Review
Genetics & Heredity
Xi Zhang, David Roy Smith
Summary: This article provides a summary of research tools used for detecting gene duplicates, including metrics, computational approaches, and the latest developments in web tools and databases.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yuxing Xu, Jingxiong Zhang, Canrong Ma, Yunting Lei, Guojing Shen, Jianjun Jin, Deren A. R. Eaton, Jianqiang Wu
Summary: This study provides high-quality genomes for three parasitic plants and establishes a robust phylogenetic framework for Orobanchaceae. The study reveals that an ancient whole-genome duplication event may have played a role in the emergence of parasitism. Contrary to previous speculations, the emergence of holoparasitism is not associated with genome duplication. The study also identifies convergent gene loss between Orobanchaceae parasites and the dodder Cuscuta australis. Additionally, the expanded gene families in Orobanchaceae parasites are enriched in functions related to haustorium development, suggesting that recent gene family expansions have facilitated adaptation to different hosts.
Article
Biochemical Research Methods
Chaitanya Aluru, Mona Singh
Summary: The study introduces a reconciliation-based framework that considers the relative positions of protein domains within extant sequences to uncover tandem domain duplications accurately. By developing an integer linear programming approach and a heuristic algorithm, the researchers are able to identify single and tandem domain duplication events with high accuracy. Through extensive simulation studies and testing on an orthogroup with complex domain duplication patterns, the effectiveness of the approach is demonstrated.
Article
Biochemistry & Molecular Biology
Qing Xiong, Angel Tsz-Yau Wan, Xiaoyu Liu, Cathy Sin-Hang Fung, Xiaojun Xiao, Nat Malainual, Jinpao Hou, Lingyi Wang, Mingqiang Wang, Kevin Yi Yang, Yubao Cui, Elaine Lai-Han Leung, Wenyan Nong, Soo-Kyung Shin, Shannon Wing-Ngor Au, Kyoung Yong Jeong, Fook-Tim Chew, Jerome Ho-Lam Hui, Ting-Fan Leung, Anchalee Tungtrongchitr, Nanshan Zhong, Zhigang Liu, Stephen Kwok-Wing Tsui
Summary: This study examines the evolutionary origin, diverse lifestyles, and quick adaptation of astigmatic mites in human household environments using six high-quality assembled and annotated genomes. The research reveals that astigmatic mites evolved from Prostigmata, notorious plant pests, and rapidly diversified from soil oribatid mites. The study also highlights the rapid expansion of gene families via tandem gene duplications in astigmatic mites, providing genetic resources for adaptation to changing household environments. Additionally, massive horizontal gene transfer events occurred during the evolution of astigmatic mites, enabling detoxification and digestive functions and offering potential drug targets for pest control.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Shane Denecke, Ivan Rankic, Olympia Driva, Megha Kalsi, Ngoc Bao Hang Luong, Benjamin Buer, Ralf Nauen, Sven Geibel, John Vontas
Summary: By annotating the ABC superfamily across more than 150 arthropod species with good quality protein annotations, specific expansions of ABC transporter families suggesting evolutionary adaptation were highlighted. Functional redundancy was observed in the transporters, with the exception of the highly conserved gene Snu, likely due to its role in cuticular formation. This analysis can be used as a resource for further understanding the ABC superfamily in arthropods.
Article
Biochemistry & Molecular Biology
Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O'Geen, Megan Y. Dennis
Summary: Evidence shows that in humans, paralogous segmental duplication genes exhibit different expression patterns, possibly due to relaxed selection or neofunctionalization. While ancestral paralogs show greater expression conservation with chimpanzee orthologs, certain derived paralogs may retain or supplant ancestral functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang, Bo Dong
Summary: Evolutionary developmental biology (evo-devo) is an interdisciplinary field that aims to understand the origin and evolution of developmental processes in different animals. EDomics is a comparative multi-omics database that provides comprehensive genomic, transcriptomic, and single-cell data for 40 representative species. It offers valuable resources and customized datasets for evo-devo research, allowing researchers to decipher the history of developmental evolution across the tree of life.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Plant Sciences
Yuanpeng Fang, Junmei Jiang, Xiaolong Hou, Jiyuan Guo, Xiangyang Li, Degang Zhao, Xin Xie
Summary: The evolution of gene families is crucial for understanding the evolutionary history and biodiversity of plants, as well as explaining their tolerance to environmental stresses. Studying the molecular evolution of plant gene families helps to gain insights into these important processes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Liangzhi Li, Zhenghua Liu, Zhicheng Zhou, Min Zhang, Delong Meng, Xueduan Liu, Ye Huang, Xiutong Li, Zhen Jiang, Shuiping Zhong, Lukasz Drewniak, Zhendong Yang, Qian Li, Yongjun Liu, Xiaolong Nan, Biguang Jiang, Chengying Jiang, Huaqun Yin
Summary: This study provides an in-depth exploration of the diversity, metabolic potential, and genetic evolution of the DPANN archaeal superphylum, revealing differences among them and the role of lateral gene transfer in shaping their genetic flexibility.
Article
Biochemistry & Molecular Biology
Junha Shin, Harald Marx, Alicia Richards, Dries Vaneechoutte, Dhileepkumar Jayaraman, Junko Maeda, Sanhita Chakraborty, Michael Sussman, Klaas Vandepoele, Jean-Michel Ane, Joshua Coon, Sushmita Roy
Summary: Comparative functional genomics analyze species evolution by comparing protein and transcript levels, revealing that protein levels diverge based on phylogenetic distance and highly expressed proteins are more conserved.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Genetics & Heredity
Hongan Long, Parul Johri, Jean-Francois Gout, Jiahao Ni, Yue Hao, Timothy Licknack, Yaohai Wang, Jiao Pan, Berenice Jimenez-Marin, Michael Lynch
Summary: The ciliate genus Paramecium has played an important role in microbial eukaryotic genetics, contributing significantly to the understanding of various phenomena. Recent progress in comparative and population genomics has shed light on the unique genetic environment of Paramecium species, which allows for efficient selection. The streamlined genomes of Paramecium and its ancient species complex provide a valuable platform for studying the fate of duplicate genes.
ANNUAL REVIEW OF GENETICS
(2023)
Article
Evolutionary Biology
Alex Dornburg, Zheng Wang, Junrui Wang, Elizabeth S. Mo, Francesc Lopez-Giraldez, Jeffrey P. Townsend
Summary: Comparative genomic analyses are crucial in identifying key genes related to human health, such as those involved in cancer development. The study investigates the evolutionary histories of ALK and LTK genes in different species, revealing functional convergences between actinopterygians and sarcopterygians. These findings offer important insights into the role and biology of these critical receptors, guiding future investigations in model organisms.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Alejandro Alvarez-Lugo, Arturo Becerra
Summary: Gene duplication is a crucial process in the emergence of new genes and functions, with a high ratio of paralogs found in certain enzymatic classes among prokaryotes. Around 20-40% of prokaryotic enzymes are estimated to have paralogs, with free-living enzymes showing higher ratios compared to intracellular organisms. Similar genomic and biochemical traits are shared among phylogenetically close phyla and even some unrelated phyla with similar lifestyles, suggesting gene duplication is associated with environmental adaptation.
FRONTIERS IN GENETICS
(2021)
Article
Microbiology
Dahe Zhao, Shengjie Zhang, Sumit Kumar, Heng Zhou, Qiong Xue, Wurunze Sun, Jian Zhou, Hua Xiang
Summary: By studying two novel families within the Candidatus Nanohaloarchaeota phylum, we have gained insights into the evolutionary process of this phylum and its symbiotic relationship with Halobacteria. This research contributes to the understanding of symbiosis evolution in Candidatus Nanohaloarchaeota and provides a model for the evolution of other DPANN lineages.
Review
Plant Sciences
James W. Clark
Summary: Plant evolution has led to increased complexity through major innovations in vegetative and reproductive traits. Genome evolution has played a crucial role, with instances of gene and whole-genome duplication, horizontal gene transfer, and gene loss shaping plant diversity. The coevolution of plant genomes and phenotypes at a macroevolutionary scale has been observed during periods of dynamic genome evolution. While the role of gene duplication has been extensively studied, the association between gene loss and plant phenotypic diversity deserves more attention, especially considering reductive evolution in multiple plant lineages.
Article
Biochemistry & Molecular Biology
Huapu Chen, Shuisheng Li, Ling Xiao, Yong Zhang, Guangli Li, Xiaochun Liu, Haoran Lin
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY
(2015)
Article
Endocrinology & Metabolism
Haipei Tang, Yun Liu, Daji Luo, Satoshi Ogawa, Yike Yin, Shuisheng Li, Yong Zhang, Wei Hu, Ishwar S. Parhar, Haoran Lin, Xiaochun Liu, Christopher H. K. Cheng
Article
Endocrinology & Metabolism
Qingqing Wang, Xin Qi, Yin Guo, Shuisheng Li, Yong Zhang, Xiaochun Liu, Haoran Lin
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2015)
Article
Endocrinology & Metabolism
Xin Qi, Wenyi Zhou, Shuisheng Li, Yun Liu, Gang Ye, Xiaochun Liu, Chun Peng, Yong Zhang, Haoran Lin
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Yanan Shi, Xiaochun Liu, Pei Zhu, Jianzhen Li, Kathy W. Y. Sham, Shuk Han Cheng, Shuisheng Li, Yong Zhang, Christopher H. K. Cheng, Haoran Lin
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2013)
Article
Reproductive Biology
Xin Qi, Wenyi Zhou, Danqi Lu, Qingqing Wang, Huixian Zhang, Shuisheng Li, Xiaochun Liu, Yong Zhang, Haoran Lin
BIOLOGY OF REPRODUCTION
(2013)
Article
Biochemistry & Molecular Biology
Yun Li, Xiaochun Liu, Yong Zhang, Xilan Ma, Haoran Lin
FISH PHYSIOLOGY AND BIOCHEMISTRY
(2013)
Article
Endocrinology & Metabolism
Yun Liu, Shuisheng Li, Xigui Huang, Danqi Lu, Xiaochun Liu, Wing-hung Ko, Yong Zhang, Christopher H. K. Cheng, Haoran Lin
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2013)
Article
Endocrinology & Metabolism
Huixian Zhang, Huapu Chen, Yong Zhang, Shuisheng Li, Danqi Lu, Haifa Zhang, Zining Meng, Xiaochun Liu, Haoran Lin
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2013)
Article
Biochemistry & Molecular Biology
Hai Huang, Yun Wei, Zining Meng, Yong Zhang, Xiaochun Liu, Liang Guo, Jian Luo, Guohua Chen, Haoran Lin
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2014)
Article
Fisheries
D. Q. Lu, M. Yao, S. B. Yi, Y. W. Li, X. C. Liu, Y. Zhang, H. R. Lin
JOURNAL OF FISH BIOLOGY
(2013)
Article
Cell Biology
Xin Qi, Wenyi Zhou, Shuisheng Li, Danqi Lu, Shibai Yi, Rui Xie, Xiaochun Liu, Yong Zhang, Haoran Lin
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2013)
Article
Cell Biology
Yun Liu, Shuisheng Li, Xing Qi, Wenyi Zhou, Xiaochun Liu, Haoran Lin, Yong Zhang, Christopher H. K. Cheng
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2013)
Article
Biochemistry & Molecular Biology
Ke Chai, Xiaochun Liu, Yong Zhang, Haoran Lin
MOLECULAR REPRODUCTION AND DEVELOPMENT
(2013)
Article
Multidisciplinary Sciences
Haipei Tang, Yun Liu, Jianzhen Li, Yike Yin, Gaofei Li, Yu Chen, Shuisheng Li, Yong Zhang, Haoran Lin, Xiaochun Liu, Christopher H. K. Cheng
SCIENTIFIC REPORTS
(2016)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.
