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Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-20 Tristan Cumer, Charles Pouchon, Frédéric Boyer, Glenn Yannic, Delphine Rioux, Aurélie Bonin, Thibaut Capblancq
Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory
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Saccharomyces cerevisiae RNA lariat debranching enzyme, Dbr1p, is required for completion of reverse transcription by the retrovirus-like element Ty1 and cleaves branched Ty1 RNAs Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-19 Thomas M. Menees
RNA debranching enzymes are 2′-5′ phosphodiesterases found in all eukaryotes. Their main role is cleavage of intron RNA lariat branch points, promoting RNA turnover via exonucleases. Consistent with this role, cells with reduced RNA debranching enzyme activity accumulate intron RNA lariats. The Saccharomyces cerevisiae RNA debranching enzyme Dbr1p is also a host factor for the yeast long terminal repeat
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Identification of genetic variation for salt tolerance in Brassica napus using genome-wide association mapping Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-19 Ghulam Mustafa Wassan, Hira Khanzada, Qinghong Zhou, Annaliese S. Mason, Ayaz Ali Keerio, Saba Khanzada, Abdul Malik Solangi, Muhammad Faheem, Donghui Fu, Haohua He
Soil salinity negatively impacts rapeseed (Brassica napus) crop production. In particular, high soil salinity is known to hinder seedling growth and establishment. Identifying natural genetic variation for high salt tolerance in Brassica napus seedlings is an effective way to breed for improved productivity under salt stress. To identify genetic variants involved in differential response to salt stress
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Regulation of flowering under short photoperiods based on transcriptomic and metabolomic analysis in Phaseolus vulgaris L. Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-15 Xiaoxu Yang, Dajun Liu, Zhishan Yan, Chang Liu, Guojun Feng
Common bean (Phaseolus vulgaris L.) is a short-day plant and its flowering time, and consequently, pod yield and quality is influenced by photoperiod. In this study, the photoperiodic-sensitive variety ‘Hong jin gou’, which flowers 31 days (d) earlier in short-day than in long-day, was used as the experimental material. Samples were collected to determine the growth and photosynthetic parameters in
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Cost-efficiency tradeoff is optimized in various cancer types revealed by genome-wide analysis Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-15 Shufen Zhao, Shanai Song, Qi Qi, Wei Lei
The tradeoff between cost and efficiency is omnipresent in organisms. Specifically, how the evolutionary force shapes the tradeoff between biosynthetic cost and translation efficiency remains unclear. In the cancer community, whether the adjustment of cost-efficiency tradeoff acts as a strategy to facilitate tumor proliferation and contributes to oncogenesis is uninvestigated. To address this issue
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The cellulose synthase ( CesA ) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-13 Sujun Zhang, Zhenxing Jiang, Jie Chen, Zongfu Han, Jina Chi, Xihua Li, Jiwen Yu, Chaozhu Xing, Mingzhou Song, Jianyong Wu, Feng Liu, Xiangyun Zhang, Jinfa Zhang, Jianhong Zhang
Cellulose synthases (CesAs) are multi-subunit enzymes found on the plasma membrane of plant cells and play a pivotal role in cellulose production. The cotton fiber is mainly composed of cellulose, and the genetic relationships between CesA genes and cotton fiber yield and quality are not fully understood. Through a phylogenetic analysis, the CesA gene family in diploid Gossypium arboreum and Gossypium
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Profiling transcriptomic changes and signaling pathways in atopic dermatitis by integrative analyses on multiple databases Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-13 Yubin Xu, Saizhen Chen, Jinguang Chen
Atopic dermatitis (AD) is a condition driven by T cell-mediated immune response. Targeted therapy of AD is challenging due to its complex pathogenesis. In the current study, by analyzing multiple expression and network datasets, we aimed at: (1) identifying important transcriptomic signatures/profiles for AD to seek potential therapeutic targets and (2) discovering key regulators in the pathogenesis
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Whole-genome resequencing reveals loci with allelic transmission ratio distortion in F 1 chicken population Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-06 Peng Ren, Feilong Deng, Shiyi Chen, Jinshan Ran, Jingjing Li, Lingqian Yin, Yan Wang, Huadong Yin, Qing Zhu, Yiping Liu
Allelic transmission ratio distortion (TRD) is the significant deviation from the expected ratio under Mendelian inheritance theory, which may be resulted from multiple disrupted biological processes, including germline selection, meiotic drive, gametic competition, imprint error, and embryo lethality. However, it is less known that whether or what extent the allelic TRD is present in farm animals
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Evolutionary QTL-allele changes in main stem node number among geographic and seasonal subpopulations of Chinese cultivated soybeans Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-04 Abbas Muhammad Fahim, Fangdong Liu, Jianbo He, Wubing Wang, Guangnan Xing, Junyi Gai
The main stem node number (MSN) is a trait related to geographic adaptation, plant architecture and yield potential of soybean. The QTL-allele constitution of the Chinese Cultivated Soybean Population (CCSP) was identified using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) procedure, from which a QTL-allele matrix was established and then separated into submatrices
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Cluster II che genes of Pseudomonas syringae pv. tabaci 6605, orthologs of cluster I in Pseudomonas aeruginosa, are required for chemotaxis and virulence Mol. Genet. Genomics (IF 2.797) Pub Date : 2021-01-02 Stephany Angelia Tumewu, Yujiro Ogawa, Takumi Okamoto, Yuka Sugihara, Hajime Yamada, Fumiko Taguchi, Hidenori Matsui, Mikihiro Yamamoto, Yoshiteru Noutoshi, Kazuhiro Toyoda, Yuki Ichinose
Pseudomonas syringae pv. tabaci 6605 (Pta6605) is a causal agent of wildfire disease in host tobacco plants and is highly motile. Pta6605 has multiple clusters of chemotaxis genes including cheA, a gene encoding a histidine kinase, cheY, a gene encoding a response regulator, mcp, a gene for a methyl-accepting chemotaxis protein, as well as flagellar and pili biogenesis genes. However, only two major
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TaNAC35 acts as a negative regulator for leaf rust resistance in a compatible interaction between common wheat and Puccinia triticina Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-11-27 Na Zhang, Shengliang Yuan, Chenguang Zhao, Robert F. Park, Xiaolei Wen, Wenxiang Yang, Na Zhang, Daqun Liu
NAC (NAM, AFAT1/2, and CUC2) transcription factors play important roles in plant growth and in resistance to abiotic and biotic stresses. Here, we show that the TaNAC35 gene negatively regulates leaf rust resistance in the wheat line Thatcher + Lr14b (TcLr14b) when challenged with a virulent isolate of Puccinia triticina (Pt). The TaNAC35 gene was cloned from this line, and blastp results showed that
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Unpredictable recombination of PB transposon in Silkworm: a potential risk Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-11-17 Xuehua Jia, Xiaoyu Pang, Yajie Yuan, Qiang Gao, Ming Lu, Guangxian Zhang, FangYing Dai, Tianfu Zhao
The piggyBac (PB) transposon is the most widely used vector for generating transgenic silkworms. The stability of the PB transposon in the receptor is a serious concern that requires attention because of biosafety concerns. In this study, we found that the transgene silkworm developed loss of reporter gene traits. To further investigate the regularity, we traced the genes and traits of this silkworm
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Molecular variation among virulent and avirulent strains of the quarantine nematode Bursaphelenchus xylophilus Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-11-10 Anna Filipiak, Tadeusz Malewski, Ewa Matczyńska, Marek Tomalak
Bursaphelenchus xylophilus is an emerging pathogenic nematode that is responsible for a devastating epidemic of pine wilt disease worldwide, causing severe ecological damage and economic losses to forestry. Two forms of this nematode have been reported, i.e., with strong and weak virulence, commonly referred as virulent and avirulent strains. However, the pathogenicity-related genes of B. xylophilus
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iCDA-CMG: identifying circRNA-disease associations by federating multi-similarity fusion and collective matrix completion Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-11-06 Qiu Xiao, Jiancheng Zhong, Xiwei Tang, Jiawei Luo
Circular RNAs (circRNAs) are a special class of non-coding RNAs with covalently closed-loop structures. Studies prove that circRNAs perform critical roles in various biological processes, and the aberrant expression of circRNAs is closely related to tumorigenesis. Therefore, identifying potential circRNA-disease associations is beneficial to understand the pathogenesis of complex diseases at the circRNA
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Compound heterozygous PLA2G6 loss-of-function variants in Swaledale sheep with neuroaxonal dystrophy Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-11-06 Anna Letko, Ben Strugnell, Irene M. Häfliger, Julia M. Paris, Katie Waine, Cord Drögemüller, Sandra Scholes
Sporadic occurrences of neurodegenerative disorders including neuroaxonal dystrophy (NAD) have been previously reported in sheep. However, so far no causative genetic variant has been found for ovine NAD. The aim of this study was to characterize the phenotype and the genetic aetiology of an early-onset neurodegenerative disorder observed in several lambs of purebred Swaledale sheep, a native English
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A potential endogenous gibberellin-mediated signaling cascade regulated floral transition in Magnolia × soulangeana ‘Changchun’ Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-11-04 Liyong Sun, Zheng Jiang, Ye Ju, Xuan Zou, Xiaoxia Wan, Yao Chen, Zengfang Yin
The floral transition is a critical developmental switch in plants, and has profound effects on the flower production and yield. Magnolia × soulangeana ‘Changchun’ is known as a woody ornamental plant, which can bloom in spring and summer, respectively. In this study, anatomical observation, physiological measurement, transcriptome, and small RNA sequencing were performed to investigate potential endogenous
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Elucidation of sequence polymorphism in fuzzless-seed cotton lines Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-11-03 Marina Naoumkina, Gregory N. Thyssen, David D. Fang, Ping Li, Christopher B. Florane
Most commercially produced cotton cultivars have two types of fibers on the seed coat, short fuzz and long lint. Lint fiber is used in the textile industry, while fuzz is considered an undesirable trait. Both types of fibers are believed to be controlled by the same regulators; however, their mechanisms of actions are still obscure. Cotton fiber mutants provide an excellent system to study the genes
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A celery transcriptional repressor AgERF8 negatively modulates abscisic acid and salt tolerance Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-11-01 Jie-Xia Liu, Bei Wu, Kai Feng, Meng-Yao Li, Ao-Qi Duan, Di Shen, Lian Yin, Zhi-Sheng Xu, Ai-Sheng Xiong
Ethylene response factors (ERFs) widely exist in plants and have been reported to be an important regulator of plant abiotic stress. Celery, a common economic vegetable of Apiaceae, contains lots of ERF transcription factors (TFs) with various functions. AP2/ERF TFs play positive or negative roles in plant growth and stress response. Here, AgERF8, a gene encoding EAR-type AP2/ERF TF, was identified
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Effects of shading on lignin biosynthesis in the leaf of tea plant ( Camellia sinensis (L.) O. Kuntze) Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-10-28 Rui-Min Teng, Yong-Xin Wang, Hui Li, Shi-Jia Lin, Hao Liu, Jing Zhuang
Shading can effectively reduce photoinhibition and improve the quality of tea. Lignin is one of the most important secondary metabolites that play vital functions in plant growth and development. However, little is known about the relationship between shading and xylogenesis in tea plant. To investigate the effects of shading on lignin accumulation in tea plants, ‘Longjing 43’ was treated with no shading
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Low expression of carotenoids cleavage dioxygenase 1 ( ccd1 ) gene improves the retention of provitamin-A in maize grains during storage Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-10-17 Suman Dutta, Vignesh Muthusamy, Rashmi Chhabra, Aanchal Baveja, Rajkumar U. Zunjare, Tapan K. Mondal, Devendra K. Yadava, Firoz Hossain
Provitamin-A (proA) is essentially required for vision in humans but its deficiency affects children and pregnant women especially in the developing world. Biofortified maize rich in proA provides new opportunity for sustainable and cost-effective solution to alleviate malnutrition, however, significant loss of carotenoids during storage reduces its efficacy. Here, we studied the role of carotenoid
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Functional characterization of the AGL1 aegerolysin in the mycoparasitic fungus Trichoderma atroviride reveals a role in conidiation and antagonism Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-10-14 Mukesh Dubey, Dan Funck Jensen, Magnus Karlsson
Aegerolysins are small secreted pore-forming proteins that are found in both prokaryotes and eukaryotes. The role of aegerolysins in sporulation, fruit body formation, and in lysis of cellular membrane is suggested in fungi. The aim of the present study was to characterize the biological function of the aegerolysin gene agl1 in the mycoparasitic fungus Trichoderma atroviride, used for biological control
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GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of 11 Upland cotton ( Gossypium hirsutum ) parents Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-10-13 Abdelraheem Abdelraheem, Gregory N. Thyssen, David D. Fang, Johnie N. Jenkins, Jack C. McCarty, Tom Wedegaertner, Jinfa Zhang
Cotton is grown in arid and semi-arid regions where abiotic stresses such as drought and salt are prevalent. There is a lack of studies that simultaneously address the genetic and genomic basis of tolerance to drought and salt stress. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs) together with their 11 Upland cotton parents with
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SARS-CoV-2 has the advantage of competing the iMet–tRNAs with human hosts to allow efficient translation Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-10-10 Yan Wang, Yanhong Gai, Yuefan Li, Chunxiao Li, Ziliang Li, Xuekun Wang
To better understand the interaction between SARS-CoV-2 and human host and find potential ways to block the pandemic, one of the unresolved questions is that how the virus economically utilizes the resources of the hosts. Particularly, the tRNA pool has been adapted to the host genes. If the virus intends to translate its own RNA, then it has to compete with the abundant host mRNAs for the tRNA molecules
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A heterozygous hypomorphic mutation of Fanca causes impaired follicle development and subfertility in female mice Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-10-06 Yuncheng Pan, Xi Yang, Feng Zhang, Siyuan Chen, Zixue Zhou, Hao Yin, Hui Ma, Lingyue Shang, Jialin Yang, Guoqing Li, Yingchen Wang, Li Jin, Qinghua Shi, Yanhua Wu
Reduced fertility is a common clinical feature of the individuals with Fanconi anemia (FA), a rare autosomal recessive disorder due to deficiency in FA pathway during DNA repair. Our previous study reported that the heterozygous pathogenic variants in FANCA (Fanconi anemia complementation group A) induced premature ovarian insufficiency (POI). However, the genotype–phenotype correlation in POI caused
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Recent advances on the machine learning methods in predicting ncRNA-protein interactions Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-10-02 Lin Zhong, Meiqin Zhen, Jianqiang Sun, Qi Zhao
Recent transcriptomics and bioinformatics studies have shown that ncRNAs can affect chromosome structure and gene transcription, participate in the epigenetic regulation, and take part in diseases such as tumorigenesis. Biologists have found that most ncRNAs usually work by interacting with the corresponding RNA-binding proteins. Therefore, ncRNA-protein interaction is a very popular study in both
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Marker genotyping error effects on genomic predictions under different genetic architectures Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-29 Tahere Akbarpour, Navid Ghavi Hossein-Zadeh, Abdol Ahad Shadparvar
This study aimed to determine the effect of different rates of marker genotyping error on the accuracy of genomic prediction that was examined under distinct marker and quantitative trait loci (QTL) densities and different heritability estimates using a stochastic simulation approach. For each scenario of simulation, a reference population with phenotypic and genotypic records and a validation population
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Insights into the microbiota of larval and postlarval Pacific white shrimp ( Penaeus vannamei ) along early developmental stages: a case in pond level Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-08-14 Hailiang Wang, Jie Huang, Ping Wang, Ting Li
Increasing studies have revealed strong links among gut microbiota, health status, and shrimp development, but they mainly focus on the microbiota of Pacific white shrimp, Penaeus vannamei, during life stages from juveniles to adults. Little is known about shrimp microbiota dynamics at early developmental stages. In this study, with an aim to profile shrimp microbiota and its dynamics at stages nauplius
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The critical region for viral RNA encapsidation in leader promoter of Nipah virus Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-08-07 Lian Yih Pong, Amir Rabu, Nazlina Ibrahim
Encapsidation by nucleocapsid (N) protein is crucial for viral RNA to serve as a functional template for virus replication. However, the potential region that is vital for RNA encapsidation of Nipah virus (NiV) is still unknown. Thus, this study was aimed to identify these regions using a NiV minireplicon system. A series of broad range internal deletion mutations was generated in the 5′ non-translated
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Y-DNA genetic evidence reveals several different ancient origins in the Brahmin population. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-25 David G Mahal
The ancient geographical origins of Brahmins—a prominent ethnic group in the Indian subcontinent—have remained controversial for a long time. This study employed the AMOVA (analysis of molecular variance) test to evaluate genetic affinities of this group with thirty populations of Central Asia and Europe. A domestic comparison was performed with fifty non-Brahmin groups in India. The results showed
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Three pleiotropic loci associated with bone mineral density and lean body mass. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-24 Yu-Xue Zhang,Shan-Shan Zhang,Shu Ran,Yu Liu,Hong Zhang,Xiao-Lin Yang,Rong Hai,Hui Shen,Qing Tian,Hong-Wen Deng,Lei Zhang,Yu-Fang Pei
Both bone mineral density (BMD) and lean body mass (LBM) are important physiological measures with strong genetic determination. Besides, BMD and LBM might have common genetic factors. Aiming to identify pleiotropic genomic loci underlying BMD and LBM, we performed bivariate genome-wide association study meta-analyses of femoral neck bone mineral density and LBM at arms and legs, and replicated in
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Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-21 Li'ang Yu,Xiaokai Ma,Ban Deng,Jingjing Yue,Ray Ming
Spinach (Spinacia olracea L.) is a dioecious leafy vegetable with a highly repetitive genome of around 990 Mb, which is challenging for de-novo genome assembly. In our study, a segregating F1 (double pseudo-testcross) population from ‘Viroflay’ × ‘Cornell-NO. 9′ was used for genetic mapping by resequencing genotyping. In the paternal ‘Cornell-NO. 9′ map, 212,414 SNPs were mapped, and the total linkage
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Mig1 localization exhibits biphasic behavior which is controlled by both metabolic and regulatory roles of the sugar kinases. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-19 Gregor W Schmidt,Niek Welkenhuysen,Tian Ye,Marija Cvijovic,Stefan Hohmann
Glucose, fructose and mannose are the preferred carbon/energy sources for the yeast Saccharomyces cerevisiae. Absence of preferred energy sources activates glucose derepression, which is regulated by the kinase Snf1. Snf1 phosphorylates the transcriptional repressor Mig1, which results in its exit from the nucleus and subsequent derepression of genes. In contrast, Snf1 is inactive when preferred carbon
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A rare mutant of OFD1 gene responsible for Joubert syndrome with significant phenotype variation. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-18 Yang-Wei Zhang,Hai-Bo Qu,Ning Long,Xiang-You Leng,Yun-Qiang Liu,Yuan Yang
Joubert syndrome (JBTS), a rare genetic disorder resulted from primary cilium defects or basal-body dysfunction, is characterized by agenesis of cerebellar vermis and abnormal brain stem. Both genotypes and phenotypes of JBTS are highly heterogeneous. The identification of pathogenic gene variation is essential for making a definite diagnosis on JBTS. Here, we found that hypoplasia of cerebellar vermis
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Comparative analysis of the pulmonary microbiome in healthy and diseased pigs. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-17 Zongjie Li,Xin Wang,Di Di,Ruyi Pan,Yun Gao,Changguang Xiao,Beibei Li,Jianchao Wei,Ke Liu,Yafeng Qiu,Zhiyong Ma
The lungs possess an effective antimicrobial system and a strong ability to eliminate microorganisms in healthy organisms, and were once considered sterile. With the development of culture-independent sequencing technology, the richness and diversity of porcine lung microbiota have been gaining attention. In order to study the relationship between lung microbiota and porcine respiratory disease complex
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Identification and expression profile of microRNA in seven tissues of the Golden snub-nosed monkey (Rhinopithecus roxellanae). Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-11 Qiao Yang,Jianqiu Yu,Lan Jiang,Xuanzhen Liu,Fangyuan Liu,Yansen Cai,Lili Niu,Megan Price,Jing Li
MicroRNAs (miRNAs) are key in the post-transcriptional regulation of gene expression and thus characterization of miRNAs and investigation of the relative abundance and specificity of tissue expression are essential for understanding gene expression in the golden snub-nosed monkey (GSM, Rhinopithecus roxellanae). Here, we report the first dataset of GSM miRNAs where we identified 460 miRNAs in seven
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Genomic analysis suggests Salinispora is a rich source of novel lanthipeptides. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-07 Caroline G Kittrell,Shailey C Shah,Matthew E Halbert,Dylan H Scott,Emilianne M Limbrick
Lanthipeptides are a subgroup of ribosomally encoded and post-translationally modified peptides (RiPPs) which frequently possess potent biological activity. Here we provide the first comprehensive bioinformatic analysis of the lanthipeptide-producing capability of the Salinispora genus, a marine actinomycete. One hundred twenty-two Salinispora arenicola, tropica, and pacifica genomic sequences were
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Harnessing the power of genetics: fast forward genetics in Caenorhabditis elegans. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-04 Jogender Singh
Forward genetics is a powerful tool to unravel molecular mechanisms of diverse biological processes. The success of genetic screens primarily relies on the ease of genetic manipulation of an organism and the availability of a plethora of genetic tools. The roundworm Caenorhabditis elegans has been one of the favorite models for genetic studies due to its hermaphroditic lifestyle, ease of maintenance
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GC usage of SARS-CoV-2 genes might adapt to the environment of human lung expressed genes. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-09-04 Yue Li,Xinai Yang,Na Wang,Haiyan Wang,Bin Yin,Xiaoping Yang,Wenqing Jiang
Understanding how SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) efficiently reproduces itself by taking resources from the human host could facilitate the development of drugs against the virus. SARS-CoV-2 translates its own proteins by using the host tRNAs, so that its GC or codon usage should fit that of the host cells. It is necessary to study both the virus and human genomes in the
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Drug repositioning based on the target microRNAs using bilateral-inductive matrix completion. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-24 K Deepthi,A S Jereesh
Identifying the cause-and-effect mechanism behind the drug–disease associations is a challenging task. Recent studies indicate that microRNAs (miRNAs) play critical roles in human diseases. Targeting specific miRNAs with drugs to treat diseases provides a new aspect for drug repositioning. Drug repositioning provides a way to identify new clinical applications for approved drugs. Drug discovery is
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Characterization of the promoter of the nitrate transporter-encoding gene nrtA in Aspergillus nidulans Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-19 Yangyi Liu, Haoxiang Li, Jingyi Li, Yao Zhou, Zhemin Zhou, Ping Wang, Shengmin Zhou
Aspergillus nidulans nrtA encodes a nitrate transporter that plays an important role in the \({\text{NO}}_{{3}}^{ - }\) assimilatory process. Many studies have focused on protein functions rather than gene regulation. The knowledge of nrtA\({\text{NO}}_{{3}}^{ - }\) uptake process, particularly in the regulation mechanism of transcription factors AreA and NirA on nrtA transcription, is very limited
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Genetic analysis of tri-allelic patterns at the CODIS STR loci Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-16 Qinrui Yang, Yiwen Shen, Chengchen Shao, Yidong Liu, Hongmei Xu, Yueqin Zhou, Zhiping Liu, Kuan Sun, Qiqun Tang, Jianhui Xie
In the routine of autosomal STR genotyping for forensic aims, tri-allelic patterns could be occasionally observed at a single locus in phenotypically normal individuals. Two predominant types of tri-allelic variants have been nominated. Uneven intensities of three alleles are normally considered as the Type 1 pattern, and balanced height of three alleles are considered as the Type 2 pattern. In this
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Characterization and application of a putative transcription factor (SUT2) in Pichia pastoris Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-21 Yankun Yang, Yating Zheng, Pengcheng Wang, Xiang Li, Chunjun Zhan, Robert J. Linhardt, Fuming Zhang, Xiuxia Liu, Jinling Zhan, Zhonghu Bai
Pichia pastoris is able to metabolize methanol via a specific MUT (methanol utilization) pathway. Based on the powerful AOX1 (Alcohol Oxidase 1) promoter, the P. pastoris expression system has become one of the most widely used eukaryotic expression systems. The molecular mechanisms of methanol metabolic regulation remain unclearly understood, so it is important to identify and develop new transcriptional
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A novel gene in early childhood diabetes: EDEM2 silencing decreases SLC2A2 and PXD1 expression, leading to impaired insulin secretion Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-16 Yazeid Alhaidan, Henrik Thybo Christesen, Kurt Højlund, Mohammed A. Al Balwi, Klaus Brusgaard
Monogenic diabetes is a rare type of diabetes resulting from mutations in a single gene. To date, most cases remain genetically unexplained, posing a challenge for accurate diabetes treatment, which leads to on a molecular diagnosis. Therefore, a trio exome scan was performed in a lean, nonsyndromic Caucasian girl with diabetes onset at 2½ years who was negative for autoantibodies. The lean father
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Characterization of the primate TRIM gene family reveals the recent evolution in primates Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-20 Shi Qiu, Hua Liu, Zuoyi Jian, Zhenxin Fan, Sanxu Liu, Jinchuan Xing, Jing Li
The tripartite motif (TRIM) gene family encodes diverse distinct proteins that play important roles in many biological processes. However, the molecular evolution and phylogenetic relationships of TRIM genes in primates are still elusive. We performed a genomic approach to identify and characterize TRIM genes in human and other six primate genomes. In total, 537 putative functional TRIM genes were
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Technical benefit on apple fruit of controlled atmosphere influenced by 1-MCP at molecular levels. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-22 Camila Francine Paes Nunes,Isadora Rubin de Oliveira,Tatiane Timm Storch,Cesar Valmor Rombaldi,Mathilde Orsel-Baldwin,Jean-Pierre Renou,François Laurens,César Luis Girardi
Abstract The apple is a highly perishable fruit after harvesting and, therefore, several storage technologies have been studied to provide the consumer market with a quality product with a longer shelf life. However, little is known about the apple genome that is submitted to the storage, and even less with the application of ripening inhibitors. Due to these factors, this study sought to elucidate
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Polymorphisms of the growth hormone gene and their association with growth traits and sex in Sarcocheilichthys sinensis. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-22 Chuankun Zhu,Zhengjun Pan,Guoliang Chang,Hui Wang,Huaiyu Ding,Nan Wu,Xiaogang Qiang,Xiangsheng Yu,Long Wang,Ji Zhang
The growth hormone gene (gh) of Sarcocheilichthys sinensis was cloned and characterized in this study. The cDNA length of gh was 973 bp, containing a 5′-UTR of 15 bp, a 3′-UTR of 325 bp and an open reading frame of 633 bp. The genomic DNA of gh was 2135 bp in length containing five exons and four introns. The precursor peptide of gh contained 210 amino acids (aa), including a signal peptide of 22 aa
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Investigation of genes associated with petal variations between diploid and autotetraploid in Chinese cabbage (Brassica rapa L. ssp. pekinensis) by RNA-seq and sRNA-seq. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-19 Fengyan Shi,Yiheng Wang,Shengnan Huang,Shiyao Dong,Zhiyong Liu,Hui Feng
Polyploidy promotes morphological, physiological, and reproductive diversity in plants. The imminent effect of chromosome doubling in plants is the enlargement of organs such as flowers and fruits, which increases the commercial value of crops. Flowering plays a vital role in the growth and development of angiosperms. Here, we prepared an isolated microspore culture of ‘FT’, a doubled haploid (DH)
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Use Chou's 5-steps rule to identify DNase I hypersensitive sites via dinucleotide property matrix and extreme gradient boosting. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-19 Shengli Zhang,Tian Xue
DNase I hypersensitive sites (DHSs) are highly sensitive active chromatin regions to DNase I enzymes, which provide the basis for the study of gene transcriptional regulation mechanism and play an important role in the analysis of gene expression regulatory elements. The identification of DHSs has contributed to biomedical research and genome analysis. There are already southern blotting technology
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Reanalysis and integration of public microarray datasets reveals novel host genes modulated in leprosy. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-13 Thyago Leal-Calvo,Milton Ozório Moraes
Due to multiple hypothesis testing with often limited sample size, microarrays and other—omics technologies can sometimes produce irreproducible findings. Complementary to better experimental design, reanalysis and integration of gene expression datasets may help overcome reproducibility issues by identifying consistent differentially expressed genes from independent studies. In this work, after a
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Comprehensive temporal reprogramming ensures dynamicity of transcriptomic profile for adaptive response in Taxus contorta. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-13 Aasim Majeed,Amandeep Singh,Ram Kumar Sharma,Vikas Jaitak,Pankaj Bhardwaj
Plants respond to the environmental perturbations by triggering the dynamic changes within the transcriptome. The assessment of these oscillations within the transcriptome would offer insights into the ecological adaptation of the plants. We evaluated how the transcriptome of Taxus contorta swings under natural conditions to elucidate its adaptive response. Thus, our study provides new insights into
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Multiple transcriptomic analyses and characterization of pathogen-related core effectors and LysM family members reveal their differential roles in fungal growth and pathogenicity in Penicillium expansum. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-12 Danyang Chen,Guangwei Li,Jia Liu,Michael Wisniewski,Samir Droby,Elena Levin,Shengxiong Huang,Yongsheng Liu
Penicillium expansum is a destructive phytopathogen causing postharvest decay on many stored fruits. To develop effective and safe management strategies, it is important to investigate its pathogenicity-related mechanisms. In this study, a bioinformatic pipeline was constructed and 50 core effector genes were identified in P. expansum using multiple RNA-seq data sets and their putative functions were
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MTNR1B gene on susceptibility to gestational diabetes mellitus: a two-stage hospital-based study in Southern China. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-12 Yulong Jia,Yi Shen,Xiuying Shi,Xuefeng Gu,Peng Zhang,Yuanlin Liu,Aiyong Zhu,Liying Jiang
Large-scale studies on genetic risk loci for melatonin receptor 1B (MTNR1B) gene and GDM risk have not been well generalized to the Chinese population. In this study, we performed two-stage case–control study: 1.429 pregnant women: 753 GDM/676 controls in the Southern Chinese population by genotyping 5 SNPs (rs10830963, rs1387153, rs2166706, rs1447352, and rs4753426) in MTNR1B. Genotypes were determined
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A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-grown carrot taproot. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-12 Daniela Arias,Jonathan Maldonado,Herman Silva,Claudia Stange
Carotenoids are terpenoid pigments synthesized by all photosynthetic and some non-photosynthetic organisms. In plants, these lipophilic compounds are involved in photosynthesis, photoprotection, and phytohormone synthesis. In plants, carotenoid biosynthesis is induced by several environmental factors such as light including photoreceptors, such as phytochromes (PHYs) and negatively regulated by phytochrome
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Up-regulation of GhPAP1A results in moderate anthocyanin accumulation and pigmentation in sub-red cotton. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-07-10 Aimin Liang,Jia Zhao,Xin Li,Fulin Yan,Zhong Chen,Xusheng Chen,Yi Wang,Yaohua Li,Chuannan Wang,Yuehua Xiao
Anthocyanins are a group of important secondary metabolites, functioning as colorant in plant organs as well as protective agents against several stresses. Sub-red plant (Rs) cottons, accumulating moderate level of anthocyanins in shoots, had increased photosynthesis efficiency compared to green- (GL) and red-plant (R1) cottons. The present work aimed to clarify the molecular base of anthocyanin regulation
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Blocked chlorophyll synthesis leads to the production of golden snap bean pods Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-30 Chang Liu, Yanmei Li, Dajun Liu, Zhishan Yan, Guojun Feng, Xiaoxu Yang
The main edible organ of snap bean (Phaseolus vulgaris L.) is the pod, whose color is a main characteristic affecting its commercial use. Golden pods are popular with consumers; however, color instability affects their commercial exploitation and causes economic losses to the planters. In this study, we focused on the different pod color of two varieties of snap bean. The golden yellow color of snap
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Diverse mobilome of Dichotomius ( Luederwaldtinia ) schiffleri (Coleoptera: Scarabaeidae) reveals long-range horizontal transfer events of DNA transposons Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-29 I. C. Amorim, E. S. Melo, R. C. Moura, G. L. Wallau
Transposable elements (TEs) are mobile DNA sequences that are able to move from one genomic location to another. These selfish elements are known as genomic parasites, since they hijack the host molecular machinery to generate new copies of themselves. The mobilization of TEs can be seen as a natural mutagen because new TE copies can insert into different loci and impact host genomic structure through
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Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-25 Noora R. Al-Snan, Safia A. Messaoudi, Yahya M. Khubrani, Jon H. Wetton, Mark A. Jobling, Moiz Bakhiet
We have determined the distribution of Y-chromosomal haplotypes and predicted haplogroups in the ethnically diverse Kingdom of Bahrain, a small archipelago in the Arabian Gulf. Paternal population structure within Bahrain was investigated using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit to generate haplotypes from 562 unrelated Bahraini males, sub-divided into four geographical regions—Northern
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Transcription from a gene desert in a melanoma porcine model. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-11 S Marthey,J Estellé,A Blin,P Wahlberg,F Créchet,J Lecardonnel,F Tessiot,C Rogel-Gaillard,E Bourneuf
The genetic mechanisms underlying cutaneous melanoma onset and progression need to be further understood to improve patients’ care. Several studies have focused on the genetic determinism of melanoma development in the MeLiM pig, a biomedical model of cutaneous melanoma. The objective of this study was to better describe the influence of a particular genomic region on melanoma progression in the MeliM
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A transcriptome atlas of silkworm silk glands revealed by PacBio single-molecule long-read sequencing. Mol. Genet. Genomics (IF 2.797) Pub Date : 2020-06-10 Tao Chen,Qiwei Sun,Yan Ma,Wenhui Zeng,Rongpeng Liu,Dawei Qu,Lihua Huang,Hanfu Xu
The silk gland of the silkworm Bombyx mori is a specialized organ where silk proteins are efficiently synthesized under precise regulation that largely determines the properties of silk fibers. To understand the genes involved in the regulation of silk protein synthesis, considerable research has focused on the transcripts expressed in silk glands; however, the complete transcriptome profile of this