences and morphological information gathered. The strains grouped into 60 genetically distinct species, thus providing a dataset of validated Chaetocerotacean 18S reference barcodes. Inferred molecular phylogenies showed monophyletic Chaetocerotaceae as well as monophyletic Bacteriastrum inside paraphyletic Chaetoceros, and the presence of cryptic diversity. To start with taxonomic updates, the species C. sporotruncatus and C. dichatoensis were described within the C. socialis species-complex based on spore morphology and sequence differences. Several rDNA sequences contained spliceosomal introns (ca. 100bp) and/or group-I introns (ca. 400bp). Phylogenies inferred from the introns did not corroborate rDNA phylogenies, suggesting horizontal gene transfer. Presence/absence of introns in conspecific strains sampled in different seasons suggests population differentiation between these seasons. A HTS dataset consisting of V4-sequences (part of 18S) from 48 seawater samples taken over the seasons in the GoN revealed 76 terminal clades of which 46 grouped with a reference barcode. Some of these species occur year-round whereas most others are seasonal. Surprisingly, of the 30 clades belonging to unknown Chaetocerotacean species, two appear to be among the most abundant in the GoN.

Item Type: Thesis (PhD)
Copyright Holders: 2016 The Author
Keywords: genetic markers; bar coding
Academic Unit/School: Faculty of Science, Technology, Engineering and Mathematics (STEM)
Associated Research Centre: Stazione Zoologica Anton Dohrn
Item ID: 50352
Depositing User: Chetan Chandrakant Gaonkar
Date Deposited: 25 Aug 2017 15:13
Last Modified: 02 May 2018 14:31
URI: http://oro.open.ac.uk/id/eprint/50352
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