Complete mitochondrial genome of Yunnan-Guizhou Plateau endemic fish, Discogobio macrophysallidos, in China.
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ABSTRACT:
SUBMITTER: Qiu Y
PROVIDER: S-EPMC7782877 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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.
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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.
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Project description:Two new toad species of the genus Leptobrachella are described from the Yunnan-Guizhou Plateau of China, based on the combination of molecular and morphological data. The description of Leptobrachella aspera Wang, Lyu, Qi & Wang, sp. nov. from Huanglianshan Nature Reserve represents the thirteenth Leptobrachella species known from Yunnan Province, and the description of Leptobrachella dorsospina Wang, Lyu, Qi & Wang, sp. nov. from Yushe Forest Park represents the sixth Leptobrachella species known from Guizhou Province. These new discoveries further emphasize the extremely high diversity of the Leptobrachella toads in these regions.
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Project description:Four new fungi of the family Peniophoraceae, viz., Peniophora roseoalba, P. yunnanensis, Vararia daweishanensis, and V. fragilis are herein proposed, based on a combination of morphological features and molecular evidence. Peniophora roseoalba is characterized by resupinate, membranaceous basidiomata with a rose pink to pale pinkish grey hymenophore, a monomitic hyphal system with clamped generative hyphae, the presence of cystidia, and ellipsoid basidiospores. However, P. yunnanensis differs in being tuberculate, with a pale cream to cream hymenial surface, small lamprocystidia (18-29 × 4.5-7 µm), and subcylindrical basidiospores. Vararia daweishanensis is characterized by resupinate, membranous basidiomata with a pale yellowish hymenial surface, a dimitic hyphal system with clamped generative hyphae, strongly dextrinoid dichohyphae, and allantoid basidiospores; V. fragilis is characterized by resupinate, brittle basidiomata, with a buff to ochraceous hymenial surface and small ellipsoid basidiospores measuring 3.5-5.5 × 2.5-3.5 µm. Sequences of the ITS and nLSU rRNA markers of the studied samples were generated, and phylogenetic analyses were performed with the maximum likelihood, maximum parsimony, and Bayesian inference methods. The nLSU analysis revealed that the four new species can be clustered into the family Peniophoraceae (Russulales), in the genera Peniophora and Vararia. Further studies based on the ITS dataset showed that four fungi of the family Peniophoraceae were new to science.
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Project description:Chimonobambusa luzhiensis (Poaceae: Bambusoideae) is an endangered plant endemic to Guizhou Province, China. Here, we report the complete chloroplast genome of C. luzhiensis. The plastid genome revealed a typical quadripartite structure with a length of 139,896 bp, including a large single-copy (LSC, 83,191 bp) region, a small single-copy (SSC, 12,811 bp) region, and a pair of inverted repeat (IR) regions (IRa and IRb, 21,797 bp). A total of 131 genes, including 86 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes were annotated, and the overall GC content was 38.8%. Phylogenetic analysis showed that the relationship between C. luzhiensis is sister to C. tumidisinoda.
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Project description:The Mugilogobius myxodermus is an endemic freshwater fish in china. Herein, we sequenced and assembled the first complete mitogenome of M. myxodermus. The total length of the mitogenome is 16,495?bp, containing 13 protein-coding genes, two ribosomal RNAs (rRNA), two non-coding regions (control region and origin of light-strand replication), and 22 transfer RNAs (tRNA). The overall base composition of M. myxodermus is 26.76% T, 28.97% C, 27.81% A, and 16.45% G, respectively. A phylogenetic tree showed that M. myxodermus clustered closest to M. abei. The complete mitogenome of M. myxodermus provides a resource for studies on biogeography and evolution of this gobiid fish.
| S-EPMC7800397 | biostudies-literature
Project description:Passiflora xishuangbannaensis, Passiflora subgenus Decaloba, is a very rare endemic to the Yunnan, China. Here we report and characterize the complete chloroplast (cp) genome sequence of P. xishuangbannaensis to provide genomic resources useful for promoting its conservation and systematics. The complete genome is 135,742 bp in length and the overall GC content is 37.1%. The cp genome sequence has a typical quadripartite structure, comprising two inverted repeats (IRs: 20,604 bp) regions, which are separated by a small single-copy (SSC: 13,159 bp) region and a large single-copy (LSC: 81,375 bp) region. Moreover, a total of 122 functional genes were annotated, including 77 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis recovered P. xishuangbannaensis as a member of subgenus Decaloba.
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Project description:Background:Mechanisms for high-altitude adaption have attracted widespread interest among evolutionary biologists. Several genome-wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds, and amphibians. However, little information is available about the adaptive evolution of highland fishes. Glyptosternon maculatum (Regan 1905), also known as Regan or barkley and endemic to the Tibetan Plateau, belongs to the Sisoridae family, order Siluriformes (catfishes). This species lives at an elevation ranging from roughly 2,800 m to 4,200 m. Hence, a high-quality reference genome of G. maculatum provides an opportunity to investigate high-altitude adaption mechanisms of fishes. Findings:To obtain a high-quality reference genome sequence of G. maculatum, we combined Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads, and BioNano optical map techniques. In total, 603.99 Gb sequencing data were generated. The assembled genome was about 662.34 Mb with scaffold and contig N50 sizes of 20.90 Mb and 993.67 kb, respectively, which captured 83% complete and 3.9% partial vertebrate Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 35.88% of the genome, and ?22,066 protein-coding genes were predicted from the genome, of which 91.7% have been functionally annotated. Conclusions:We present the first comprehensive de novo genome of G. maculatum. This genetic resource is fundamental for investigating the origin of G. maculatum and will improve our understanding of high-altitude adaption of fishes. The assembled genome can also be used as reference for future population genetic studies of G. maculatum.
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Project description:Longchuanacris curvifurculus (L. curvifurculus) was once a dominating grasshopper in the Yunnan province (People's Republic of China) that occupy important ecological niche. However, its population has severely declined because of the deterioration of ecological environment. Identifying the species and source of L. curvifurculus is important for biodiversity conservation and ecological/environmental preservation. In the study, the complete mitochondrial genome of L. curvifurculus was assembled from high-coverage (36.8×) Illumina MiSeq sequencing data. The circular genome is 15,450?bp in length, harboring 37 typical mitochondrial genes and one control region. The nucleotide composition is asymmetric (43.0% A, 14.3% C, 10.5% G, and 32.2% T), with an overall A?+?T content of 75.2%. All the protein-coding genes (PCGs) are initiated with typical ATN start codons and terminated by the typical TAA codons or the incomplete T(aa) codon. The control region has a remarkably high A?+?T content (84.9%) and is located between genes rrnS and trnV.
| S-EPMC7800574 | biostudies-literature
Project description:Abstract The complete plastid genome of Scutellaria microviolacea C. Y. Wu was firstly reported. The full length of the plastid genome was 152,092 bp and comprised of a large single-copy (LSC) region of 84,090 bp, a small single-copy (SSC) region of 17,534 bp, and two inverted repeat regions (IRs) of 25,234 bp. A total of 131 genes were encoded, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of the S. microviolacea plastid genome was 38.3%. Further phylogenetic analysis based on 18 accessions inferred that the genus Scutellaria can be divided into two clades, and S. microviolacea is evolutionarily close to Scutellaria tsinyunensis. Our study provided essential genetic resources for further studies on the evolution and genetic diversity of the genus Scutellaria and its related taxa.
| S-EPMC9090395 | biostudies-literature