CONGRUENCE BETWEEN THE MORPHOLOGIC TREE AND MOLECULAR TREE: A CASE STUDY OF CLYPEASTEROIDA BASED ON THE NEW AND COMPLETE MITOCHONDRIAL GENOME OF SINAECHINOCYAMUS MAI (ECHINODERMATA: ECHINOIDEA)

Morphological and molecular data often lead to distinct hypotheses for phylogenetic relationships. This is also true in the Echinoderm class Echinoidea. In particular, the phylogenetic position of the order Clypeasteroida is not well resolved. Complete mitochondrial genomes are currently available for 29 echinoid species, but no clypeasteroid echinoid has so far been sequenced. Twenty years after the last study of the enigmatic, miniature sand dollar Sinaechinocyamus mai, live individuals from the west coast of Taiwan were captured. DNA extracted from a single live individual was sequenced with 10X Genomics technology. The first complete mitochondrial genome (mitogenome) of Sinaechinocyamus mai is reported here. To test current hypotheses pertaining the phylogenetic position of the order Clypeasteroida, a phylogenetic analysis was conducted, including the first complete mitogenome of a clypeasteroid species and 34 other ingroup taxa belonging to 9 orders of the class Echinoidea.

Our study shows a strong congruence between the molecular and morphologic phylogenetic trees. In order to achieve this, we have applied different filtering methods to rule out possible contaminations from other taxa, including human genomes, to reconstruct the mitogenome four times, and then to conduct the phylogenetic analyses by maximizing the genetic information (> 15,000 bp) within a mitochondrion. By getting good support values for the deep nodes it is evident that the tree of Echinoidea is stabilizing at the family level and higher. It is further supported by previous morphologic trees based on morphologic characters. Important highlights are: 1) The first complete mitochondrial genome from a member of the Clypeasteroida was reconstructed; 2) Based on 871 million sequence reads recovered, four mitogenome assemblies and annotations using different assembly strategies and filtering methods were reconstructed; the final mitogenome assembly for Sinaechinocyamus mai is 15,756 bp in length; 3) Our results do not agree with previous phylogenetic interpretations based on molecular data. Instead, it shows congruence with older interpretations based on morphologic characters with high fidelity; and 4) Absence of lantern in Irregularia is an early event, and that the lantern in adult clypeasteroids has re-appeared and is secondarily modified.