Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group

Complete mitochondrial genome of critically endangered catfish Hemibagrus punctatus (Jerdon, 1849) and comparative analysis for insights into the phylogeny of hemibagrids through mitogenomic approach

BACKGROUND

Hemibagrus punctatus (Jerdon, 1849) is a critically endangered bagrid catfish endemic to the Western Ghats of India, whose population is declining due to anthropogenic activities. The current study aims to compare the mitogenome of H. punctatus with that of other Bagrid catfishes and provide insights into their evolutionary relationships.

METHODS AND RESULTS

Samples were collected from Hemmige Karnataka, India. In the present study, the mitogenome of H. punctatus was successfully assembled, and its phylogenetic relationships with other Bagridae species were studied. The total genomic DNA of samples was extracted following the phenol-chloroform isoamyl alcohol method. Samples were sequenced, and the Illumina paired-end reads were assembled to a contig length of 16,517 bp. The mitochondrial genome was annotated using MitoFish and MitoAnnotator (Iwasaki et al., 2013). A robust phylogenetic analysis employing NJ (Maximum composite likelihood) and ASAP methods supports the classification of H. punctatus within the Bagridae family, which validates the taxonomic status of this species. In conclusion, this research enriches our understanding of H. punctatus mitogenome, shedding light on its evolutionary dynamics within the Bagridae family and contributing to the broader knowledge of mitochondrial genes in the context of evolutionary biology.

CONCLUSIONS

The study's findings contribute to a better understanding of the mitogenome of H. punctatus and provide insights into the evolutionary relationships within other Hemibagrids.

DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees

This study introduces a new method to construct phylogenetic trees by combining both of the Simple Sequence Repeats (SSRs) and sequence alignments. The purpose of this work is to present the DendroSSR program and show it via a case study involving diverse Aspergillus species. To show how the DendroSSR program works to resolve complicated species relationships in phylogenetic trees, we employed the Aspergillus species as an example of a research case. The DendroSSR employs a technique containing multiple phases beginning with, detecting SSRs, computing SSRs similarities, sequences alignment, building a distance matrix based on SSRs similarity and sequences alignments, and then hierarchical clustering, and presenting the findings in a dendrogram. Sometimes sequence alignments alone may not give adequate information to generate a phylogenetic tree to resolve complicated species relationships. Therefore, establishing a distance matrix that is formed of addition of SSRs similarity across sequences to the traditional sequence alignment helps the process substantially and resolves the connections of complex species on phylogenetic trees. Additionally, it may be hard to distinguish complex relationships across species when studying conserved sequences, which could lead to an incomplete representation of their evolutionary relationships. These limitations are addressed by DendroSSR, which offers a technique to produce phylogenetic trees by incorporating SSRs similarity across species into the approach of generating phylogenetic trees. As it is known, SSRs are extensively scattered across the genomes of species and exhibit a great variation. Therefore, SSRs may support the knowledge gathered from sequence alignments by providing more information on genetic variation and even evolutionary relationships. The use of DendroSSR analysis might be considered for creating phylogenetic trees as a complementary or secondary strategy among the species under examination in circumstances where traditional phylogenetic analysis fails to clarify the species complex phylogenetic relationships.

Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

The Characidae family contains the largest number of tropical fish species. Morphological similarities make species identification difficult within this family. Here, the complete mitogenomes of two Characidae fish were determined and comparatively analyzed with those of nine other Characidae fish species. The two newly sequenced complete mitogenomes are circular DNA molecules with sizes of 16,701 bp (Hyphessobrycon amandae; MT484069) and 16,710 bp (Hemigrammus erythrozonus; MT484070); both have a highly conserved structure typical of Characidae, with the start codon ATN (ATG/ATT) and stop codon TAR (TAA/TAG) or an incomplete T--/TA-. Most protein-coding genes of the 11 Characidae mitogenomes showed significant codon usage bias, and the protein-coding gene cox1 was found to be a comparatively slow-evolving gene. Phylogenetic analyses via the maximum likelihood and Bayesian inference methods confirmed that H. amandae and H. erythrozonus belong to the family Characidae. In all Characidae species studied, one genus was well supported; whereas other two genera showed marked differentiation. These findings provide a phylogenetic basis for improved classification of the family Characidae. Determining the mitogenomes of H. erythrozonus and H. amandae improves our understanding of the phylogeny and evolution of fish species.

DNA barcoding and phylogenetics of freshwater fish fauna of Ranganadi River, Arunachal Pradesh

Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Fish diversity and species identification is utmost important for fisheries management. But, in some cases morphological characteristics based identification is difficult for a non-specialist to perform. In view of the above, the present study emphasized on the assessment of DNA barcoding, phylogenetics and genetic diversity of fish species in the Ranganadi River, Arunachal Pradesh, India. India. Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Altogether 114 specimens, representing 22 species, belonging to 3 orders and 5 families were successfully barcoded and found to be 98-100% identical from both GenBank and BOLD databases. Out of these 22 fish species, it was found that one species assessed was Endangered, three species as Near Threatened and one species as Vulnerable. A Neighbour Joining (NJ) tree was constructed using Rstudio for the purpose of a phylogenetic analysis of the identified species. The barcoding gap analysis using K2P, P-distance and Jukes-Cantor was done to detect the presence of cryptic species and barcoding success. The nucleotide base composition and genetic distance analysis were also performed, using MEGA 6.0. DNA Sequence Polymorphism v6.12.03 analysis revealed the nucleotide diversity (p) and haplotype diversity (Hd). The Hd for the whole dataset was found to be 0.975, which showed high genetic diversity in the Ranganadi River. Both morphological key identifying characters and molecular data corroborated the phylogenetic analysis. This COI barcode library, generated in the present study, not only helped in species identification and molecular study, but also in cryptic species identification.

The mitogenome of freshwater loach Homatula laxiclathra (Teleostei: Nemacheilidae) with phylogenetic analysis of Nemacheilidae

The complete mitogenome can provide valuable genetic information to reconstruct relationships between species. In this study, we sequenced a stone loach, Homatula laxiclathra (Teleostei: Nemacheilidae), which is found in the northern region of the Qinling Mountains in China. The size of the H. laxiclathra mitogenome is 16,570 bp, which contains 37 typical mitochondrial genes including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (D-loop) with a total AT content of 55.8%. This is similar to other Nemacheilidae sequences published in GenBank. Furthermore, a mito-phylogenomic analysis of 46 Nemacheilidae species places H. laxiclathra in a robust monophyletic Homatula cluster with other Homatula species. Our results contribute toward a better understanding of a true phylogeny of these species based on large-scale taxonomic samplings as well as to help grasp the evolution of fish mitogenomes.