Genomics, Proteomics & Bioinformatics最新文献

{"title":"Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves","authors":"Yang Zhang ,&nbsp;Fan Mao ,&nbsp;Shu Xiao ,&nbsp;Haiyan Yu ,&nbsp;Zhiming Xiang ,&nbsp;Fei Xu ,&nbsp;Jun Li ,&nbsp;Lili Wang ,&nbsp;Yuanyan Xiong ,&nbsp;Mengqiu Chen ,&nbsp;Yongbo Bao ,&nbsp;Yuewen Deng ,&nbsp;Quan Huo ,&nbsp;Lvping Zhang ,&nbsp;Wenguang Liu ,&nbsp;Xuming Li ,&nbsp;Haitao Ma ,&nbsp;Yuehuan Zhang ,&nbsp;Xiyu Mu ,&nbsp;Min Liu ,&nbsp;Ziniu Yu","doi":"10.1016/j.gpb.2021.10.005","DOIUrl":"10.1016/j.gpb.2021.10.005","url":null,"abstract":"<div><p><strong>Bivalves</strong> are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented <strong>attachment</strong>. The latter mode of sessile life is strongly molded by left-right <strong>shell asymmetry</strong> during larval development of <strong>Ostreoida oysters</strong> such as <em>Crassostrea hongkongensis</em>. Here, we sequenced the genome of <em>C. hongkongensis</em> in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene <em>Antennapedia</em> (<em>Antp</em>) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Comparative transcriptomic analysis shows a conspicuous divergence between left-right asymmetrical <em>C. hongkongensis</em> and symmetrical <em>Pinctada fucata</em> in their expression profiles. Especially, a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated, and may cooperatively govern asymmetrical shell formation in Ostreoida oysters.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1078-1091"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225672/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9545852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Epidemiology of Carbapenemase-producing Klebsiella pneumoniae in China","authors":"Cuidan Li ,&nbsp;Xiaoyuan Jiang ,&nbsp;Tingting Yang ,&nbsp;Yingjiao Ju ,&nbsp;Zhe Yin ,&nbsp;Liya Yue ,&nbsp;Guannan Ma ,&nbsp;Xuebing Wang ,&nbsp;Ying Jing ,&nbsp;Xinhua Luo ,&nbsp;Shuangshuang Li ,&nbsp;Xue Yang ,&nbsp;Fei Chen ,&nbsp;Dongsheng Zhou","doi":"10.1016/j.gpb.2022.02.005","DOIUrl":"10.1016/j.gpb.2022.02.005","url":null,"abstract":"<div><p>The rapid spread of <strong>carbapenemase</strong>-producing <strong><em>Klebsiella pneumoniae</em></strong> (cpKP) poses serious threats to public health; however, the underlying genetic basis for its dissemination is still unknown. We conducted a comprehensive <strong>genomic epidemiology</strong> analysis on 420 cpKP isolates collected from 70 hospitals in 24 provinces/autonomous regions/municipalities of China during 2009–2017 by short-/long-read sequencing. The results showed that most cpKP isolates were categorized into clonal group 258 (CG258), in which ST11 was the dominant clone. Phylogenetic analysis revealed three major clades including the top one of Clade 3 for CG258 cpKP isolates. Additionally, carbapenemase gene analysis indicated that <em>bla</em>_KPC was dominant in the cpKP isolates, and most <em>bla</em>_KPC genes were located in five major incompatibility (Inc) groups of <em>bla</em>_KPC-harboring plasmids. Importantly, three advantageous combinations of host–<em>bla</em>_KPC-carrying plasmid (Clade 3.1+3.2–IncFII_pHN7A8, Clade 3.1+3.2–IncFII_pHN7A8:IncR, and Clade 3.3–IncFII_pHN7A8:Inc_pA1763-KPC) were identified to confer cpKP isolates the advantages in both genotypes (strong correlation/coevolution) and phenotypes (resistance/growth/competition) to facilitate the nationwide spread of ST11/CG258 cpKP. Intriguingly, Bayesian skyline analysis illustrated that the three advantageous combinations might be directly associated with the strong population expansion during 2007–2008 and subsequent maintenance of the population of ST11/CG258 cpKP after 2008. We then examined <strong>drug resistance</strong> profiles of these cpKP isolates and proposed combination treatment regimens for CG258/non-CG258 cpKP infections. Thus, the findings of our systematical analysis shed light on the molecular epidemiology and genetic basis for the dissemination of ST11/CG258 cpKP in China, and much emphasis should be given to the close monitoring of advantageous cpKP–<strong>plasmid</strong> combinations.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1154-1167"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9896350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell Sequencing Reveals Clearance of Blastula Chromosomal Mosaicism in In Vitro Fertilization Babies","authors":"Yuan Gao ,&nbsp;Jinning Zhang ,&nbsp;Zhenyu Liu ,&nbsp;Shuyue Qi ,&nbsp;Xinmeng Guo ,&nbsp;Hui Wang ,&nbsp;Yanfei Cheng ,&nbsp;Shuang Tian ,&nbsp;Minyue Ma ,&nbsp;Hongmei Peng ,&nbsp;Lu Wen ,&nbsp;Fuchou Tang ,&nbsp;Yuanqing Yao","doi":"10.1016/j.gpb.2022.07.004","DOIUrl":"10.1016/j.gpb.2022.07.004","url":null,"abstract":"<div><p>Although chromosomal mosaic embryos detected by trophectoderm (TE) biopsy offer healthy embryos available for transfer, high-resolution postnatal karyotyping and chromosome testing of the transferred embryos are insufficient. Here, we applied <strong>single-cell multi-omics sequencing</strong> for seven infants with blastula chromosomal <strong>mosaicism</strong> detected by TE biopsy. The chromosome ploidy was examined by single-cell genome analysis, with the cellular identity being identified by single-cell transcriptome analysis. A total of 1616 peripheral leukocytes from seven infants with embryonic chromosomal mosaicism and three control ones with euploid TE biopsy were analyzed. A small number of blood cells showed copy number alterations (CNAs) on seemingly random locations at a frequency of 0%−2.5% per infant. However, none of the cells showed CNAs that were the same as those of the corresponding TE biopsies. The blastula chromosomal mosaicism may be fully self-corrected, probably through the selective loss of the aneuploid cells during development, and the transferred embryos can be born as euploid infants without mosaic CNAs corresponding to the TE biopsies. The results provide a new reference for the evaluations of transferring chromosomal mosaic embryos in certain situations.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1224-1231"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9542403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes","authors":"Yali Hou ,&nbsp;Shilei Zhao ,&nbsp;Qi Liu ,&nbsp;Xiaolong Zhang ,&nbsp;Tong Sha ,&nbsp;Yankai Su ,&nbsp;Wenming Zhao ,&nbsp;Yiming Bao ,&nbsp;Yongbiao Xue ,&nbsp;Hua Chen","doi":"10.1016/j.gpb.2022.05.009","DOIUrl":"10.1016/j.gpb.2022.05.009","url":null,"abstract":"<div><p><strong>SARS-CoV-2</strong> is a new RNA virus affecting humans and spreads extensively throughout the world since its first outbreak in December, 2019. Whether the transmissibility and pathogenicity of SARS-CoV-2 in humans after zoonotic transfer are actively evolving, and driven by adaptation to the new host and environments is still under debate. Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of <strong>COVID-19</strong> is essential for predicting the epidemic trend, and providing guidance for disease control and treatments. Interrogating novel strategies for identifying <strong>natural selection</strong> using within-species polymorphisms and 3,674,076 SARS-CoV-2 genome sequences of 169 countries as of December 30, 2021, we demonstrate with population genetic evidence that during the course of SARS-CoV-2 pandemic in humans, 1) SARS-CoV-2 genomes are overall conserved under purifying selection, especially for the 14 genes related to viral RNA replication, transcription, and assembly; 2) ongoing positive selection is actively driving the evolution of 6 genes (<em>e.g.</em>, <em>S</em>, <em>ORF3a</em>, and <em>N</em>) that play critical roles in molecular processes involving pathogen–host interactions, including viral invasion into and egress from host cells, and viral inhibition and evasion of host immune response, possibly leading to high transmissibility and mild symptom in SARS-CoV-2 evolution. According to an established haplotype phylogenetic relationship of 138 viral clusters, a spatial and temporal landscape of 556 critical mutations is constructed based on their divergence among viral haplotype clusters or repeatedly increase in frequency within at least 2 clusters, of which multiple mutations potentially conferring alterations in viral transmissibility, pathogenicity, and virulence of SARS-CoV-2 are highlighted, warranting attention.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1214-1223"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9233880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9559383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants","authors":"Zhongqiang Xia ,&nbsp;Xuelei Dai ,&nbsp;Wei Fan ,&nbsp;Changying Liu ,&nbsp;Meirong Zhang ,&nbsp;Peipei Bian ,&nbsp;Yuping Zhou ,&nbsp;Liang Li ,&nbsp;Baozhong Zhu ,&nbsp;Shuman Liu ,&nbsp;Zhengang Li ,&nbsp;Xiling Wang ,&nbsp;Maode Yu ,&nbsp;Zhonghuai Xiang ,&nbsp;Yu Jiang ,&nbsp;Aichun Zhao","doi":"10.1016/j.gpb.2022.08.005","DOIUrl":"10.1016/j.gpb.2022.08.005","url":null,"abstract":"<div><p>Multiple plant lineages have independently evolved sex chromosomes and variable karyotypes to maintain their sessile lifestyles through constant biological innovation. <em>Morus notabilis</em>, a dioecious <strong>mulberry</strong> species, has the fewest chromosomes among <em>Morus</em> spp., but the genetic basis of <strong>sex determination</strong> and <strong>karyotype evolution</strong> in this species has not been identified. In this study, three high-quality genome assemblies were generated for <em>Morus</em> spp. [including dioecious <em>M</em>. <em>notabilis</em> (male and female) and <em>Morus yunnanensis</em> (female)] with genome sizes of 301–329 Mb and were grouped into six pseudochromosomes. Using a combination of genomic approaches, we found that the putative ancestral karyotype of <em>Morus</em> species was close to 14 protochromosomes, and that several chromosome fusion events resulted in descending dysploidy (2<em>n</em> = 2<em>x</em> = 12). We also characterized a ∼ 6.2-Mb sex-determining region on chromosome 3. Four potential male-specific genes, a partially duplicated<!--> <!-->DNA helicase gene (named <em>MSDH</em>) and three <em>Ty3_Gypsy</em> long terminal repeat retrotransposons (named <em>MSTG1/2/3</em>), were identified in the Y-linked area and considered to be strong candidate genes for sex determination or differentiation. Population genomic analysis showed that Guangdong accessions in China were genetically similar to Japanese accessions of mulberry. In addition, genomic areas containing selective sweeps that distinguish domesticated mulberry from wild populations in terms of flowering and disease resistance were identified. Our study provides an important genetic resource for sex identification research and molecular breeding in mulberry.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1119-1137"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9542415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins","authors":"Mei-Jing Dong ,&nbsp;Hao Luo ,&nbsp;Feng Gao","doi":"10.1016/j.gpb.2022.10.002","DOIUrl":"10.1016/j.gpb.2022.10.002","url":null,"abstract":"<div><p>The replication of DNA is a complex biological process that is essential for life. Bacterial <strong>DNA replication</strong> is initiated at genomic loci referred to as <strong>replication origins</strong> (<em>oriC</em>s). Integrating the <strong>Z-curve</strong> method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial <em>oriC</em>s in 2008 called Ori-Finder, which is helpful to clarify the characteristics of bacterial <em>oriC</em>s. The <em>oriC</em>s of hundreds of sequenced bacterial genomes have been annotated in the genome reports using Ori-Finder and the predicted results have been deposited in DoriC, a manually curated database of <em>oriC</em>s. This has facilitated large-scale data mining of functional elements in <em>oriC</em>s and strand-biased analysis. Here, we describe Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. More species-specific indicator genes and functional elements of <em>oriC</em>s are integrated into the updated framework, which has also been redesigned to predict <em>oriC</em>s in draft genomes. The interactive visualization module displays more genomic information related to <em>oriC</em>s and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous <em>oriC</em> search, and strand-biased analyses. The redesigned interface provides additional customization options for <em>oriC</em> prediction. Ori-Finder 2022 is freely available at <span>http://tubic.tju.edu.cn/Ori-Finder/</span><svg><path></path></svg> and <span>https://tubic.org/Ori-Finder/</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1207-1213"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9542431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage","authors":"Yingbo Shen ,&nbsp;Rong Zhang ,&nbsp;Dongyan Shao ,&nbsp;Lu Yang ,&nbsp;Jiayue Lu ,&nbsp;Congcong Liu ,&nbsp;Xueyang Wang ,&nbsp;Junyao Jiang ,&nbsp;Boxuan Wang ,&nbsp;Congming Wu ,&nbsp;Julian Parkhill ,&nbsp;Yang Wang ,&nbsp;Timothy R. Walsh ,&nbsp;George F. Gao ,&nbsp;Zhangqi Shen","doi":"10.1016/j.gpb.2022.11.006","DOIUrl":"10.1016/j.gpb.2022.11.006","url":null,"abstract":"<div><p>Emergence of the <strong>colistin</strong> resistance gene, <strong><em>mcr</em>-<em>1</em></strong>, has attracted worldwide attention. Despite the prevalence of <em>mcr</em>-<em>1</em>-positive <strong><em>Escherichia coli</em></strong> (MCRPEC) strains in <strong>human</strong> carriage showing a significant decrease between 2016 and 2019, genetic differences in MCRPEC strains remain largely unknown. We therefore conducted a comparative <strong>genomic</strong> study on MCRPEC strains from fecal samples of healthy human subjects in 2016 and 2019. We identified three major differences in MCRPEC strains between these two time points. First, the insertion sequence IS<em>Apl1</em> was often deleted and the percentage of <em>mcr</em>-<em>1</em>-carrying IncI2 plasmids was increased in MCRPEC strains in 2019. Second, the antibiotic resistance genes (ARGs), <em>aac(3)-IVa</em> and <em>bla</em>_CTX-M-1, emerged and coexisted with <em>mcr</em>-<em>1</em> in 2019. Third, MCRPEC strains in 2019 contained more virulence genes, resulting in an increased proportion of extraintestinal pathogenic <em>E. coli</em> (ExPEC) strains (36.1%) in MCRPEC strains in 2019 compared to that in 2016 (10.5%), implying that these strains could occupy intestinal ecological niches by competing with other commensal bacteria. Our results suggest that despite the significant reduction in the prevalence of MCRPEC strains in humans from 2016 to 2019, MCRPEC exhibits increased resistance to other clinically important ARGs and contains more virulence genes, which may pose a potential public health threat.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1168-1179"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/bf/33/main.PMC10225485.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9913392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomes of Two Flying Squid Species Provide Novel Insights into Adaptations of Cephalopods to Pelagic Life","authors":"Min Li ,&nbsp;Baosheng Wu ,&nbsp;Peng Zhang ,&nbsp;Ye Li ,&nbsp;Wenjie Xu ,&nbsp;Kun Wang ,&nbsp;Qiang Qiu ,&nbsp;Jun Zhang ,&nbsp;Jie Li ,&nbsp;Chi Zhang ,&nbsp;Jiangtao Fan ,&nbsp;Chenguang Feng ,&nbsp;Zuozhi Chen","doi":"10.1016/j.gpb.2022.09.009","DOIUrl":"10.1016/j.gpb.2022.09.009","url":null,"abstract":"<div><p>Pelagic cephalopods have evolved a series of fascinating traits, such as excellent visual acuity, high-speed agility, and <strong>photophores</strong> for adaptation to open pelagic oceans. However, the genetic mechanisms underpinning these traits are not well understood. Thus, in this study, we obtained high-quality <strong>genomes</strong> of two purpleback <strong>flying squid</strong> species (<em>Sthenoteuthis oualaniensis</em> and <em>Sthenoteuthis</em> sp.), with sizes of 5450 Mb and 5651 Mb, respectively. Comparative genomic analyses revealed that the <em>S</em>-crystallin subfamily <em>SL20-1</em> associated with visual acuity in the purpleback flying squid lineage was significantly expanded, and the <strong>evolution</strong> of high-speed agility for the species was accompanied by significant positive selection pressure on genes related to energy metabolism. These molecular signals might have contributed to the evolution of their adaptative predatory and anti-predatory traits. In addition, the transcriptomic analysis provided clear indications of the evolution of the photophores of purpleback flying squids, especially the recruitment of new genes and energy metabolism-related genes which may have played key functional roles in the process.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1053-1065"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9541158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptive Bird-like Genome Miniaturization During the Evolution of Scallop Swimming Lifestyle","authors":"Yuli Li ,&nbsp;Yaran Liu ,&nbsp;Hongwei Yu ,&nbsp;Fuyun Liu ,&nbsp;Wentao Han ,&nbsp;Qifan Zeng ,&nbsp;Yuehuan Zhang ,&nbsp;Lingling Zhang ,&nbsp;Jingjie Hu ,&nbsp;Zhenmin Bao ,&nbsp;Shi Wang","doi":"10.1016/j.gpb.2022.07.001","DOIUrl":"10.1016/j.gpb.2022.07.001","url":null,"abstract":"<div><p>Genome miniaturization drives key evolutionary innovations of adaptive traits in vertebrates, such as the flight evolution of <strong>birds</strong>. However, whether similar evolutionary processes exist in invertebrates remains poorly understood. Derived from the second-largest animal phylum, <strong>scallops</strong> are a special group of bivalve molluscs and acquire the evolutionary novelty of the swimming lifestyle, providing excellent models for investigating the coordinated genome and <strong>lifestyle evolution</strong>. Here, we show for the first time that <strong>genome sizes</strong> of scallops exhibit a generally negative correlation with locomotion activity. To elucidate the co-evolution of genome size and swimming lifestyle, we focus on the Asian moon scallop (<em>Amusium pleuronectes</em>) that possesses the smallest known scallop genome while being among scallops with the highest swimming activity. Whole-<strong>genome sequencing</strong> of <em>A. pleuronectes</em> reveals highly conserved chromosomal macrosynteny and microsynteny, suggestive of a highly contracted but not degenerated genome. Genome reduction of <em>A. pleuronectes</em> is facilitated by significant inactivation of transposable elements, leading to reduced gene length, elevated expression of genes involved in energy-producing pathways, and decreased copy numbers and expression levels of biomineralization-related genes. Similar evolutionary changes of relevant pathways are also observed for bird genome reduction with flight evolution. The striking mimicry of genome miniaturization underlying the evolution of bird flight and scallop swimming unveils the potentially common, pivotal role of genome size fluctuation in the evolution of novel lifestyles in the animal kingdom.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1066-1077"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9545890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reprogramming Mycobacterium tuberculosis CRISPR System for Gene Editing and Genome-wide RNA Interference Screening","authors":"Khaista Rahman ,&nbsp;Muhammad Jamal ,&nbsp;Xi Chen ,&nbsp;Wei Zhou ,&nbsp;Bin Yang ,&nbsp;Yanyan Zou ,&nbsp;Weize Xu ,&nbsp;Yingying Lei ,&nbsp;Chengchao Wu ,&nbsp;Xiaojian Cao ,&nbsp;Rohit Tyagi ,&nbsp;Muhammad Ahsan Naeem ,&nbsp;Da Lin ,&nbsp;Zeshan Habib ,&nbsp;Nan Peng ,&nbsp;Zhen F. Fu ,&nbsp;Gang Cao","doi":"10.1016/j.gpb.2021.01.008","DOIUrl":"10.1016/j.gpb.2021.01.008","url":null,"abstract":"<div><p><strong><em>Mycobacterium tuberculosis</em></strong> is the causative agent of tuberculosis (TB), which is still the leading cause of mortality from a single infectious disease worldwide. The development of novel anti-TB drugs and vaccines is severely hampered by the complicated and time-consuming genetic manipulation techniques for <em>M. tuberculosis.</em> Here, we harnessed an endogenous type III-A CRISPR/Cas10 system of <em>M. tuberculosis</em> for efficient <strong>gene editing</strong> and RNA interference (RNAi). This simple and easy method only needs to transform a single mini-CRISPR array plasmid, thus avoiding the introduction of exogenous protein and minimizing proteotoxicity. We demonstrated that <em>M. tuberculosis</em> genes can be efficiently and specifically knocked in/out by this system as confirmed by DNA high-throughput sequencing. This system was further applied to single- and multiple-gene RNAi. Moreover, we successfully performed <strong>genome-wide RNAi screening</strong> to identify <em>M. tuberculosis</em> genes regulating <em>in vitro</em> and intracellular growth. This system can be extensively used for exploring the functional genomics of <em>M. tuberculosis</em> and facilitate the development of novel anti-TB drugs and vaccines.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1180-1196"},"PeriodicalIF":9.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9594363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}