Comparative and Functional Genomics of Macronutrient Utilization in Marine Diatoms

Abstract

Song and Ward, 2007). Additional sequences from Chaetoceros tenuissimus, Pseudo-nitzschia multistriata, and Skeletonema costatum were obtained by a blastp search of Phatr2_26029 against diatoms (taxid:2836) in the NCBI nr database. Outgroup sequences were identified as top non-diatom hits with a blastp search of Phatr2_26029 against the NCBI nr database. Amino acid transporter (AMT) sequences were obtained from Phycocosm (Bacillariophyta) using the TCDB accessions TC 1.A.11.2 (AMT1/2) and TC 1.A.11.4 (AMT -Rhesus type). Additionally, putative AMT sequences were identified from the non-assembled scaffolds of P. tricornutum (Phatr2_bd, https://mycocosm.jgi.doe.gov/Phatr2_bd/Phatr2_bd.home.html) using tblastn with other P. tricornutum AMTs as the query sequences. Pn. multistriata AMT sequences were retrieved with blastp search of Pn. multiseries sequences against NCBI nr against diatoms (taxid:2836). For construction of the phylogenetic tree, phosphate transporter sequences were identified in Phycocosm using TC 2.A.58 (Phosphate:Na+ Symporter or SLC34), TC 2.A.20 (Inorganic phosphate transporter, PiT or SLC20), and TC 2.A.1.9 (Phosphate: H+ symporter family) annotations and using accessions identified in (Cruz de Carvalho et al., 2016). Amino acid sequences and accessions can be downloaded from figshare (Smith, 2021). Alignments and Phylogenetic TreeCLC Genomics Workbench (20.0.2) was used for all alignments and trees. Sequences were aligned with Gap cost settings as follows: Gap open cost = 10.0, Gap extension cost = 1.0, with the End gap cost = free. Alignment was run as Very accurate (slow). Short sequences, sequences with large gaps, and sequences with low coverage over consensus regions were removed from the alignments and long sequences were trimmed. Alignments used in construction of the NRT2 tree versions (see below) and the AMT tree can be accessed from figshare (Smith, 2021). The neighbor joining method was used for a start tree, the protein substitution model chosen was WAG, and Estimation was set to estimate topology. Bootstrap analysis was performed with 100 replicates, and only nodes with bootstrap support >50 are indicated.

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

“…Genome‐enabled exploration of Phaeodactylum tricorutum has also revealed important features of diatom nutrient metabolism (Coale et al., 2022; Kroth & Matsuda, 2022; Smith & Allen, 2022). Examples include the discovery of a functional urea cycle involved in the metabolism optimization under nitrogen limitation (Allen et al., 2011), or the role of the nitrate reductase in controlling the balance between nitrate transport and assimilation, and the distribution of carbon flux (Levitan et al., 2015; McCarthy et al., 2017).…”

Patterns and drivers of diatom diversity and abundance in the global ocean

“…Their cells possess a rigid silica cell wall denoted frustule, which makes them the world's largest contributors to biosilicification 8 . They are also important players in the nitrogen cycle because they have efficient strategies for nitrogen capture and utilization 9,10 . Furthermore, some species even harbor nitrogen-fixing symbionts [11][12][13][14] .…”