Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae)
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ABSTRACT:
SUBMITTER: Gao T
PROVIDER: S-EPMC10671150 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Jia-Guang Xiao, Na Song, Zhi-Qiang Han, and Tian-Xiang Gao (2016) Reliance only on morphology to identify fishes to the species level is challenging when the diagnostic characters are similar among related taxa. Within the genus Sillago, differences among some nominal species are generally small and restricted to a few characters. In this study, a new species of Sillago (Sillago shaoi sp. nov.) was described using morphology and genetic analysis of DNA barcoding. The morphological results differentiated S. shaoi sp. nov. from eight other Sillago spp. Genetic analysis verified both the validity of the current taxonomy and the relationships between the new species and other Sillago species. S. shaoi sp. nov. formed a monophyletic group as a distinct phylogenetic species and showed strong genetic divergence from others. The present study also revealed that the COI gene was an effective molecular marker for identifying Sillago species.
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Project description:A new Sillago species, the black-banded sillago, Sillago nigrofasciata sp. nov., is described based on 302 specimens sampled from the southern coast of China. Morphological comparisons have been conducted between the new species and ten other Sillago species. The results show that the new species is characterized by a black mid-lateral band below the lateral line when fresh; other characteristics are similar to those of Sillago sihama but subtle differences exist on the swim bladder between Sillago nigrofasciata sp. nov. and S. sihama. A detailed description and illustrations are provided for the new species. The validity of this new species is also supported by a genetic comparison using sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene.
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Project description:BackgroundSillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica), have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to set up a platform for comparative analysis of all species in this family.FindingsUsing the single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) Sequel, we generated ∼27.3 Gb genomic DNA sequences for the Chinese sillago. We reconstructed a genome assembly of 534 Mb using a strategy that takes advantage of complementary strengths of two genome assembly programs, Canu and FALCON. The genome size was consistent with the estimated genome size based on k-mer analysis. The assembled genome consisted of 802 contigs with a contig N50 length of 2.6 Mb. We annotated 22,122 protein-coding genes in the Chinese sillago genomes using a de novo method as well as RNA sequencing data and homologies to other teleosts. According to the phylogenetic analysis using protein-coding genes, the Chinese sillago is closely related to Larimichthys crocea and Dicentrarchus labrax and diverged from their ancestor around 69.5-82.6 million years ago.ConclusionsUsing long reads generated with PacBio sequencing technology, we have built a draft genome assembly for the Chinese sillago, which is the first reference genome for Sillaginidae species. This genome assembly sets a stage for comparative analysis of the diversification and adaptation of fishes in Sillaginidae.
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Project description:Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co-occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next-generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein-encoding genes, with the Complex IV genes (coxI-III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species.
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Project description:To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species.
| S-EPMC4632788 | biostudies-literature
Project description:BackgroundDNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library.Methodology/principal findingsHere, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32-4.82%) than mean estimates (0.24-0.39%), indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region's suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P) distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata.Conclusion/significanceThis study confirms that COI is an effective tool for species identification of Carangidae from the IMA. There were moderate levels of cryptic diversity among putative species within the central IMA. However, to explain the hypothesis of species richness in the IMA, it is necessary to sample the whole family across their broad geographic range. Such insights are helpful not only to document mechanisms driving diversification and recruitment in Carangidae, but also to provide a scientific framework for management strategies and conservation of commercially-important fisheries resources.
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Project description:The complete mitochondrial genome of Sillaginopsis panijus has been determined for the first time using Sanger Dideoxy DNA sequencing. The mitogenome is a circular molecule of 16,529 bp in length. It contains 37 mitochondrial genes (13 protein-coding genes, two ribosomal RNA, and 22 transfer RNA) and a control region as other bony fishes. In the phylogenetic analysis using 12H-strand protein-coding genes, monotypic S. panijus is situated separately from the genus Sillago. The present phylogeny supports its taxonomic position according to morphology and will be helpful for evolutionary analysis.
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Project description:Silver sillago (Sillago sihama) is a commercially important marine fish species in East Asia. In this study, we compared the transcriptome response to hypoxia stress in the gill tissue of S. sihama. The fish were divided into four groups, such as 1 h of hypoxia (hypoxia1h, DO = 1.5 ± 0.1 mg/L), 4 h of hypoxia (hypoxia4h, DO = 1.5 ± 0.1 mg/L), 4 h of reoxygen (reoxygen4h, DO = 8.0 ± 0.2 mg/L) after 4 h of hypoxia (DO = 1.5 mg/L), and normoxia or control (DO = 8.0 ± 0.2 mg/L) groups. Compared to the normoxia group, a total of 3550 genes were identified as differentially expressed genes (DEGs) (log2foldchange > 1 and padj < 0.05), including 1103, 1451 and 996 genes in hypoxia1h, hypoxia4h and reoxygen4h groups, respectively. Only 247 DEGs were differentially co-expressed in all treatment groups. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, DEGs were significantly enriched in steroid biosynthesis, biosynthesis of amino acids, glutathione metabolism and metabolism of xenobiotics by cytochrome P450, ferroptosis and drug metabolism-cytochrome P450 pathways. Of these, the cytochrome P450 (CYP) and glutathione S-transferase (GST) gene families were widely expressed. Our study represents the insights into the underlying molecular mechanisms of hypoxia stress.
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