Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

“…Organismal scope or featured taxon Cunha & Giribet (2019) yes Gastropods Laumer et al (2019) yes Animals Lemer et al (2019) yes Bivalves Lozano-Fernandez et al (2019) yes Chelicerates Marlétaz et al (2019) yes Spiralia Philippe et al (2019) yes Bilateria Narayanan Kutty et al (2019) no Calyptratae Uribe et al (2019) no Gastropods Wolfe et al (2019) no Decapod crustaceans Zverkov et al (2019) no Dicyemida and Orthonectida Aouad et al (2018) yes Archaea Laumer et al (2018) yes Placozoa Otero-Bravo et al (2018) yes Pantoea Puttick et al (2018) yes Land plants Schwentner et al (2018) yes Pancrustacea Sousa et al (2018) yes Land plants Bennett & Mao (2018) no Fulgoroidea symbionts Eitel et al (2018) no Placozoa Manzano-Marín et al (2018) no Cinara strobi symbionts Feuda et al (2017) yes Animals Szabó et al (2017) yes Pseudococcidae symbionts Williams et al (2017) yes Archaea Schwentner et al (2017) no Pancrustacea Shin et al (2017) no Curculionoidea Simion et al (2017) no Animals Yoshida et al (2017) no Tardigrades Leliaert et al (2016) yes Viridiplantae Zhang et al (2016) yes Roseobacter CHAB-I-5 lineage He et al (2016) no Rhizaria Song et al (2016) no Holometabola Domman et al (2015) yes Plastids Luo (2015) yes SAR11 Petitjean et al (2015) yes Archaea Borowiec et al (2015) no Animals Derelle et al (2015) no Eukaryotes Wang & Wu (2015) no Mitochondria…”

Ecotype diversification of an abundant Roseobacter lineage

“…Many roseobacters are non-obligate lithotrophs, which meet part of the energy requirement by oxidizing reduced inorganic compounds, including reduced sulfur compounds and carbon monoxide (CO) (Luo and Moran, 2014). The sox gene cluster (soxRSVWXYZABCDEGH) responsible for sulfur oxidation is prevalent among cultured and uncultivated roseobacters (Luo and Moran, 2014;Zhang et al, 2016). It is therefore interesting that this gene cluster is completely missing in the S.O.…”

“…This finding was consolidated by the genomic analyses of single cells and novel cultures of four largely uncultivated pelagic Roseobacter lineages DC5‐80‐3 (also known as the RCA clade), SAG‐O19, CHAB‐I‐5 and NAC11‐7 (Luo et al ., ; Voget et al ., ; Billerbeck et al ., ; Zhang et al ., ). These lineages differ in phylogenetic position, genome size, and base composition (Zhang et al ., ). Although a major difference in global ocean distribution among them was shown (Zhang et al ., ), an attempt to link this ecological pattern to differences in genome content was not successful.…”

“…Using an assembly-free bioinformatics procedure to unambiguously assign metagenomic gene fragments to the Roseobacter clade, it was shown that wild planktonic roseobacters differ systematically in genome content and base composition from Roseobacter isolates readily growing in high nutrient media (Luo et al, 2012). This finding was consolidated by the genomic analyses of single cells and novel cultures of four largely uncultivated pelagic Roseobacter lineages DC5-80-3 (also known as the RCA clade), SAG-O19, CHAB-I-5 and NAC11-7 (Luo et al, 2014a,b;Voget et al, 2015;Billerbeck et al, 2016;Zhang et al, 2016). These lineages differ in phylogenetic position, genome size, and base composition (Zhang et al, 2016).…”

“…These lineages differ in phylogenetic position, genome size, and base composition (Zhang et al, 2016). Although a major difference in global ocean distribution among them was shown (Zhang et al, 2016), an attempt to link this ecological pattern to differences in genome content was not successful.…”