Dataset Information

Complete mitochondrial genome of Yunnan-Guizhou Plateau endemic fish, Discogobio macrophysallidos, in China.

ABSTRACT: The complete mitochondrial genome of Discogobio macrophysallidos was first determined and analyzed in this work. Its mitochondrial genome is 16,593 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region, and its gene order was consistent with other fishes. Phylogenetic analysis showed that D. macrophysallidos were clustered with other three species of Discogobio. The complete mitogenome of D. macrophysallidos provides new molecular data for the further phylogenetic study of the genus of Discogobio.

SUBMITTER: Qiu Y

PROVIDER: S-EPMC7782877 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Complete mitochondrial genome of Yunnan-Guizhou Plateau endemic fish, Discogobio macrophysallidos, in China.

Qiu Yuping Y Jin Jinjin J Chen Guozhu G

Mitochondrial DNA. Part B, Resources 20200702 3

The complete mitochondrial genome of Discogobio macrophysallidos was first determined and analyzed in this work. Its mitochondrial genome is 16,593 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region, and its gene order was consistent with other fishes. Phylogenetic analysis showed that D. macrophysallidos were clustered with other three species of Discogobio. The complete mitogeno ...[more]

PMID: 33457887

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Project description:Background: Lung cancer has inherited susceptibility and show familial aggregation, the characteristics of familial lung cancer exhibit population heterogeneity. Despite previous studies, familial lung cancer in China's Yunnan-Guizhou plateau remains understudied. Methods: Between 2015 and 2017, 1,023 lung cancer patients (residents of Yunnan-Guizhou plateau) were enrolled with no limitation on other parameters, 152 subjects had familial lung cancer. Clinicopathologic parameters were analyzed and compared, 4,754 lung cancer patients from NCI-GDC were used to represent a general population. Results: Familial lung cancer (FLC) subjects showed unique characters: early-onset; increased rate of female, adenocarcinoma, stage IV and other cancer history; unbalance in anatomic sites; all ruling out significant difference in smoking status. Unbalanced distribution of co-existing diseases or symptoms was also discovered. FLC patients were more likely to develop benign lesions (polyps, nodules, cysts) early in life, especially early-growth of multiple pulmonary nodules at higher frequency. Typical diseases with family history like diabetes and hypertension were also increased in FLC population. Compared to GDC data, our subject population was younger: the age peak of our FLC group was in 50-59; our sporadic group had an age peak around 60; while GDC patients' age peak was in 60-69. Importantly, the biggest difference happened in age 40-49: our FLC group and sporadic group had 3 times and 2 times higher ratio than GDC population, respectively. Moreover, the age peaks of our FLC males and FLC females were both in 50-59; while our sporadic females had the age peak in 50-59, much earlier than sporadic males (around 60-69); reflecting gender-specific or age-specific characters in our subject population. Conclusions: Familial lung cancer in China's Yunnan-Guizhou plateau showed unique clinicopathologic characters, differences were found in gender, age, histologic type, TNM stage and co-existing diseases or symptoms. Identification of hereditary factors which lead to increased lung cancer risk will be a challenge of both scientific and clinical significance.

Project description:A Yunnan-Guizhou Plateau fish, the Kanglang white minnow (Anabarilius grahami), is a typical "3E" (Endangered, Endemic, and Economic) species in China. Its distribution is limited to Fuxian Lake, the nation's second deepest lake, with a significant local economic value but a drastically declining wild population. This species has been evaluated as VU (Vulnerable) in the China Species Red List. As one of the "Four Famous Fish" in Yunnan province, the artificial breeding has been achieved since 2003. It has not only re-established its wild natural populations by reintroduction of the artificial breeding stocks, but also brought a wide and popular utilization of this species to the local fish farms. A. grahami has become one of the main native aquaculture species in Yunnan province, and the artificial production has been emerging in steady growth each year. To promote the conservation and sustainable utilization of this fish, we initiated its whole genome sequencing project using an Illumina Hiseq2500 platform. The assembled genome size of A. grahami is 1.006 Gb, accounting for 98.63% of the estimated genome size (1.020 Gb), with contig N50 and scaffold N50 values of 26.4 kb and 4.41 Mb, respectively. Approximately about 50.38% of the genome was repetitive. A total of 25,520 protein-coding genes were subsequently predicted. A phylogenetic tree based on 4,580 single-copy genes from A. grahami and 18 other cyprinids revealed three well-supported subclades within the Cyprinidae. This is the first inter-subfamily relationship of cyprinids at genome level, providing a simple yet useful framework for understanding the traditional but popular subfamily classification systems. Interestingly, a further population demography of A. grahami uncovered a historical relationship between this fish and Fuxian Lake, suggesting that range expansion or shrinkage of the habitat has had a remarkable impact on the population size of endemic plateau fishes. Additionally, a total of 33,836 simple sequence repeats (SSR) markers were identified, and 11 loci were evaluated for a preliminary genetic diversity analysis in this study, thus providing another useful genetic resource for studying this "3E" species.

Dataset Information

Complete mitochondrial genome of Yunnan-Guizhou Plateau endemic fish, Discogobio macrophysallidos, in China.

Publications

Complete mitochondrial genome of Yunnan-Guizhou Plateau endemic fish, <i>Discogobio macrophysallidos</i>, in China.

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