Li, L.-L. | Search bioRxiv

bioRxiv2024

Telomere-to-telomere, gap-free genome of mung beans (Vigna radiata) provides insights into domestication under structural variation

Mung bean (Vigna radiata), an essential annual legume, holds substantial value in global agriculture due to its short growth cycle, low input requirements, and nutritional benefits. Despite extensive domestication, the genetic mechanisms underlying its morphological and physiological evolution remain incompletely understood. In this study, we present a gap-free, telomere-to-telomere genome assembly of the mung bean cultivar Weilv-9, achieved through the integration of PacBio HiFi, Oxford Nanopore, and Hi-C sequencing technologies. The 500 Mb assembly, encompassing 11 chromosomes and containing 28,740 protein-coding genes, reveals that 49.17% of the genome comprises repetitive sequences. Within the genome, we found the recent amplification of transposable elements significantly impacts the expression of nearby genes. Furthermore, integrating structural variation and SNP data from resequencing, we identified that the fatty acid synthesis, suberin biosynthetic, and phenylpropanoid metabolic processes have undergone strong selection during domestication. These findings provide valuable insights into the genetic mechanisms driving domestication and offer a foundation for future genetic enhancement and breeding programs in mung beans and related species.

genomics↗

bioRxiv2020

Whole Genome Sequencing of 5 Tibetan Sheep Breeds Identifies Selective Signatures to Adaptability at Different High-Altitude Areas in Qinghai-Tibetan Plateau

Tibetan sheep is one of primitive Chinese sheep breeds, which achieved the divergence about 2500 years ago in Qinghai plateau region. According to different geographic conditions, especially altitudes, Tibetan sheep evolved into different breeds. In this study, we performed pooled whole genome resequencing of 125 individuals from 5 representative Tibetan sheep breeds. Comparative genomic analysis showed that they can be divided into different clades with a close genetic relationship. However, some genes with common selective regions were enriched for hypoxic adaptability in different breeds living at higher altitude, including GHR, BMP15 and CPLANE1. Furthermore, breed-specific selective regions about physical characteristics, especially wool growth, were found in genes such as BSND, USP24, NCAPG and LCORL. This study could contribute to our understanding about trait formation and offer a reference for breeding of Tibetan sheep.

genomics↗

bioRxiv2019

Hsa-mir-210 as a novel signature predicts survival in lung squamous cell carcinoma using bioinformatics analysis

In recent years, more and more studies have shown that the expression of miRNAs is closely related to the occurrence of tumors and plays an irreplaceable role in the development and metastasis of tumors. The research was focused on lung squamous cell carcinoma. The data information is downloaded from the TCGA database and analyzed for variance, which is then verified in the GEO database. Then differential expression of miRNAs was found and survival analysis was performed, through the cut - off standard(P<0.05,|logFC|[≥]2), we screen the 38 up-regulated miRNAs and 14 down-regulated miRNAs from the TCGA. Finally, after the verification on the GEO database, four up-regulated miRNAs (hsa-mir-205, hsa-mir-210, hsa-mir-182, hsa-mir-224) and one down-regulated miRNA (hsa-mir-451) were obtained, which provide a new direction for the diagnosis of lung squamous cell carcinoma. In the survival analysis, it was found that the expression state of hsamir-210 was significantly correlated with patient survival. The results in the univariate and multivariate Cox analysis indicated that hsa-mir-210 was an independent prognostic factor on lung squamous cell carcinoma. The functional enrichment analysis showed that hsa-mir-210 was closely related to positive and negative regulation of cell proliferation, DNA transcription, VEGF signaling pathway, MAPK signaling pathway, hif-1 signaling pathway and choline metabolic pathway. In summary, this study suggested that hsa-mir-210 could be a potential prognostic factor for lung squamous cell carcinoma.\n\nAuthor SummaryMicroRNAs are single-stranded small molecular RNA that participate in the regulation of various biological functions through indirect regulation of gene expression, and have been reported to play an important role in the occurrence, development, invasion and metastasis of tumors. In recent years, the research on miRNAs has become increasingly hot, and the role of miRNAs in tumor has been proved more and more. The subjects of this study were squamous cell carcinoma in lung cancer with relatively few studies on miRNAs. Through high-throughput data analysis, miRNAs with differential expression between lung squamous cell carcinoma tissues and normal tissues were found. These differentially expressed miRNAs provide a new direction for the early diagnosis of patients. Then, survival analysis was conducted to find the miRNAs significantly correlated with the total survival time of patients, and multi-factor analysis was conducted to exclude the influence of other clinical factors, and independent risk factors (miRNAs) affecting the survival of patients were determined, so as to provide new targets for the treatment and survival prediction of patients.

bioinformatics↗