Description and phylogenetic implications of a de novo mitochondrial genome of Rhinichthys atratulus (Teleostei: Leuciscidae) from Connecticut

Abstract

We present a de novo mitogenome assembly from a specimen of Rhinichthys atratulus, the Eastern Blacknose Dace, collected in the Connecticut River drainage. R. atratulus is a fish species widely distributed across Atlantic slope drainages from Nova Scotia, Canada to the Roanoke River Drainage, Virginia, United States. The assembly has a total length of 16,646 bp; consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a 974 bp D-loop; and has a GC content of 45.7%. We performed two phylogenetic analyses using the de novo assembly and 28 additional cyprinoid mitochondrial genomes: with and without the D-loop. The resulting phylogenetic trees showed the same branching patterns. However, inclusion of the D-loop resulted in nodes with equal or greater support. The trees largely match previously published analyses, while offering new insights into relationships among leuciscid genera. Our findings indicate that the inclusion of the D-loop in mitogenome phylogenetic analyses can help improve bootstrap support at otherwise unresolved nodes.

Fig. 1

Annotation of our de novo R. atratulus mitogenome assembly using MitoFish, visualized with Chloroplot (Zheng et al., 2020). The innermost ring represents the GC content of a given 100 bp interval of the sequence, with the subdivided rings representing increasing 25% intervals. The arrows in this section correspond to the direction of transcription for the genes and RNAs displayed in the outer ring, with the inner features transcribed clockwise (forward strand) and the outer features transcribed counterclockwise (reverse strand). Features are color coded by their product, per the key. The inset photograph is of a male R. atratulus individual in breeding colors. This individual was collected and photographed by the authors from the same locality as the sequenced individual in May 2023.

Fig. 2

Comparison of nucleic acid composition (as percent of total sequence, y-axis) between each mitochondrial genome (x-axis). The differently colored sections of each bar represent the proportion of A (blue), T (green), G (gold), and C (pink) in each mitogenome. The species are ordered according to the phylogenetic results shown in Fig. 3. *This specimen (NC_033943.1) is labeled as Rhinichthys atratulus in the Genbank but is properly identified as R. obtusus; see Study Material and Species Identification for further information.

Fig. 3

Phylogenetic estimates from mitogenomes of 27 ingroup cyprinoid taxa (see Table 1 for complete list of NCBI accessions). The de novo Rhinichthys atratulus (PP958238) mitogenome is highlighted in gold. The trees were rooted at the two outgroups of the genus Catostomus. Trees were constructed (A) with D-loops and (B) without D-loops. Bootstrap values are displayed adjacent to each node. *This specimen (NC_033943.1) is labeled as Rhinichthys atratulus in the Genbank but is properly identified as R. obtusus; see Study Material and Species Identification for further information.