1
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Yang W, Cui J, Chen Y, Wang C, Yin Y, Zhang W, Liu S, Sun C, Li H, Duan Y, Song F, Cai W, Hines HM, Tian L. Genetic Modification of a Hox Locus Drives Mimetic Color Pattern Variation in a Highly Polymorphic Bumble Bee. Mol Biol Evol 2023; 40:msad261. [PMID: 38039153 PMCID: PMC10724181 DOI: 10.1093/molbev/msad261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/11/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Müllerian mimicry provides natural replicates ideal for exploring mechanisms underlying adaptive phenotypic divergence and convergence, yet the genetic mechanisms underlying mimetic variation remain largely unknown. The current study investigates the genetic basis of mimetic color pattern variation in a highly polymorphic bumble bee, Bombus breviceps (Hymenoptera, Apidae). In South Asia, this species and multiple comimetic species converge onto local Müllerian mimicry patterns by shifting the abdominal setal color from orange to black. Genetic crossing between the orange and black phenotypes suggested the color dimorphism being controlled by a single Mendelian locus, with the orange allele being dominant over black. Genome-wide association suggests that a locus at the intergenic region between 2 abdominal fate-determining Hox genes, abd-A and Abd-B, is associated with the color change. This locus is therefore in the same intergenic region but not the same exact locus as found to drive red black midabdominal variation in a distantly related bumble bee species, Bombus melanopygus. Gene expression analysis and RNA interferences suggest that differential expression of an intergenic long noncoding RNA between abd-A and Abd-B at the onset setal color differentiation may drive the orange black color variation by causing a homeotic shift late in development. Analysis of this same color locus in comimetic species reveals no sequence association with the same color shift, suggesting that mimetic convergence is achieved through distinct genetic routes. Our study establishes Hox regions as genomic hotspots for color pattern evolution in bumble bees and demonstrates how pleiotropic developmental loci can drive adaptive radiations in nature.
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Affiliation(s)
- Wanhu Yang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jixiang Cui
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuxin Chen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chao Wang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuanzhi Yin
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shanlin Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Heather M Hines
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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2
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Shippy TD, Hosmani PS, Flores-Gonzalez M, Mueller LA, Hunter WB, Brown SJ, D’Elia T, Saha S. Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features. GIGABYTE 2022; 2022:gigabyte49. [PMID: 36824511 PMCID: PMC9933525 DOI: 10.46471/gigabyte.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
Hox genes and their cofactors are essential developmental genes specifying regional identity in animals. Hox genes have a conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. A few insect species have breaks in the cluster, but these are exceptions. We annotated the 10 Hox genes of the Asian citrus psyllid Diaphorina citri, and found a split in its Hox cluster between the Deformed and Sex combs reduced genes - the first time a break at this position has been observed in an insect Hox cluster. We also annotated D. citri orthologs of the Hox cofactor genes homothorax, PKNOX and extradenticle and found an additional copy of extradenticle in D. citri that appears to be a retrogene. Expression data and sequence conservation suggest that the extradenticle retrogene may have retained the original extradenticle function and allowed divergence of the parental extradenticle gene.
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Affiliation(s)
- Teresa D. Shippy
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | | | | | | | - Wayne B. Hunter
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Susan J. Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Tom D’Elia
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Surya Saha
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
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3
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Li C, Nong W, Zhao S, Lin X, Xie Y, Cheung MY, Xiao Z, Wong AYP, Chan TF, Hui JHL, Lam HM. Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean. BMC Genomics 2022; 23:65. [PMID: 35057741 PMCID: PMC8780314 DOI: 10.1186/s12864-022-08308-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Soybean is a major legume crop with high nutritional and environmental values suitable for sustainable agriculture. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are important regulators of gene functions in eukaryotes. However, the interactions between these two types of ncRNAs in the context of plant physiology, especially in response to salinity stress, are poorly understood. RESULTS Here, we challenged a cultivated soybean accession (C08) and a wild one (W05) with salt treatment and obtained their small RNA transcriptomes at six time points from both root and leaf tissues. In addition to thoroughly analyzing the differentially expressed miRNAs, we also documented the first case of miRNA arm-switching (miR166m), the swapping of dominant miRNA arm expression, in soybean in different tissues. Two arms of miR166m target different genes related to salinity stress (chloroplastic beta-amylase 1 targeted by miR166m-5p and calcium-dependent protein kinase 1 targeted by miR166m-3p), suggesting arm-switching of miR166m play roles in soybean in response to salinity stress. Furthermore, two pairs of miRNA:lncRNA interacting partners (miR166i-5p and lncRNA Gmax_MSTRG.35921.1; and miR394a-3p and lncRNA Gmax_MSTRG.18616.1) were also discovered in reaction to salinity stress. CONCLUSIONS This study demonstrates how ncRNA involves in salinity stress responses in soybean by miRNA arm switching and miRNA:lncRNA interactions. The behaviors of ncRNAs revealed in this study will shed new light on molecular regulatory mechanisms of stress responses in plants, and hence provide potential new strategies for crop improvement.
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Affiliation(s)
- Chade Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Wenyan Nong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Shancen Zhao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, P.R. China
| | - Xiao Lin
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Yichun Xie
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ming-Yan Cheung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Zhixia Xiao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Annette Y P Wong
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ting Fung Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Jerome H L Hui
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
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Repression of the Hox gene abd-A by ELAV-mediated Transcriptional Interference. PLoS Genet 2021; 17:e1009843. [PMID: 34780465 PMCID: PMC8629391 DOI: 10.1371/journal.pgen.1009843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/29/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Intergenic transcription is a common feature of eukaryotic genomes and performs important and diverse cellular functions. Here, we investigate the iab-8 ncRNA from the Drosophila Bithorax Complex and show that this RNA is able to repress the transcription of genes located at its 3’ end by a sequence-independent, transcriptional interference mechanism. Although this RNA is expressed in the early epidermis and CNS, we find that its repressive activity is limited to the CNS, where, in wild-type embryos, it acts on the Hox gene, abd-A, located immediately downstream of it. The CNS specificity is achieved through a 3’ extension of the transcript, mediated by the neuronal-specific, RNA-binding protein, ELAV. Loss of ELAV activity eliminates the 3’ extension and results in the ectopic activation of abd-A. Thus, a tissue-specific change in the length of a ncRNA is used to generate a precise pattern of gene expression in a higher eukaryote. Although all of the cells making up complex organisms contain the same genetic material, they are nevertheless able to create the diverse tissues of the body. They do this by changing the genes they express. Thus, understanding how genes are controlled in a tissue-specific fashion is one of the primary interests of molecular genetics. Within the bithorax homeotic complex of the fruit fly Drosophila melanogaster, we, and others, previously showed that a >92 kb-long non-coding RNA, called the iab-8 ncRNA, downregulates many important developmental genes, including its genomic downstream neighbor, the homeotic gene abd-A. This downregulation is important as its loss is linked to female sterility. Interestingly, we find that the iab-8 ncRNA regulates abd-A through a mechanism called transcriptional interference, where one gene downregulates a target gene by transcribing over it. In the case of iab-8, this process is limited to the posterior central nervous system, where the iab-8 ncRNA is specifically extended into the abd-A gene by the action of the neuronal-specific RNA binding protein, ELAV. Overall, our work highlights a largely unexplored mechanism by which tissue-specific gene regulation is achieved.
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5
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Castro Alvarez JJ, Revel M, Cléard F, Pauli D, Karch F, Maeda RK. Repression of the Hox gene abd-A by ELAV-mediated Transcriptional Interference.. [DOI: 10.1101/2021.09.29.462302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
ABSTRACTIntergenic transcription is a common feature of eukaryotic genomes and performs important and diverse cellular functions. Here, we investigate the iab-8 ncRNA from the Drosophila Bithorax Complex and show that this RNA is able to repress the transcription of genes located at its 3’ end by a sequence-independent, transcriptional interference mechanism. Although this RNA is expressed in the early epidermis and CNS, we find that its repressive activity is limited to the CNS, where in wild-type embryos, it acts on the Hox gene, abd-A located immediately downstream of it. The CNS specificity is achieved through a 3’ extension of the transcript, mediated by the neuronal-specific, RNA-binding protein, ELAV. Loss of ELAV activity eliminates the 3’ extension and results in the ectopic activation of abd-A. Thus, a tissue-specific change in the length of a ncRNA is used to generate a precise pattern of gene expression in a higher eukaryote.
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6
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Evolution and Phylogeny of MicroRNAs - Protocols, Pitfalls, and Problems. Methods Mol Biol 2021. [PMID: 34432281 DOI: 10.1007/978-1-0716-1170-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
MicroRNAs are important regulators in many eukaryotic lineages. Typical miRNAs have a length of about 22nt and are processed from precursors that form a characteristic hairpin structure. Once they appear in a genome, miRNAs are among the best-conserved elements in both animal and plant genomes. Functionally, they play an important role in particular in development. In contrast to protein-coding genes, miRNAs frequently emerge de novo. The genomes of animals and plants harbor hundreds of mutually unrelated families of homologous miRNAs that tend to be persistent throughout evolution. The evolution of their genomic miRNA complement closely correlates with important morphological innovation. In addition, miRNAs have been used as valuable characters in phylogenetic studies. An accurate and comprehensive annotation of miRNAs is required as a basis to understand their impact on phenotypic evolution. Since experimental data on miRNA expression are limited to relatively few species and are subject to unavoidable ascertainment biases, it is inevitable to complement miRNA sequencing by homology based annotation methods. This chapter reviews the state of the art workflows for homology based miRNA annotation, with an emphasis on their limitations and open problems.
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7
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Novikova EL, Kulakova MA. There and Back Again: Hox Clusters Use Both DNA Strands. J Dev Biol 2021; 9:28. [PMID: 34287306 PMCID: PMC8293171 DOI: 10.3390/jdb9030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.
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Affiliation(s)
- Elena L. Novikova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Milana A. Kulakova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
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8
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Abstract
MicroRNA target sites are often conserved during evolution and purifying selection to maintain such sites is expected. On the other hand, comparative analyses identified a paucity of microRNA target sites in coexpressed transcripts, and novel target sites can potentially be deleterious. We proposed that selection against novel target sites pervasive. The analysis of derived allele frequencies revealed that, when the derived allele is a target site, the proportion of nontarget sites is higher than expected, particularly for highly expressed microRNAs. Thus, new alleles generating novel microRNA target sites can be deleterious and selected against. When we analyzed ancestral target sites, the derived (nontarget) allele frequency does not show statistical support for microRNA target allele conservation. We investigated the joint effects of microRNA conservation and expression and found that selection against microRNA target sites depends mostly on the expression level of the microRNA. We identified microRNA target sites with relatively high levels of population differentiation. However, when we analyze separately target sites in which the target allele is ancestral to the population, the proportion of single-nucleotide polymorphisms with high Fst significantly increases. These findings support that population differentiation is more likely in target sites that are lost than in the gain of new target sites. Our results indicate that selection against novel microRNA target sites is prevalent and, although individual sites may have a weak selective pressure, the overall effect across untranslated regions is not negligible and should be accounted when studying the evolution of genomic sequences.
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Affiliation(s)
- Andrea Hatlen
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Antonio Marco
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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9
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Zhe Q, Yiu WC, Yip HY, Nong W, Yu CWC, Lee IHT, Wong AYP, Wong NWY, Cheung FKM, Chan TF, Lau KF, Zhong S, Chu KH, Tobe SS, Ferrier DEK, Bendena WG, Hui JHL. Micro-RNA Clusters Integrate Evolutionary Constraints on Expression and Target Affinities: The miR-6/5/4/286/3/309 Cluster in Drosophila. Mol Biol Evol 2020; 37:2955-2965. [PMID: 32521021 DOI: 10.1093/molbev/msaa146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A striking feature of micro-RNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a micro-RNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this micro-RNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of micro-RNA cluster members were also constructed. Expression of individual micro-RNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient micro-RNAs together (miR-5/4/286/3/309) or more recently evolved clustered micro-RNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed downregulation of leg-patterning gene cassettes in generation of the leg-shortening phenotype. Furthermore, cell transfection with different combinations of micro-RNA cluster members revealed a suite of downstream genes targeted by all cluster members, as well as complements of targets that are unique for distinct micro-RNAs. Considered together, the micro-RNA targets and the evolutionary ages of each micro-RNA in the cluster demonstrate the importance of micro-RNA clustering, where new members can reinforce and modify the selection forces on both the cluster regulation and the gene regulatory network of existing micro-RNAs. Key words: micro-RNA, cluster, evolution.
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Affiliation(s)
- Qu Zhe
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Wing Chung Yiu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Clare W C Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Ivy H T Lee
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Annette Y P Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Nicola W Y Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Fiona K M Cheung
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Kwok Fai Lau
- School of Life Sciences, The Chinese University of Hong Kong
| | - Silin Zhong
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Ka Hou Chu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, The Chinese University of Hong Kong
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Canada
| | | | | | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
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10
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Qu Z, Nong W, So WL, Barton-Owen T, Li Y, Leung TCN, Li C, Baril T, Wong AYP, Swale T, Chan TF, Hayward A, Ngai SM, Hui JHL. Millipede genomes reveal unique adaptations during myriapod evolution. PLoS Biol 2020; 18:e3000636. [PMID: 32991578 PMCID: PMC7523956 DOI: 10.1371/journal.pbio.3000636] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 08/24/2020] [Indexed: 01/27/2023] Open
Abstract
The Myriapoda, composed of millipedes and centipedes, is a fascinating but poorly understood branch of life, including species with a highly unusual body plan and a range of unique adaptations to their environment. Here, we sequenced and assembled 2 chromosomal-level genomes of the millipedes Helicorthomorpha holstii (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] = 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (assembly size = 449 Mb, N50 = 26.78 Mb mainly on 17 pseudomolecules). Unique genomic features, patterns of gene regulation, and defence systems in millipedes, not observed in other arthropods, are revealed. Both repeat content and intron size are major contributors to the observed differences in millipede genome size. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute (AGO) proteins for loading small RNAs are duplicated in both millipedes, but unlike in insects, an AGO duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs—including species-specific microRNA arm switching—providing differential gene regulation is also obtained. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules found in centipedes. We identify sets of genes associated with the ozadene that play roles in chemical defence as well as antimicrobial activity. Macro-synteny analyses revealed highly conserved genomic blocks between the 2 millipedes and deuterostomes. Collectively, our analyses of millipede genomes reveal that a series of unique adaptations have occurred in this major lineage of arthropod diversity. The 2 high-quality millipede genomes provided here shed new light on the conserved and lineage-specific features of millipedes and centipedes. These findings demonstrate the importance of the consideration of both centipede and millipede genomes—and in particular the reconstruction of the myriapod ancestral situation—for future research to improve understanding of arthropod evolution, and animal evolutionary genomics more widely. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes. This study describes the genome sequences of two millipedes, Helicorthomorpha holstii and Trigoniulus corallinus, revealing unique adaptations not found in other arthropods.
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Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Tom Barton-Owen
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Thomas C. N. Leung
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Chade Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Tobias Baril
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, United Kingdom
| | - Annette Y. P. Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Thomas Swale
- Dovetail Genomics, Scotts Valley, California, United States of America
| | - Ting-Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Alexander Hayward
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, United Kingdom
| | - Sai-Ming Ngai
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Jerome H. L. Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
- * E-mail:
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11
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Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing. Nat Commun 2020; 11:3051. [PMID: 32561724 PMCID: PMC7305137 DOI: 10.1038/s41467-020-16801-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/22/2020] [Indexed: 12/30/2022] Open
Abstract
The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.
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12
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RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res 2020; 47:D221-D229. [PMID: 30395267 PMCID: PMC6324050 DOI: 10.1093/nar/gky1034] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022] Open
Abstract
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org.
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Affiliation(s)
- The RNAcentral Consortium
http://orcid.org/0000-0002-6497-2883SweeneyBlake Ahttp://orcid.org/0000-0001-7279-2682PetrovAnton IBurkovBorishttp://orcid.org/0000-0001-8626-2148FinnRobert Dhttp://orcid.org/0000-0002-6982-4660BatemanAlexSzymanskiMaciejKarlowskiWojciech MGorodkinJanSeemannStefan ECannoneJamie JGutellRobin RFeyPetraBasuSiddharthaKaySimonhttp://orcid.org/0000-0001-7954-7057CochraneGuyBillisKostantinosEmmertDavidMarygoldSteven Jhttp://orcid.org/0000-0001-6718-3559HuntleyRachael Phttp://orcid.org/0000-0002-9791-0064LoveringRuth CFrankishAdamChanPatricia Phttp://orcid.org/0000-0003-3253-6021LoweTodd Mhttp://orcid.org/0000-0002-8380-5247BrufordElspethSealRuthhttp://orcid.org/0000-0001-6274-0184VandesompeleJohttp://orcid.org/0000-0002-2685-2637VoldersPieter-JanParaskevopoulouMariaMaLinaZhangZhangGriffiths-JonesSamBujnickiJanusz MBoccalettoPietrohttp://orcid.org/0000-0001-8522-334XBlakeJudith ABultCarol JChenRunshengZhaoYiWoodValerieRutherfordKimhttp://orcid.org/0000-0002-2084-269XRivasElenaColeJameshttp://orcid.org/0000-0001-5356-4174LaulederkindStanley J FShimoyamaMaryGillespieMarc EOrlic-MilacicMarijahttp://orcid.org/0000-0001-9424-9197KalvariIoannahttp://orcid.org/0000-0002-2497-3427NawrockiEricEngelStacia Rhttp://orcid.org/0000-0001-9163-5180CherryJ MichaelTeamSILVABerardiniTanya ZHatzigeorgiouArtemisKaragkouniDimitrahttp://orcid.org/0000-0002-1751-9226HoweKevinDavisPaulDingerMarcelhttp://orcid.org/0000-0002-7294-0865HeShunminYoshihamaMakiKenmochiNaoyaStadlerPeter FWilliamsKelly P
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Institute for Cellular and Molecular Biology, and the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
- dictyBase, Northwestern University, 420 E. Superior St., Chicago, IL 60611, USA
- Department of Molecular and Cellular Biology, Harvard University, Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02140, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
- Institute of Cardiovascular Science, University College London, London, UK
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece
- Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
- Ghent University and Cancer Research Institute Ghent, 9000 Ghent, Belgium
- St Vincent's Clinical School, UNSW Sydney, Sydney, Australia
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609, USA
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
- Cambridge Systems Biology and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, Cambridgeshire CB2 1GA, UK
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI 53226, USA
- Department of Genetics, Stanford University, Palo Alto, CA 94304 USA
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen
- Jacobs University Bremen, School of Engineering and Science, D-28759 Bremen
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
- Phoenix Bioinformatics, Fremont, CA 94538, USA
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstr. 1618, 04107 Leipzig, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Ritterstrasse 9–13, 04109 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Insel Strasse 22, 04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, 04103 Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
- Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- To whom correspondence should be addressed. Tel: +44 1223 492550; Fax: +44 1223 494468;
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Tian L, Rahman SR, Ezray BD, Franzini L, Strange JP, Lhomme P, Hines HM. A homeotic shift late in development drives mimetic color variation in a bumble bee. Proc Natl Acad Sci U S A 2019; 116:11857-11865. [PMID: 31043564 PMCID: PMC6575597 DOI: 10.1073/pnas.1900365116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural phenotypic radiations, with their high diversity and convergence, are well-suited for informing how genomic changes translate to natural phenotypic variation. New genomic tools enable discovery in such traditionally nonmodel systems. Here, we characterize the genomic basis of color pattern variation in bumble bees (Hymenoptera, Apidae, Bombus), a group that has undergone extensive convergence of setal color patterns as a result of Müllerian mimicry. In western North America, multiple species converge on local mimicry patterns through parallel shifts of midabdominal segments from red to black. Using genome-wide association, we establish that a cis-regulatory locus between the abdominal fate-determining Hox genes, abd-A and Abd-B, controls the red-black color switch in a western species, Bombus melanopygus Gene expression analysis reveals distinct shifts in Abd-B aligned with the duration of setal pigmentation at the pupal-adult transition. This results in atypical anterior Abd-B expression, a late developmental homeotic shift. Changing expression of Hox genes can have widespread effects, given their important role across segmental phenotypes; however, the late timing reduces this pleiotropy, making Hox genes suitable targets. Analysis of this locus across mimics and relatives reveals that other species follow independent genetic routes to obtain the same phenotypes.
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Affiliation(s)
- Li Tian
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | | | - Briana D Ezray
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - Luca Franzini
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - James P Strange
- United States Department of Agriculture-Agricultural Research Service Pollinating Insects Research Unit, Utah State University, Logan, UT 84322
| | - Patrick Lhomme
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Biodiversity and Crop Improvement Program, International Center of Agricultural Research in the Dry Areas, 10112 Rabat, Morocco
| | - Heather M Hines
- Department of Biology, The Pennsylvania State University, University Park, PA 16802;
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
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Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J. Identification and characterization of novel conserved RNA structures in Drosophila. BMC Genomics 2018; 19:899. [PMID: 30537930 PMCID: PMC6288889 DOI: 10.1186/s12864-018-5234-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 11/08/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Comparative genomics approaches have facilitated the discovery of many novel non-coding and structured RNAs (ncRNAs). The increasing availability of related genomes now makes it possible to systematically search for compensatory base changes - and thus for conserved secondary structures - even in genomic regions that are poorly alignable in the primary sequence. The wealth of available transcriptome data can add valuable insight into expression and possible function for new ncRNA candidates. Earlier work identifying ncRNAs in Drosophila melanogaster made use of sequence-based alignments and employed a sliding window approach, inevitably biasing identification toward RNAs encoded in the more conserved parts of the genome. RESULTS To search for conserved RNA structures (CRSs) that may not be highly conserved in sequence and to assess the expression of CRSs, we conducted a genome-wide structural alignment screen of 27 insect genomes including D. melanogaster and integrated this with an extensive set of tiling array data. The structural alignment screen revealed ∼30,000 novel candidate CRSs at an estimated false discovery rate of less than 10%. With more than one quarter of all individual CRS motifs showing sequence identities below 60%, the predicted CRSs largely complement the findings of sliding window approaches applied previously. While a sixth of the CRSs were ubiquitously expressed, we found that most were expressed in specific developmental stages or cell lines. Notably, most statistically significant enrichment of CRSs were observed in pupae, mainly in exons of untranslated regions, promotors, enhancers, and long ncRNAs. Interestingly, cell lines were found to express a different set of CRSs than were found in vivo. Only a small fraction of intergenic CRSs were co-expressed with the adjacent protein coding genes, which suggests that most intergenic CRSs are independent genetic units. CONCLUSIONS This study provides a more comprehensive view of the ncRNA transcriptome in fly as well as evidence for differential expression of CRSs during development and in cell lines.
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Affiliation(s)
- Rebecca Kirsch
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Department of Veterinary and Animal Science, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, D-04107 Germany
| | - Stefan E. Seemann
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Department of Veterinary and Animal Science, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
| | - Walter L. Ruzzo
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- School of Computer Science and Engineering, University of Washington, Box 352350, Seattle, 98195-2350 WA USA
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, 98195-5065 WA USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, 98109-1024 WA USA
| | - Stephen M. Cohen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen N, DK-2200 Denmark
| | - Peter F. Stadler
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, D-04107 Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103 Germany
- Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, COL-111321 D.C. Colombia
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090 Austria
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501 USA
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Department of Veterinary and Animal Science, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
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15
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Qu Z, Bendena WG, Tobe SS, Hui JHL. Juvenile hormone and sesquiterpenoids in arthropods: Biosynthesis, signaling, and role of MicroRNA. J Steroid Biochem Mol Biol 2018; 184:69-76. [PMID: 29355708 DOI: 10.1016/j.jsbmb.2018.01.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/03/2018] [Accepted: 01/16/2018] [Indexed: 12/21/2022]
Abstract
Arthropod molting and reproduction are precisely controlled by the levels of sesquiterpenoids, a class of C15 hormones derived from three isoprene units. The two major functional arthropod sesquiterpenoids are juvenile hormone (JH) and methyl farnesoate (MF). In hemimetabolous insects (such as the aphids, bugs, and cockroaches) and holometabolous insects (such as beetles, bees, butterflies, and flies), dramatic decrease in the titers of JH and/or MF promote metamorphosis from larvae to adults either directly or through an intermediate pupal stage, respectively. JH is absent in crustaceans (lobster, shrimp, crab) and other arthropods (chelicerates such as ticks, mites, spiders, scorpions and myriapods such as millipede and centipedes). In some crustaceans, molting and reproduction is dependent on changing levels of MF. The regulation of sesquiterpenoid production is thus crucial in the life cycle of arthropods. Dynamic and complex mechanisms have evolved to regulate sesquiterpenoid production. Noncoding RNAs such as the microRNAs are primary regulators. This article provides an overview of microRNAs that are known to regulate sesquiterpenoid production in arthropods.
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Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | | | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Canada.
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong.
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16
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Maeda RK, Sitnik JL, Frei Y, Prince E, Gligorov D, Wolfner MF, Karch F. The lncRNA male-specific abdominal plays a critical role in Drosophila accessory gland development and male fertility. PLoS Genet 2018; 14:e1007519. [PMID: 30011265 PMCID: PMC6067764 DOI: 10.1371/journal.pgen.1007519] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 07/31/2018] [Accepted: 06/27/2018] [Indexed: 12/19/2022] Open
Abstract
Although thousands of long non-coding RNAs (lncRNA) have been identified in the genomes of higher eukaryotes, the precise function of most of them is still unclear. Here, we show that a >65 kb, male-specific, lncRNA, called male-specific abdominal (msa) is required for the development of the secondary cells of the Drosophila male accessory gland (AG). msa is transcribed from within the Drosophila bithorax complex and shares much of its sequence with another lncRNA, the iab-8 lncRNA, which is involved in the development of the central nervous system (CNS). Both lncRNAs perform much of their functions via a shared miRNA embedded within their sequences. Loss of msa, or of the miRNA it contains, causes defects in secondary cell morphology and reduces male fertility. Although both lncRNAs express the same miRNA, the phenotype in the secondary cells and the CNS seem to reflect misregulation of different targets in the two tissues. In many animals, the male seminal fluid induces physiology changes in the mated female that increase a male’s reproductive success. These changes are often referred to as the post-mating response (PMR). In Drosophila, the seminal fluid proteins responsible for generating the PMR are made in a specialized gland, analogous to the mammalian seminal vesicle and prostate, called the accessory gland (AG). In this work, we show that a male-specific, long, non-coding RNA (lncRNA), called msa, plays a critical role in the development and function of this gland, primarily through a microRNA (miRNA) encoded within its sequence. This same miRNA had previously been shown to be expressed in the central nervous system (CNS) via an alternative promoter, where its ability to repress homeotic genes is required for both male and female fertility. Here, we present evidence that the targets of this miRNA in the AG are likely different from those found in the CNS. Thus, the same miRNA seems to have been selected to affect Drosophila fertility through two different mechanisms. Although many non-coding RNAs have now been identified, very few can be shown to have function. Our work highlights a lncRNA that has multiple biological functions, affecting cellular morphology and fertility.
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Affiliation(s)
- Robert K. Maeda
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- * E-mail: (RKM); (FK)
| | - Jessica L. Sitnik
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Yohan Frei
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Elodie Prince
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Dragan Gligorov
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mariana F. Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - François Karch
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- * E-mail: (RKM); (FK)
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17
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Qu Z, Bendena WG, Nong W, Siggens KW, Noriega FG, Kai ZP, Zang YY, Koon AC, Chan HYE, Chan TF, Chu KH, Lam HM, Akam M, Tobe SS, Lam Hui JH. MicroRNAs regulate the sesquiterpenoid hormonal pathway in Drosophila and other arthropods. Proc Biol Sci 2018; 284:rspb.2017.1827. [PMID: 29237851 DOI: 10.1098/rspb.2017.1827] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022] Open
Abstract
Arthropods comprise the majority of all described animal species, and understanding their evolution is a central question in biology. Their developmental processes are under the precise control of distinct hormonal regulators, including the sesquiterpenoids juvenile hormone (JH) and methyl farnesoate. The control of the synthesis and mode of action of these hormones played important roles in the evolution of arthropods and their adaptation to diverse habitats. However, the precise roles of non-coding RNAs, such as microRNAs (miRNAs), controlling arthropod hormonal pathways are unknown. Here, we investigated the miRNA regulation of the expression of the juvenile hormone acid methyltransferase gene (JHAMT), which encodes a rate-determining sesquiterpenoid biosynthetic enzyme. Loss of function of the miRNA bantam in the fly Drosophila melanogaster increased JHAMT expression, while overexpression of the bantam repressed JHAMT expression and resulted in pupal lethality. The male genital organs of the pupae were malformed, and exogenous sesquiterpenoid application partially rescued the genital deformities. The role of the bantam in the regulation of sesquiterpenoid biosynthesis was validated by transcriptomic, qPCR and hormone titre (JHB3 and JH III) analyses. In addition, we found a conserved set of miRNAs that interacted with JHAMT, and the sesquiterpenoid receptor methoprene-tolerant (Met) in different arthropod lineages, including insects (fly, mosquito and beetle), crustaceans (water flea and shrimp), myriapod (centipede) and chelicerate (horseshoe crab). This suggests that these miRNAs might have conserved roles in the post-transcriptional regulation of genes in sesquiterpenoid pathways across the Panarthropoda. Some of the identified lineage-specific miRNAs are potential targets for the development of new strategies in aquaculture and agricultural pest control.
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Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | | | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | | | - Fernando G Noriega
- Department of Biological Sciences and Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Zhen-Peng Kai
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, People's Republic of China
| | - Yang-Yang Zang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, People's Republic of China
| | - Alex C Koon
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Ho Yin Edwin Chan
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Ting Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Hon Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Michael Akam
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada M5S 3G5
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
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18
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Mohammed J, Flynt AS, Panzarino AM, Mondal MMH, DeCruz M, Siepel A, Lai EC. Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Res 2017; 28:52-65. [PMID: 29233922 PMCID: PMC5749182 DOI: 10.1101/gr.226068.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/20/2017] [Indexed: 11/24/2022]
Abstract
To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5' end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3' untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.
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Affiliation(s)
- Jaaved Mohammed
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10021, USA.,Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Alex S Flynt
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA.,Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Alexandra M Panzarino
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | | | - Matthew DeCruz
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Eric C Lai
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10021, USA.,Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
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19
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Yazbeck AM, Tout KR, Stadler PF, Hertel J. Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution. J Integr Bioinform 2017. [PMID: 28637930 PMCID: PMC6042801 DOI: 10.1515/jib-2016-0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The miRBase currently reports more than 25,000 microRNAs in several hundred genomes that belong to more than 1000 families of homologous sequences. Quantitative investigations of miRNA gene evolution requires the construction of data sets that are consistent in their coverage and include those genomes that are of interest in a given study. Given the size and structure of data, this can be achieved only with the help of a fully automatic pipeline that improves the available seed alignments, extends the set of available sequences by homology search, and reliably identifies true positive homology search results. Here we describe the current progress towards such a system, emphasizing the task of improving and completing the initial seed alignment.
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Kenny NJ, Sin YW, Hayward A, Paps J, Chu KH, Hui JHL. The phylogenetic utility and functional constraint of microRNA flanking sequences. Proc Biol Sci 2015; 282:20142983. [PMID: 25694624 DOI: 10.1098/rspb.2014.2983] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
MicroRNAs (miRNAs) have recently risen to prominence as novel factors responsible for post-transcriptional regulation of gene expression. miRNA genes have been posited as highly conserved in the clades in which they exist. Consequently, miRNAs have been used as rare genome change characters to estimate phylogeny by tracking their gain and loss. However, their short length (21-23 bp) has limited their perceived utility in sequenced-based phylogenetic inference. Here, using reference taxa with established phylogenetic relationships, we demonstrate that miRNA sequences are of high utility in quantitative, rather than in qualitative, phylogenetic analysis. The clear orthology among miRNA genes from different species makes it straightforward to identify and align these sequences from even fragmentary datasets. We also identify significant sequence conservation in the regions directly flanking miRNA genes, and show that this too is of utility in phylogenetic analysis, as well as highlighting conserved regions that will be of interest to other fields. Employing miRNA sequences from 12 sequenced drosophilid genomes, together with a Tribolium castaneum outgroup, we demonstrate that this approach is robust using Bayesian and maximum-likelihood methods. The utility of these characters is further demonstrated in the rhabditid nematodes and primates. As next-generation sequencing makes it more cost-effective to sequence genomes and small RNA libraries, this methodology provides an alternative data source for phylogenetic analysis. The approach allows rapid resolution of relationships between both closely related and rapidly evolving species, and provides an additional tool for investigation of relationships within the tree of life.
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Affiliation(s)
- Nathan J Kenny
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yung Wa Sin
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Alexander Hayward
- Department of Medical Biochemistry and Microbiology, Uppsala Universitet, Uppsala, Sweden
| | - Jordi Paps
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jerome H L Hui
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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21
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Quah S, Holland PWH. The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution. EvoDevo 2015; 6:31. [PMID: 26451238 PMCID: PMC4597612 DOI: 10.1186/s13227-015-0027-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/25/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Introns represent a potentially rich source of existing transcription for the evolution of novel microRNAs (miRNAs). Within the Hox gene clusters, a miRNA gene, miR-615, is located within the intron of the Hoxc5 gene. This miRNA has a restricted phylogenetic distribution, providing an opportunity to examine the origin and evolution of a new miRNA within the intron of a developmentally-important homeobox gene. RESULTS Alignment and structural analyses show that the sequence is highly conserved across eutherian mammals and absent in non-mammalian tetrapods. Marsupials possess a similar sequence which we predict will not be efficiently processed as a miRNA. Our analyses suggest that transcription of HOXC5 in humans is accompanied by expression of miR-615 in all cases, but that the miRNA can also be transcribed independently of its host gene through the use of an intragenic promoter. We present scenarios for the evolution of miR-615 through intronic exaptation, and speculate on the acquisition of independent transcriptional regulation. Target prediction and transcriptomic analyses suggest that the dominant product of miR-615 is involved in the regulation of growth and a range of developmental processes. CONCLUSIONS The miR-615 gene evolved within the intron of Hoxc5 in the ancestor of placental mammals. Using miR-615 as a case study, we propose a model by which a functional miRNA can emerge within an intron gradually, by selection on secondary structure followed by evolution of an independent miRNA promoter. The location within a Hox gene intron is of particular interest as the miRNA is specific to placental mammals, is co-expressed with its host gene and may share complementary functions.
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Affiliation(s)
- Shan Quah
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Peter W. H. Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
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22
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Kenny NJ, Namigai EKO, Marlétaz F, Hui JHL, Shimeld SM. Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Mar Genomics 2015; 24 Pt 2:139-46. [PMID: 26319627 DOI: 10.1016/j.margen.2015.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/19/2015] [Accepted: 07/14/2015] [Indexed: 12/01/2022]
Abstract
MicroRNAs (miRNA) are small non-coding RNAs that act post-transcriptionally to regulate gene expression levels. Some studies have indicated that microRNAs may have low homoplasy, and as a consequence the phylogenetic distribution of microRNA families has been used to study animal evolutionary relationships. Limited levels of lineage sampling, however, may distort such analyses. Lophotrochozoa is an under-sampled taxon that includes molluscs, annelids and nemerteans, among other phyla. Here, we present two novel draft genomes, those of the limpet Patella vulgata and polychaete Spirobranchus (Pomatoceros) lamarcki. Surveying these genomes for known microRNAs identifies numerous potential orthologues, including a number that have been considered to be confined to other lineages. RT-PCR demonstrates that some of these (miR-1285, miR-1287, miR-1957, miR-1983 and miR-3533), previously thought to be found only in vertebrates, are expressed. This study provides genomic resources for two lophotrochozoans and reveals patterns of microRNA evolution that could be hidden by more restricted sampling.
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Affiliation(s)
- Nathan J Kenny
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | | | | | - Jerome H L Hui
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Hox miRNA regulation within the Drosophila Bithorax complex: Patterning behavior. Mech Dev 2015; 138 Pt 2:151-159. [PMID: 26311219 DOI: 10.1016/j.mod.2015.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 01/02/2023]
Abstract
The study of Drosophila Hox genes, located in the Antennapedia complex (ANT-C) and Bithorax complex (BX-C), has provided fundamental insights into mechanisms of how the segments of the animal body plan are specified. Notably, even though the analysis of the BX-C formally began over a century ago, surprises continue to emerge regarding its regulation and function. Even simply the gene content of the BX-C has been regularly revised in past years, especially with regard to non-coding RNAs (ncRNAs), including microRNAs. In this perspective, we review the history of studies of non-coding transcription in the BX-C, and highlight recent studies of its miRNAs that provide new insights into their tissue-specific roles in Hox gene regulation. In particular, we have demonstrated unexpected importance of endogenous BX-C miRNAs to restrict the spatial accumulation of Hox proteins and their TALE cofactors in the ventral nerve cord, and link this to aberrant neural differentiation and reproductive behavior. These findings open new directions on studying Hox miRNA function, and we speculate that further understanding of their roles in insect models may provide new leads for studying the enigmatic biological functions of analogous miRNAs located in vertebrate Hox clusters.
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Javeed N, Tardi NJ, Maher M, Singari S, Edwards KA. Controlled expression of Drosophila homeobox loci using the Hostile takeover system. Dev Dyn 2015; 244:808-25. [PMID: 25820349 PMCID: PMC4449281 DOI: 10.1002/dvdy.24279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 03/12/2015] [Accepted: 03/16/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Hostile takeover (Hto) is a Drosophila protein trapping system that allows the investigator to both induce a gene and tag its product. The Hto transposon carries a GAL4-regulated promoter expressing an exon encoding a FLAG-mCherry tag. Upon expression, the Hto exon can splice to a downstream genomic exon, generating a fusion transcript and tagged protein. RESULTS Using rough-eye phenotypic screens, Hto inserts were recovered at eight homeobox or Pax loci: cut, Drgx/CG34340, Pox neuro, araucan, shaven/D-Pax2, Zn finger homeodomain 2, Sex combs reduced (Scr), and the abdominal-A region. The collection yields diverse misexpression phenotypes. Ectopic Drgx was found to alter the cytoskeleton and cell adhesion in ovary follicle cells. Hto expression of cut, araucan, or shaven gives phenotypes similar to those of the corresponding UAS-cDNA constructs. The cut and Pox neuro phenotypes are suppressed by the corresponding RNAi constructs. The Scr and abdominal-A inserts do not make fusion proteins, but may act by chromatin- or RNA-based mechanisms. CONCLUSIONS Hto can effectively express tagged homeodomain proteins from their endogenous loci; the Minos vector allows inserts to be obtained even in transposon cold-spots. Hto screens may recover homeobox genes at high rates because they are particularly sensitive to misexpression.
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Affiliation(s)
- Naureen Javeed
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Nicholas J. Tardi
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Maggie Maher
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Swetha Singari
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Kevin A. Edwards
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
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Quah S, Hui JHL, Holland PWH. A Burst of miRNA Innovation in the Early Evolution of Butterflies and Moths. Mol Biol Evol 2015; 32:1161-74. [PMID: 25576364 PMCID: PMC4408404 DOI: 10.1093/molbev/msv004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in posttranscriptional regulation of gene expression. Because several miRNAs are known to affect the stability or translation of developmental regulatory genes, the origin of novel miRNAs may have contributed to the evolution of developmental processes and morphology. Lepidoptera (butterflies and moths) is a species-rich clade with a well-established phylogeny and abundant genomic resources, thereby representing an ideal system in which to study miRNA evolution. We sequenced small RNA libraries from developmental stages of two divergent lepidopterans, Cameraria ohridella (Horse chestnut Leafminer) and Pararge aegeria (Speckled Wood butterfly), discovering 90 and 81 conserved miRNAs, respectively, and many species-specific miRNA sequences. Mapping miRNAs onto the lepidopteran phylogeny reveals rapid miRNA turnover and an episode of miRNA fixation early in lepidopteran evolution, implying that miRNA acquisition accompanied the early radiation of the Lepidoptera. One lepidopteran-specific miRNA gene, miR-2768, is located within an intron of the homeobox gene invected, involved in insect segmental and wing patterning. We identified cubitus interruptus (ci) as a likely direct target of miR-2768, and validated this suppression using a luciferase assay system. We propose a model by which miR-2768 modulates expression of ci in the segmentation pathway and in patterning of lepidopteran wing primordia.
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Affiliation(s)
- Shan Quah
- Department of Zoology, University of Oxford
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Marco A, Kozomara A, Hui JHL, Emery AM, Rollinson D, Griffiths-Jones S, Ronshaugen M. Sex-biased expression of microRNAs in Schistosoma mansoni. PLoS Negl Trop Dis 2013; 7:e2402. [PMID: 24069470 PMCID: PMC3772069 DOI: 10.1371/journal.pntd.0002402] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 07/23/2013] [Indexed: 11/22/2022] Open
Abstract
Schistosomiasis is an important neglected tropical disease caused by digenean helminth parasites of the genus Schistosoma. Schistosomes are unusual in that they are dioecious and the adult worms live in the blood system. MicroRNAs play crucial roles during gene regulation and are likely to be important in sex differentiation in dioecious species. Here we characterize 112 microRNAs from adult Schistosoma mansoni individuals, including 84 novel microRNA families, and investigate the expression pattern in different sexes. By deep sequencing, we measured the relative expression levels of conserved and newly identified microRNAs between male and female samples. We observed that 13 microRNAs exhibited sex-biased expression, 10 of which are more abundant in females than in males. Sex chromosomes showed a paucity of female-biased genes, as predicted by theoretical evolutionary models. We propose that the recent emergence of separate sexes in Schistosoma had an effect on the chromosomal distribution and evolution of microRNAs, and that microRNAs are likely to participate in the sex differentiation/maintenance process. Schistosomiasis is the second most common disease caused by a parasite, affecting over 200 million people. The parasites involved are flatworms of the genus Schistosoma. Unlike most non-parasitic flatworms, Schistosoma species have separate sexes, and the emergence of sex has been associated with the development of a parasitic lifestyle. The identification of gene products that are expressed in a sex-biased fashion permits the study of the origin of sexual dimorphism and, in the case of the schistosomes, the evolution of a human parasite. Here we investigated the differential expression of microRNAs in male and female individuals of the species Schistosoma mansoni. MicroRNAs are crucial gene regulators. We observed that many new microRNAs emerged in the evolutionary lineage leading to the schistosomes. However, many sex-biased microRNAs were present in the hermaphrodite ancestor of the flatworms, and therefore acquired sex-biased expression later on. Our results suggest that changes in microRNA expression patterns were associated with the emergence of separate sexes in the schistosomes.
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Affiliation(s)
- Antonio Marco
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Ana Kozomara
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
| | - Jerome H. L. Hui
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
| | - Aidan M. Emery
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - David Rollinson
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
- * E-mail: (SGJ); (MR)
| | - Matthew Ronshaugen
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
- * E-mail: (SGJ); (MR)
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27
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Tarver JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM, King BL, Pisani D, Donoghue PCJ, Peterson KJ. miRNAs: small genes with big potential in metazoan phylogenetics. Mol Biol Evol 2013; 30:2369-82. [PMID: 23913097 DOI: 10.1093/molbev/mst133] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
microRNAs (miRNAs) are a key component of gene regulatory networks and have been implicated in the regulation of virtually every biological process found in multicellular eukaryotes. What makes them interesting from a phylogenetic perspective is the high conservation of primary sequence between taxa, their accrual in metazoan genomes through evolutionary time, and the rarity of secondary loss in most metazoan taxa. Despite these properties, the use of miRNAs as phylogenetic markers has not yet been discussed within a clear conceptual framework. Here we highlight five properties of miRNAs that underlie their utility in phylogenetics: 1) The processes of miRNA biogenesis enable the identification of novel miRNAs without prior knowledge of sequence; 2) The continuous addition of miRNA families to metazoan genomes through evolutionary time; 3) The low level of secondary gene loss in most metazoan taxa; 4) The low substitution rate in the mature miRNA sequence; and 5) The small probability of convergent evolution of two miRNAs. Phylogenetic analyses using both Bayesian and parsimony methods on a eumetazoan miRNA data set highlight the potential of miRNAs to become an invaluable new tool, especially when used as an additional line of evidence, to resolve previously intractable nodes within the tree of life.
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Affiliation(s)
- James E Tarver
- Department of Biological Sciences, Dartmouth College, Hanover, NH
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