Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell-eye evolution

Abstract

Mollusca is the second-largest animal phylum with over 100,000 species among eight distinct taxonomic classes. Across 1000 living species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess "shell eyes", true eyes with a lens and retina that are embedded within the dorsal shells, which represent the most recent evolution of animal eyes. The phylogeny of major chiton clades is mostly well established, in a set of superfamily and higher-level taxa supported by various approaches including multiple gene markers, mitogenome-phylogeny and phylotranscritomic approaches as well as morphological studies. However, one critical lineage has remained unclear: Schizochiton was controversially suggested as a potential independent origin of chiton shell eyes. Here, with the draft genome sequencing of Schizochiton incisus (superfamily Schizochitonoidea) plus assembly of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. Phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. A consistent robust topology was generated with protein coding genes using different models and methods. Our results support Schizochitonoidea is a sister group to other Chitonoidea in Chitonina, in agreement with established classification. This suggests that the earliest origin of shell eyes is in Schizochitonoidea, which were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding on the evolution of Polyplacophora.

Still waters run deep: Large scale genome rearrangements in the evolution of morphologically conservative Polyplacophora

“…Four new chiton genomes represent the most complete genomes sequenced for the class, adding to several previously published partial or complete genomes(6, 8–10)(SI Appendix, Tables S1-S3). We sequenced chromosome-level genomes of Deshayesiella sirenkoi (Lepidopleurida) from the Daikoku vent field, Western Pacific Ocean, Callochiton septemvalvis (Callochitonida) and Acanthochitona discrepans (Chitonida) both from the intertidal of Strangford Lough, N. Ireland, and the congener A. rubrolineata from the intertidal of Qingdao, China.…”

Extracellular chemosymbiont populations in a shallow-water thyasirid clam potentially shaped by priority effect

“…In addition, to find the taxonomy of two strains of symbiont in chemosynthetic sulfur-oxidizing bacteria (SOB), a total of 57 symbiont genomes assigned by GTDB-tk v.2.1.1 [59] were downloaded for phylogenomic analysis with Bathymodiolus azoricus symbiont (MOB) as an outgroup. A pipeline of phylogenomic analysis was modified from the published works [72, 73].…”

Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment

“…The taxonomy of the symbiont at the genomic level was assigned by GTDB‐Tk version 2.1.1 (Chaumeil et al, 2019) based on the tree topology and average nucleotide identity (ANI) comparison with published bacterial genomes. The bacterial proteins, predicted using Prokka version 1.14.6 in this study, were also used to construct a phylogenomic tree (Kocot et al, 2017; Liu et al, 2022). Briefly, the orthologue of proteins was predicted using OrthoFinder version 2.5.4 (Emms & Kelly, 2019) with DIAMOND blastp and then aligned using MAFFT version 7.508 (Katoh & Standley, 2013).…”