Journal of Phylogenetics & Evolutionary Biology

Since due to tremendous advancement that is being made in sequencing and phylogenetic organisms, wet research techniques single-handedly cannot keep up with the influx of genomic information therefore need of bioinformatics tools such as MEGA is a need. It is user friendly bio-computational software for sequence analysis and phylogenetic tree construction for exploration evolutionary relationships among species or populations.

DNA barcoding is an effective tool for the identification of species representing diverse taxa especially through the sequence analysis of mitochondrial cytochrome c oxidase subunit I (COI) gene. In the present study, DNA barcodes were generated from 46 species of freshwater fishes covering the Orders Cypriniformes, Siluriformes, Synbranchiformes and Perciformes representing 30 genera under 9 families. All the samples were collected from diverse sites which also includes some endemic species. A total of 47 COI sequences were generated. After amplification and sequencing of 678 base pair fragment of COI, primers were trimmed which invariably generated a 635 base pair barcode sequence. The average Kimura two-parameter (K2P) distances within-species, genera, families, and orders were 0.32%, 8.40%, 14.50%, and 18.65%, respectively. DNA barcode discriminated congeneric species without any confusion. The present study strongly supports the efficiency of COI as an ideal marker for DNA barcoding of selected freshwater fishes.

Acorssocheilus wuyiensis is an endemic south China stream-dwelling cyprinid species. In this study, we decoded the complete mitogenome of Acorssocheilus wuyiensis for the first time by using whole genome sequencing approach. The complete mitogenome is 16,594 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one D-loop control region. Only ND6 and other eight tRNA genes are encoded on the L-strand while most of these genes are located in the H-strand. Its overall base composition is A: 31.1%, C: 28.0%, G: 16.2% and T: 24.7%. The complete mitogenome of the Chinese barred species of Cyprinidae could provide a basic data for further phylogenetic and conversational analysis.

Powdery mildew (PM) caused by Podosphaera xanthii and downy mildew (DM) caused by Pseudoperonospora cubensis are two of the most economically important diseases for watermelon (Citrullus lanatus) and squash (Cucurbita pepo, C. maxima and C. moschata). Traditional breeding for resistance to PM and DM is resource intensive, often requiring decades’ long phenotyping and selection processes. As an alternative, durable and broad-spectrum resistance to PM and DM can be obtained through loss-of-function of susceptibility genes in elite breeding material. Susceptibility genes for PM [Mildew-Locus-O (MLO) and Powdery Mildew Resistance (PMR)] and DM [Downy Mildew Resistance (DMR)] have been functionally proven in model plant species. Previous studies have reported candidate MLO genes for C. lanatus and C. pepo, but none for C. maxima and C. moschata. On the contrary, no PMR or DMR candidate genes have been identified for C. lanatus or any of the Cucurbita species. The current study used bioinformatics approaches based on sequence similarity, phylogenetic relationships and presence of conserved domains to predict candidate MLO genes in C. maxima and C. moschata and PMR and DMR genes in C. lanatus, C. pepo, C. maxima and C. moschata. Four MLO homologs in C. maxima and five in C. moschata clustered within Clade V, a clade containing all MLO susceptibility genes in dicots, and had highly conserved transmembrane domains and C-terminal PM interaction motif. Sixty-three candidate PMR genes were identified among the four species, 16 of which had close similarity to functionally proven PMR homologs in model species. Similarly, 37 candidate DMR genes were identified 12 among which clustered with functionally proven DMR homologs in model species. Functional analysis of the genes identified in the current study will reveal their role in pathogenesis and assess their potential for manipulation through gene editing methods to generate novel resistant plant genotypes.