Niviventer sacer
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ABSTRACT:
PROVIDER: PRJNA780340 | ENA |
REPOSITORIES: ENA
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Project description:Comparative genomics of white-bellied rats
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Project description:Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation, thus enabling range expansion. In contrast, narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions, thus limiting their ability to expand into novel environments. However, the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood. The Niviventer niviventer species complex (NNSC), consisting of highly abundant wild rats in Southeast Asia and China, offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related. In the present study, we combined ecological niche modeling with phylogenetic analysis, which suggested that sister species cannot be both widespread and dominant within the same geographical region. Moreover, by assessing heterozygosity, linkage disequilibrium decay, and Tajima's D analysis, we found that widespread species exhibited higher genetic diversity than narrow-range species. In addition, by exploring the "genomic islands of speciation", we identified 13 genes in highly divergent regions that were shared by the two widespread species, distinguishing them from their narrow-range counterparts. Functional annotation analysis indicated that these genes are involved in nervous system development and regulation. The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.
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Project description:Niviventer sacer (Rodentia: Muridae) had been regarded as a subspecies of N. confucianus, i.e. N. c. sacer, and was raised as a distinct species recently by our laboratory. We sequenced the complete mitochondrial genome of N. sacer first and annotated the genome structure. The total length of the genome was 16,308 base pairs (bp) containing 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region. We also constructed the phylogenetic tree by maximum-likelihood method and it demonstrated that N. sacer was the sister clade of N. confucianus.
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Project description:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.
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Project description:BackgroundNiviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4). We estimated phylogenetic relationships on the basis of one mitochondrial and three nuclear genes, using concatenation and coalescent-based approaches. We also employed molecular species delimitation approaches to test the existence of cryptic and putative new species.ResultsOur phylogeny was finely resolved, especially for the N. confucianus-like species. Our data provided the first support for N. brahma and N. eha as sister species, an assignment that is congruent with their morphological similarities. Species delimitation analyses provided new insight into species diversity and systematics. Three geographic populations of N. confucianus and one of N. fulvescens were supported as genetically distinct in our species delimitation analyses, while three recognized species (N. coninga, N. huang, and N. lotipes) were not strongly supported as distinct.ConclusionsOur results suggested that several genetically distinct species may be contained within the species currently known as N. confucianus and N. fulvescens. In addition, the results of Bayesian Phylogenetics and Phylogeography (BPP) for N. coninga, N. huang, and N. lotipes indicated that either inter-specific gene flow had occurred or imperfect taxonomy was present. Morphological examinations and morphometric analyses are warranted to examine the molecular results.
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Project description:The phylogenetic structure of the genus Niviventer has been studied based on several individual mitochondrial and nuclear genes, but the results seem to be inconsistent. In order to clarify the phylogeny of Niviventer, we sequenced the complete mitochondrial genome of white-bellied rat (Niviventer andersoni of the family Muridae) by next-generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and one noncoding control region (D-Loop). Phylogenetic analyses of the nucleotide sequences of all 13 PCGs, PCGs minus ND6, and the entire mitogenome sequence except for the D-loop revealed well-resolved topologies supporting that N. andersoni was clustered with N. excelsior forming a sister division with N. confucianus, which statistically rejected the hypothesis based on the tree of cytochrome b (cytb) gene that N. confucianus is sister to N. fulvescens. Our research provides the first annotated complete mitochondrial genome of N. andersoni, extending the understanding about taxonomy and mitogenomic evolution of the genus Niviventer.
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