51
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Rajaratnam G, Supeinthiran A, Meier R, Su KFY. CRISPR/Cas9 deletions in a conserved exon of Distal-less generates gains and losses in a recently acquired morphological novelty in flies. iScience 2018; 10:222-233. [PMID: 30553946 PMCID: PMC6297884 DOI: 10.1016/j.isci.2018.11.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 01/23/2023] Open
Abstract
Distal-less has been repeatedly co-opted for the development of many novel traits. Here, we document its curious role in the development of a novel abdominal appendage (“sternite brushes”) in sepsid flies. CRISPR/Cas9 deletions in the homeodomain result in losses of sternite brushes, demonstrating that Distal-less is necessary for their development. However, deletions in the upstream coding exon (Exon 2) produce losses or gains of brushes. A dissection of Exon 2 reveals that the likely mechanism for gains involves a deletion in an exon-splicing enhancer site that leads to exon skipping. Such contradictory phenotypes are also observed in butterflies, suggesting that mutations in the conserved upstream regions have the potential to generate phenotypic variability in insects that diverged 300 million years ago. Our results demonstrate the importance of Distal-less for the development of a novel abdominal appendage in insects and highlight how site-specific mutations in the same exon can produce contradictory phenotypes. Distal-less is necessary for the development of a novel abdominal appendage CRISPR/Cas9 editing produced both losses and gains of novel abdominal appendages Gains of appendages result from mutations in exonic splicing enhancer (ESEs) sites ESE mutations likely led to exon skipping and an altered Distal-less protein
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Affiliation(s)
- Gowri Rajaratnam
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Lee Kong Chian Natural History Museum, Singapore, Singapore.
| | - Kathy F Y Su
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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52
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Developmental dynamics of butterfly wings: real-time in vivo whole-wing imaging of twelve butterfly species. Sci Rep 2018; 8:16848. [PMID: 30442931 PMCID: PMC6237780 DOI: 10.1038/s41598-018-34990-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/24/2018] [Indexed: 01/13/2023] Open
Abstract
Colour pattern development of butterfly wings has been studied from several different approaches. However, developmental changes in the pupal wing tissues have rarely been documented visually. In this study, we recorded real-time developmental changes of the pupal whole wings of 9 nymphalid, 2 lycaenid, and 1 pierid species in vivo, from immediately after pupation to eclosion, using the forewing-lift method. The developmental period was roughly divided into four sequential stages. At the very early stage, the wing tissue was transparent, but at the second stage, it became semi-transparent and showed dynamic peripheral adjustment and slow low-frequency contractions. At this stage, the wing peripheral portion diminished in size, but simultaneously, the ventral epithelium expanded in size. Likely because of scale growth, the wing tissue became deeply whitish at the second and third stages, followed by pigment deposition and structural colour expression at the fourth stage. Some red or yellow (light-colour) areas that emerged early were “overpainted” by expanding black areas, suggesting the coexistence of two morphogenic signals in some scale cells. The discal spot emerged first in some nymphalid species, as though it organised the entire development of colour patterns. These results indicated the dynamic wing developmental processes common in butterflies.
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53
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Klaassen H, Wang Y, Adamski K, Rohner N, Kowalko JE. CRISPR mutagenesis confirms the role of oca2 in melanin pigmentation in Astyanax mexicanus. Dev Biol 2018; 441:313-318. [DOI: 10.1016/j.ydbio.2018.03.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 01/02/2023]
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54
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Fujii T, Yamamoto K, Banno Y. Translucent larval integument and flaccid paralysis caused by genome editing in a gene governing molybdenum cofactor biosynthesis in Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 99:11-16. [PMID: 29803701 DOI: 10.1016/j.ibmb.2018.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/28/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
Translucency of the larval integument in Bombyx mori is caused by a lack of uric acid in the epidermis. Hime'nichi translucent (ohi) is a unique mutation causing intermediate translucency of the larval integument and male-specific flaccid paralysis. To determine the gene associated with the ohi mutation, the ohi locus was mapped to a 400-kb region containing 29 predicted genes. Among the genes in this region, we focused on Bombyx homolog of mammalian Gephyrin (BmGphn), which regulates molybdenum cofactor (MoCo) biosynthesis, because MoCo is indispensable for the activity of xanthine dehydrogenase (XDH), a key enzyme in uric acid biosynthesis. The translucent integument of ohi larvae turned opaque after injection of bovine xanthine oxidase, which is a mammalian equivalent to XDH, indicating that XDH activity is defective in ohi larvae. RT-PCR and sequencing analysis showed that (i) in ohi larvae, expression of the BmGphn gene was repressed in the fat body where uric acid is synthesized, and (ii) there was no amino acid substitution in the ohi mutant allele. Finally, we obtained BmGphn knockout alleles (hereafter denoted as BmGphnΔ) by using CRISPR/Cas9. The resulting ohi/BmGphnΔ larvae had translucent integuments, demonstrating that BmGphn is the gene responsible for the ohi phenotype. Our results show that repressed expression of BmGphn is a causative factor for the defective MoCo biosynthesis and XDH activity observed in ohi larvae. Interestingly, all male BmGphnΔ homozygotes died before pupation and showed a flaccid paralysis phenotype. The genetic and physiological mechanisms underlying this flaccid paralysis phenotype are also discussed.
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Affiliation(s)
- Tsuguru Fujii
- Laboratory of Silkworm Genetic Resources, Institute of Genetic Resources, Graduate School of Bio Resources and Bioenvironmental Science, Kyushu University, Fukuoka, 812-8581, Japan
| | - Kazunori Yamamoto
- Laboratory of Silkworm Genetic Resources, Institute of Genetic Resources, Graduate School of Bio Resources and Bioenvironmental Science, Kyushu University, Fukuoka, 812-8581, Japan
| | - Yutaka Banno
- Laboratory of Silkworm Genetic Resources, Institute of Genetic Resources, Graduate School of Bio Resources and Bioenvironmental Science, Kyushu University, Fukuoka, 812-8581, Japan.
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55
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Margres MJ, Wray KP, Hassinger ATB, Ward MJ, McGivern JJ, Moriarty Lemmon E, Lemmon AR, Rokyta DR. Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation. Mol Biol Evol 2018; 34:3099-3110. [PMID: 28962003 DOI: 10.1093/molbev/msx231] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A trait's genomic architecture can affect the rate and mechanism of adaptation, and although many ecologically-important traits are polygenic, most studies connecting genotype, phenotype, and fitness in natural populations have focused on traits with relatively simple genetic bases. To understand the genetic basis of polygenic adaptation, we must integrate genomics, phenotypic data, ecology, and fitness effects for a genetically tractable, polygenic trait; snake venoms provide such a system for studying polygenic adaptation because of their genetic tractability and vital ecological role in feeding and defense. We used a venom transcriptome-proteome map, quantitative proteomics, genomics, and fitness assays in sympatric prey to construct a genotype-phenotype-fitness map for the venoms of an island-mainland pair of rattlesnake populations. Reciprocal fitness experiments demonstrated that each population was locally adapted to sympatric prey. We identified significant expression differentiation with little to no coding-sequence variation across populations, demonstrating that expression differentiation was exclusively the genetic basis of polygenic adaptation. Previous research on the genetics of adaptation, however, has largely been biased toward investigating protein-coding regions because of the complexity of gene regulation. Our results showed that biases at the molecular level can be in the opposite direction, highlighting the need for more systematic comparisons of different molecular mechanisms underlying rapid, adaptive evolution in polygenic traits.
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Affiliation(s)
- Mark J Margres
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Kenneth P Wray
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - James J McGivern
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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56
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Melanin Pathway Genes Regulate Color and Morphology of Butterfly Wing Scales. Cell Rep 2018; 24:56-65. [DOI: 10.1016/j.celrep.2018.05.092] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/26/2018] [Accepted: 05/29/2018] [Indexed: 02/03/2023] Open
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57
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Campbell CR, Poelstra JW, Yoder AD. What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly063] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - J W Poelstra
- Department of Biology, Duke University, Durham, NC, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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58
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Perera OP, Little NS, Pierce CA. CRISPR/Cas9 mediated high efficiency knockout of the eye color gene Vermillion in Helicoverpa zea (Boddie). PLoS One 2018; 13:e0197567. [PMID: 29771955 PMCID: PMC5957398 DOI: 10.1371/journal.pone.0197567] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/04/2018] [Indexed: 12/27/2022] Open
Abstract
Among various genome editing tools available for functional genomic studies, reagents based on clustered regularly interspersed palindromic repeats (CRISPR) have gained popularity due to ease and versatility. CRISPR reagents consist of ribonucleoprotein (RNP) complexes formed by combining guide RNA (gRNA) that target specific genomics regions and a CRISPR associated nuclease (Cas). The gRNA targeting specific gene sequences may be delivered as a plasmid construct that needs to be transcribed or as a synthetic RNA. The Cas nuclease can be introduced as a plasmid construct, mRNA, or purified protein. The efficiency of target editing is dependent on intrinsic factors specific to each species, the target gene sequence, and the delivery methods of CRISPR gRNA and the Cas nuclease. Although intrinsic factors affecting genome editing may not be altered in most experiments, the delivery method for CRISPR/Cas reagents can be optimized to produce the best results. In this study, the efficiency of genome editing by CRISPR/Cas system in the bollworm, Helicoverpa zea (Boddie), was evaluated using ribonucleoprotein (RNP) complexes assembled by binding synthetic gRNA with purified Cas9 nuclease engineered with nuclear localization signals to target the vermillion (eye color) gene. Mutation rates of adults emerging from embryos microinjected with 1, 2, or 4 μM RNP complexes were compared using replicated experiments. Embryos injected with 2 or 4 μM RNP complexes displayed significantly higher mutation rates (>88%) in surviving adults compared to those injected with 1 μM. The hatch rate in embryos injected with RNP complexes and with injection buffer only (mock injections) was reduced by 19.8(±5.2)% compared to noninjected control embryos, but did not differ significantly between injected embryos. Evaluation of potential off-target sites in H. zea genome did not identify any mutations. This study demonstrates that in vitro assembled synthetic RNP complexes can be used to obtain high genome editing rates in a reproducible manner in functional genomics or genetic manipulation studies.
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Affiliation(s)
- Omaththage P. Perera
- Southern Insect Management Research Unit, USDA-ARS, Stoneville, MS, United States
| | - Nathan S. Little
- Southern Insect Management Research Unit, USDA-ARS, Stoneville, MS, United States
| | - Calvin A. Pierce
- Southern Insect Management Research Unit, USDA-ARS, Stoneville, MS, United States
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59
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Banerjee TD, Monteiro A. CRISPR-Cas9 Mediated Genome Editing in Bicyclus anynana Butterflies. Methods Protoc 2018; 1:E16. [PMID: 31164559 PMCID: PMC6526417 DOI: 10.3390/mps1020016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 01/19/2023] Open
Abstract
CRISPR-Cas9 is revolutionizing the field of genome editing in non-model organisms. The robustness, ease of use, replicability and affordability of the technology has resulted in its widespread adoption among researchers. The African butterfly Bicyclus anynana is an emerging model lepidopteran species in the field of evo-devo, with a sequenced genome and amenable to germ line transformation. However, efficient genome editing tools to accelerate the pace of functional genetic research in this species have only recently become available with CRISPR-Cas9 technology. Here, we provide a detailed explanation of the CRISPR-Cas9 protocol we follow in the lab. The technique has been successfully implemented to knock-out genes associated with eyespot development and melanin pigmentation.
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Affiliation(s)
- Tirtha Das Banerjee
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
- Yale-NUS College, 10 College Avenue West, Singapore 138609, Singapore.
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60
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Callier V. The second biennial meeting of the Pan-American Society for Evolutionary Developmental Biology. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:132-137. [PMID: 29733500 DOI: 10.1002/jez.b.22804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/21/2018] [Accepted: 04/11/2018] [Indexed: 11/11/2022]
Abstract
Evodevo is concerned with understanding how phenotypes develop and evolve, how organismal diversity is generated and maintained, and how evolutionary innovations originate. The second Pan-American Society for Evolutionary Developmental Biology (PASEDB) meeting in Calgary, Canada, showcased a great variety of species and study systems, and a variety of approaches to address these questions. Although there were, like at the first PASEDB meeting, many developmental genetic and genomic studies, much of the work moved beyond comparative developmental genetics toward more integrative studies that seek explanations at different levels of the organismal hierarchy.
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Affiliation(s)
- Viviane Callier
- Ronin Institute for Independent Scholarship, Montclair, New Jersey
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61
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Wound healing, calcium signaling, and other novel pathways are associated with the formation of butterfly eyespots. BMC Genomics 2017; 18:788. [PMID: 29037153 PMCID: PMC5644175 DOI: 10.1186/s12864-017-4175-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/05/2017] [Indexed: 01/21/2023] Open
Abstract
Background One hypothesis surrounding the origin of novel traits is that they originate from the co-option of pre-existing genes or larger gene regulatory networks into novel developmental contexts. Insights into a trait’s evolutionary origins can, thus, be gained via identification of the genes underlying trait development, and exploring whether those genes also function in other developmental contexts. Here we investigate the set of genes associated with the development of eyespot color patterns, a trait that originated once within the Nymphalid family of butterflies. Although several genes associated with eyespot development have been identified, the eyespot gene regulatory network remains largely unknown. Results In this study, next-generation sequencing and transcriptome analyses were used to identify a large set of genes associated with eyespot development of Bicyclus anynana butterflies, at 3-6 h after pupation, prior to the differentiation of the color rings. Eyespot-associated genes were identified by comparing the transcriptomes of homologous micro-dissected wing tissues that either develop or do not develop eyespots in wild-type and a mutant line of butterflies, Spotty, with extra eyespots. Overall, 186 genes were significantly up and down-regulated in wing tissues that develop eyespots compared to wing tissues that do not. Many of the differentially expressed genes have yet to be annotated. New signaling pathways, including the Toll, Fibroblast Growth Factor (FGF), extracellular signal–regulated kinase (ERK) and/or Jun N-terminal kinase (JNK) signaling pathways are associated for the first time with eyespot development. In addition, several genes involved in wound healing and calcium signaling were also found to be associated with eyespots. Conclusions Overall, this study provides the identity of many new genes and signaling pathways associated with eyespots, and suggests that the ancient wound healing gene regulatory network may have been co-opted to cells at the center of the pattern to aid in eyespot origins. New transcription factors that may be providing different identities to distinct wing sectors, and genes with sexually dimorphic expression in the eyespots were also identified. Electronic supplementary material The online version of this article (10.1186/s12864-017-4175-7) contains supplementary material, which is available to authorized users.
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62
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Shang W, Wang F, Fan G, Wang H. Key elements for designing and performing a CRISPR/Cas9-based genetic screen. J Genet Genomics 2017; 44:439-449. [PMID: 28967615 DOI: 10.1016/j.jgg.2017.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/09/2017] [Accepted: 09/04/2017] [Indexed: 12/26/2022]
Abstract
Reverse genetic screens are invaluable for uncovering gene functions, but are traditionally hampered by some technical limitations. Over the past few years, since the advent of the revolutionary CRISPR/Cas9 technology, its power in genome editing has been harnessed to overcome the traditional limitations in reverse genetic screens, with successes in various biological contexts. Here, we outline these CRISPR/Cas9-based screens, provide guidance on the design of effective screens and discuss the potential future directions of development of this field.
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Affiliation(s)
- Wanjing Shang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaofeng Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Haopeng Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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63
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Macroevolutionary shifts of WntA function potentiate butterfly wing-pattern diversity. Proc Natl Acad Sci U S A 2017; 114:10701-10706. [PMID: 28923954 DOI: 10.1073/pnas.1708149114] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Butterfly wing patterns provide a rich comparative framework to study how morphological complexity develops and evolves. Here we used CRISPR/Cas9 somatic mutagenesis to test a patterning role for WntA, a signaling ligand gene previously identified as a hotspot of shape-tuning alleles involved in wing mimicry. We show that WntA loss-of-function causes multiple modifications of pattern elements in seven nymphalid butterfly species. In three butterflies with a conserved wing-pattern arrangement, WntA is necessary for the induction of stripe-like patterns known as symmetry systems and acquired a novel eyespot activator role specific to Vanessa forewings. In two Heliconius species, WntA specifies the boundaries between melanic fields and the light-color patterns that they contour. In the passionvine butterfly Agraulis, WntA removal shows opposite effects on adjacent pattern elements, revealing a dual role across the wing field. Finally, WntA acquired a divergent role in the patterning of interveinous patterns in the monarch, a basal nymphalid butterfly that lacks stripe-like symmetry systems. These results identify WntA as an instructive signal for the prepatterning of a biological system of exuberant diversity and illustrate how shifts in the deployment and effects of a single developmental gene underlie morphological change.
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64
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Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence. Proc Natl Acad Sci U S A 2017; 114:10707-10712. [PMID: 28923944 DOI: 10.1073/pnas.1709058114] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The optix gene has been implicated in butterfly wing pattern adaptation by genetic association, mapping, and expression studies. The actual developmental function of this gene has remained unclear, however. Here we used CRISPR/Cas9 genome editing to show that optix plays a fundamental role in nymphalid butterfly wing pattern development, where it is required for determination of all chromatic coloration. optix knockouts in four species show complete replacement of color pigments with melanins, with corresponding changes in pigment-related gene expression, resulting in black and gray butterflies. We also show that optix simultaneously acts as a switch gene for blue structural iridescence in some butterflies, demonstrating simple regulatory coordination of structural and pigmentary coloration. Remarkably, these optix knockouts phenocopy the recurring "black and blue" wing pattern archetype that has arisen on many independent occasions in butterflies. Here we demonstrate a simple genetic basis for structural coloration, and show that optix plays a deeply conserved role in butterfly wing pattern development.
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65
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Deshmukh R, Baral S, Gandhimathi A, Kuwalekar M, Kunte K. Mimicry in butterflies: co-option and a bag of magnificent developmental genetic tricks. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 28913870 DOI: 10.1002/wdev.291] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 07/04/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023]
Abstract
Butterfly wing patterns are key adaptations that are controlled by remarkable developmental and genetic mechanisms that facilitate rapid evolutionary change. With swift advancements in the fields of genomics and genetic manipulations, identifying the regulators of wing development and mimetic wing patterns has become feasible even in nonmodel organisms such as butterflies. Recent mapping and gene expression studies have identified single switch loci of major effects such as transcription factors and supergenes as the main drivers of adaptive evolution of mimetic and polymorphic butterfly wing patterns. We highlight several of these examples, with emphasis on doublesex, optix, WntA and other dynamic, yet essential, master regulators that control critical color variation and sex-specific traits. Co-option emerges as a predominant theme, where typically embryonic and other early-stage developmental genes and networks have been rewired to regulate polymorphic and sex-limited mimetic wing patterns in iconic butterfly adaptations. Drawing comparisons from our knowledge of wing development in Drosophila, we illustrate the functional space of genes that have been recruited to regulate butterfly wing patterns. We also propose a developmental pathway that potentially results in dorsoventral mismatch in butterfly wing patterns. Such dorsoventrally mismatched color patterns modulate signal components of butterfly wings that are used in intra- and inter-specific communication. Recent advances-fuelled by RNAi-mediated knockdowns and CRISPR/Cas9-based genomic edits-in the developmental genetics of butterfly wing patterns, and the underlying biological diversity and complexity of wing coloration, are pushing butterflies as an emerging model system in ecological genetics and evolutionary developmental biology. WIREs Dev Biol 2018, 7:e291. doi: 10.1002/wdev.291 This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Comparative Development and Evolution > Regulation of Organ Diversity Comparative Development and Evolution > Evolutionary Novelties.
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Affiliation(s)
| | - Saurav Baral
- National Centre for Biological Sciences, Bengaluru, India
| | - A Gandhimathi
- National Centre for Biological Sciences, Bengaluru, India
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66
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Sun D, Guo Z, Liu Y, Zhang Y. Progress and Prospects of CRISPR/Cas Systems in Insects and Other Arthropods. Front Physiol 2017; 8:608. [PMID: 28932198 PMCID: PMC5592444 DOI: 10.3389/fphys.2017.00608] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/07/2017] [Indexed: 01/03/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated gene Cas9 represent an invaluable system for the precise editing of genes in diverse species. The CRISPR/Cas9 system is an adaptive mechanism that enables bacteria and archaeal species to resist invading viruses and phages or plasmids. Compared with zinc finger nucleases and transcription activator-like effector nucleases, the CRISPR/Cas9 system has the advantage of requiring less time and effort. This efficient technology has been used in many species, including diverse arthropods that are relevant to agriculture, forestry, fisheries, and public health; however, there is no review that systematically summarizes its successful application in the editing of both insect and non-insect arthropod genomes. Thus, this paper seeks to provide a comprehensive and impartial overview of the progress of the CRISPR/Cas9 system in different arthropods, reviewing not only fundamental studies related to gene function exploration and experimental optimization but also applied studies in areas such as insect modification and pest control. In addition, we also describe the latest research advances regarding two novel CRISPR/Cas systems (CRISPR/Cpf1 and CRISPR/C2c2) and discuss their future prospects for becoming crucial technologies in arthropods.
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Affiliation(s)
- Dan Sun
- Longping Branch, Graduate School of Hunan UniversityChangsha, China.,Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yong Liu
- Longping Branch, Graduate School of Hunan UniversityChangsha, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
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67
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Trizzino M, Park Y, Holsbach-Beltrame M, Aracena K, Mika K, Caliskan M, Perry GH, Lynch VJ, Brown CD. Transposable elements are the primary source of novelty in primate gene regulation. Genome Res 2017; 27:1623-1633. [PMID: 28855262 PMCID: PMC5630026 DOI: 10.1101/gr.218149.116] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 08/17/2017] [Indexed: 12/11/2022]
Abstract
Gene regulation shapes the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species using ChIP-seq (H3K27ac and H3K4me1) to profile cis-regulatory elements (CREs) and using RNA-seq to characterize gene expression in the same individuals. To quantify regulatory divergence, we compared CRE activity across species by testing differential ChIP-seq read depths directly measured for orthologous sequences. We show that the primate regulatory landscape is largely conserved across the lineage, with 63% of the tested human liver CREs showing similar activity across species. Conserved CRE function is associated with sequence conservation, proximity to coding genes, cell-type specificity, and transcription factor binding. Newly evolved CREs are enriched in immune response and neurodevelopmental functions. We further demonstrate that conserved CREs bind master regulators, suggesting that while CREs contribute to species adaptation to the environment, core functions remain intact. Newly evolved CREs are enriched in young transposable elements (TEs), including Long-Terminal-Repeats (LTRs) and SINE-VNTR-Alus (SVAs), that significantly affect gene expression. Conversely, only 16% of conserved CREs overlap TEs. We tested the cis-regulatory activity of 69 TE subfamilies by luciferase reporter assays, spanning all major TE classes, and showed that 95.6% of tested TEs can function as either transcriptional activators or repressors. In conclusion, we demonstrated the critical role of TEs in primate gene regulation and illustrated potential mechanisms underlying evolutionary divergence among the primate species through the noncoding genome.
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Affiliation(s)
- Marco Trizzino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - YoSon Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Marcia Holsbach-Beltrame
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Katherine Aracena
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Katelyn Mika
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Minal Caliskan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Vincent J Lynch
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Meccariello A, Monti SM, Romanelli A, Colonna R, Primo P, Inghilterra MG, Del Corsano G, Ramaglia A, Iazzetti G, Chiarore A, Patti F, Heinze SD, Salvemini M, Lindsay H, Chiavacci E, Burger A, Robinson MD, Mosimann C, Bopp D, Saccone G. Highly efficient DNA-free gene disruption in the agricultural pest Ceratitis capitata by CRISPR-Cas9 ribonucleoprotein complexes. Sci Rep 2017; 7:10061. [PMID: 28855635 PMCID: PMC5577161 DOI: 10.1038/s41598-017-10347-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/07/2017] [Indexed: 12/20/2022] Open
Abstract
The Mediterranean fruitfly Ceratitis capitata (medfly) is an invasive agricultural pest of high economic impact and has become an emerging model for developing new genetic control strategies as an alternative to insecticides. Here, we report the successful adaptation of CRISPR-Cas9-based gene disruption in the medfly by injecting in vitro pre-assembled, solubilized Cas9 ribonucleoprotein complexes (RNPs) loaded with gene-specific single guide RNAs (sgRNA) into early embryos. When targeting the eye pigmentation gene white eye (we), a high rate of somatic mosaicism in surviving G0 adults was observed. Germline transmission rate of mutated we alleles by G0 animals was on average above 52%, with individual cases achieving nearly 100%. We further recovered large deletions in the we gene when two sites were simultaneously targeted by two sgRNAs. CRISPR-Cas9 targeting of the Ceratitis ortholog of the Drosophila segmentation paired gene (Ccprd) caused segmental malformations in late embryos and in hatched larvae. Mutant phenotypes correlate with repair by non-homologous end-joining (NHEJ) lesions in the two targeted genes. This simple and highly effective Cas9 RNP-based gene editing to introduce mutations in C. capitata will significantly advance the design and development of new effective strategies for pest control management.
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Affiliation(s)
- Angela Meccariello
- Department of Biology, University of Naples "Federico II", 80126, Napoli, Italy
| | - Simona Maria Monti
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134, Naples, Italy
| | - Alessandra Romanelli
- Department of Pharmacy, University of Naples "Federico II", 80134, Napoli, Italy
| | - Rita Colonna
- Department of Biology, University of Naples "Federico II", 80126, Napoli, Italy
| | - Pasquale Primo
- Department of Biology, University of Naples "Federico II", 80126, Napoli, Italy
| | | | | | - Antonio Ramaglia
- Department of Physics "E. Pancini", University of Naples "Federico II", 80126, Napoli, Italy
| | - Giovanni Iazzetti
- Department of Biology, University of Naples "Federico II", 80126, Napoli, Italy
| | - Antonia Chiarore
- Stazione Zoologica Anton Dohrn, Center Villa Dohrn for Benthic Ecology, Punta San Pietro, 80077, Ischia, Italy
| | - Francesco Patti
- Stazione Zoologica Anton Dohrn, Center Villa Dohrn for Benthic Ecology, Punta San Pietro, 80077, Ischia, Italy
| | - Svenia D Heinze
- Institute of Molecular Life Sciences, University of Zürich, Zürich, 8057, Switzerland
| | - Marco Salvemini
- Department of Biology, University of Naples "Federico II", 80126, Napoli, Italy
| | - Helen Lindsay
- Institute of Molecular Life Sciences, University of Zürich, Zürich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, 8057, Switzerland
| | - Elena Chiavacci
- Institute of Molecular Life Sciences, University of Zürich, Zürich, 8057, Switzerland
| | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zürich, Zürich, 8057, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zürich, Zürich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, 8057, Switzerland
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, Zürich, 8057, Switzerland
| | - Daniel Bopp
- Institute of Molecular Life Sciences, University of Zürich, Zürich, 8057, Switzerland
| | - Giuseppe Saccone
- Department of Biology, University of Naples "Federico II", 80126, Napoli, Italy.
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69
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Yang YJ, Wang Y, Li ZF, Gong Y, Zhang P, Hu WC, Sheng DH, Li YZ. Increasing on-target cleavage efficiency for CRISPR/Cas9-induced large fragment deletion in Myxococcus xanthus. Microb Cell Fact 2017; 16:142. [PMID: 28814300 PMCID: PMC5559782 DOI: 10.1186/s12934-017-0758-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The CRISPR/Cas9 system is a powerful tool for genome editing, in which the sgRNA binds and guides the Cas9 protein for the sequence-specific cleavage. The protocol is employable in different organisms, but is often limited by cell damage due to the endonuclease activity of the introduced Cas9 and the potential off-target DNA cleavage from incorrect guide by the 20 nt spacer. RESULTS In this study, after resolving some critical limits, we have established an efficient CRISPR/Cas9 system for the deletion of large genome fragments related to the biosynthesis of secondary metabolites in Myxococcus xanthus cells. We revealed that the high expression of a codon-optimized cas9 gene in M. xanthus was cytotoxic, and developed a temporally high expression strategy to reduce the cell damage from high expressions of Cas9. We optimized the deletion protocol by using the tRNA-sgRNA-tRNA chimeric structure to ensure correct sgRNA sequence. We found that, in addition to the position-dependent nucleotide preference, the free energy of a 20 nt spacer was a key factor for the deletion efficiency. CONCLUSIONS By using the developed protocol, we achieved the CRISPR/Cas9-induced deletion of large biosynthetic gene clusters for secondary metabolites in M. xanthus DK1622 and its epothilone-producing mutant. The findings and the proposals described in this paper were suggested to be workable in other organisms, for example, other Gram negative bacteria with high GC content.
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Affiliation(s)
- Ying-jie Yang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Ye Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Zhi-feng Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Ya Gong
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Wen-chao Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Duo-hong Sheng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
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Toll ligand Spätzle3 controls melanization in the stripe pattern formation in caterpillars. Proc Natl Acad Sci U S A 2017; 114:8336-8341. [PMID: 28716921 DOI: 10.1073/pnas.1707896114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A stripe pattern is an aposematic or camouflage coloration often observed among various caterpillars. However, how this ecologically important pattern is formed is largely unknown. The silkworm dominant mutant Zebra (Ze) has a black stripe in the anterior margin of each dorsal segment. Here, fine linkage mapping of 3,135 larvae revealed a 63-kbp region responsible for the Ze locus, which contained three candidate genes, including the Toll ligand gene spätzle3 (spz-3). Both electroporation-mediated ectopic expression and RNAi analyses showed that, among candidate genes, only processed spz-3 induced melanin pigmentation and that Toll-8 was the candidate receptor gene of spz-3 This Toll ligand/receptor set is also involved in melanization of other mutant Striped (pS ), which has broader stripes. Additional knockdown of 5 other spz family and 10 Toll-related genes caused no drastic change in the pigmentation of either mutant, suggesting that only spz-3/Toll-8 is mainly involved in the melanization process rather than pattern formation. The downstream pigmentation gene yellow was specifically up-regulated in the striped region of the Ze mutant, but spz-3 showed no such region-specific expression. Toll signaling pathways are known to be involved in innate immunity, dorsoventral axis formation, and neurotrophic functions. This study provides direct evidence that a Toll signaling pathway is co-opted to control the melanization process and adaptive striped pattern formation in caterpillars.
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71
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Tan KY, Tan CH, Chanhome L, Tan NH. Comparative venom gland transcriptomics of Naja kaouthia (monocled cobra) from Malaysia and Thailand: elucidating geographical venom variation and insights into sequence novelty. PeerJ 2017; 5:e3142. [PMID: 28392982 PMCID: PMC5384570 DOI: 10.7717/peerj.3142] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/03/2017] [Indexed: 11/20/2022] Open
Abstract
Background The monocled cobra (Naja kaouthia) is a medically important venomous snake in Southeast Asia. Its venom has been shown to vary geographically in relation to venom composition and neurotoxic activity, indicating vast diversity of the toxin genes within the species. To investigate the polygenic trait of the venom and its locale-specific variation, we profiled and compared the venom gland transcriptomes of N. kaouthia from Malaysia (NK-M) and Thailand (NK-T) applying next-generation sequencing (NGS) technology. Methods The transcriptomes were sequenced on the Illumina HiSeq platform, assembled and followed by transcript clustering and annotations for gene expression and function. Pairwise or multiple sequence alignments were conducted on the toxin genes expressed. Substitution rates were studied for the major toxins co-expressed in NK-M and NK-T. Results and discussion The toxin transcripts showed high redundancy (41–82% of the total mRNA expression) and comprised 23 gene families expressed in NK-M and NK-T, respectively (22 gene families were co-expressed). Among the venom genes, three-finger toxins (3FTxs) predominated in the expression, with multiple sequences noted. Comparative analysis and selection study revealed that 3FTxs are genetically conserved between the geographical specimens whilst demonstrating distinct differential expression patterns, implying gene up-regulation for selected principal toxins, or alternatively, enhanced transcript degradation or lack of transcription of certain traits. One of the striking features that elucidates the inter-geographical venom variation is the up-regulation of α-neurotoxins (constitutes ∼80.0% of toxin’s fragments per kilobase of exon model per million mapped reads (FPKM)), particularly the long-chain α-elapitoxin-Nk2a (48.3%) in NK-T but only 1.7% was noted in NK-M. Instead, short neurotoxin isoforms were up-regulated in NK-M (46.4%). Another distinct transcriptional pattern observed is the exclusively and abundantly expressed cytotoxin CTX-3 in NK-T. The findings suggested correlation with the geographical variation in proteome and toxicity of the venom, and support the call for optimising antivenom production and use in the region. Besides, the current study uncovered full and partial sequences of numerous toxin genes from N. kaouthia which have not been reported hitherto; these include N. kaouthia-specific l-amino acid oxidase (LAAO), snake venom serine protease (SVSP), cystatin, acetylcholinesterase (AChE), hyaluronidase (HYA), waprin, phospholipase B (PLB), aminopeptidase (AP), neprilysin, etc. Taken together, the findings further enrich the snake toxin database and provide deeper insights into the genetic diversity of cobra venom toxins.
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Affiliation(s)
- Kae Yi Tan
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Choo Hock Tan
- Department of Pharmacology, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | | | - Nget Hong Tan
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
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Genetic Basis of Melanin Pigmentation in Butterfly Wings. Genetics 2017; 205:1537-1550. [PMID: 28193726 DOI: 10.1534/genetics.116.196451] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/06/2017] [Indexed: 11/18/2022] Open
Abstract
Despite the variety, prominence, and adaptive significance of butterfly wing patterns, surprisingly little is known about the genetic basis of wing color diversity. Even though there is intense interest in wing pattern evolution and development, the technical challenge of genetically manipulating butterflies has slowed efforts to functionally characterize color pattern development genes. To identify candidate wing pigmentation genes, we used RNA sequencing to characterize transcription across multiple stages of butterfly wing development, and between different color pattern elements, in the painted lady butterfly Vanessa cardui This allowed us to pinpoint genes specifically associated with red and black pigment patterns. To test the functions of a subset of genes associated with presumptive melanin pigmentation, we used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing in four different butterfly genera. pale, Ddc, and yellow knockouts displayed reduction of melanin pigmentation, consistent with previous findings in other insects. Interestingly, however, yellow-d, ebony, and black knockouts revealed that these genes have localized effects on tuning the color of red, brown, and ochre pattern elements. These results point to previously undescribed mechanisms for modulating the color of specific wing pattern elements in butterflies, and provide an expanded portrait of the insect melanin pathway.
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Beldade P, Peralta CM. Developmental and evolutionary mechanisms shaping butterfly eyespots. CURRENT OPINION IN INSECT SCIENCE 2017; 19:22-29. [PMID: 28521939 DOI: 10.1016/j.cois.2016.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 06/07/2023]
Abstract
Butterfly eyespots are visually compelling models to study the reciprocal interactions between evolutionary and developmental processes that shape phenotypic variation. They are evolutionarily diversified, ecologically relevant, and developmentally tractable, and have made key contributions to linking genotype, development, phenotype and fitness. Advances in the availability of analytical tools (e.g. gene editing and visualization techniques) and resources (e.g. genomic and transcriptomic data) are boosting the detailed dissection of the mechanisms underlying eyespot development and evolution. Here, we review current knowledge on the ecology, development, and evolution of butterfly eyespots, with focus on recent advances. We also highlight a number of unsolved mysteries in our understanding of the patterns and processes underlying the diversification of these structures.
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Affiliation(s)
- Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal; UMR5174, University of Toulouse, France.
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Worley KC, Richards S, Rogers J. The value of new genome references. Exp Cell Res 2016; 358:433-438. [PMID: 28017728 DOI: 10.1016/j.yexcr.2016.12.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/22/2016] [Indexed: 12/24/2022]
Abstract
Genomic information has become a ubiquitous and almost essential aspect of biological research. Over the last 10-15 years, the cost of generating sequence data from DNA or RNA samples has dramatically declined and our ability to interpret those data increased just as remarkably. Although it is still possible for biologists to conduct interesting and valuable research on species for which genomic data are not available, the impact of having access to a high quality whole genome reference assembly for a given species is nothing short of transformational. Research on a species for which we have no DNA or RNA sequence data is restricted in fundamental ways. In contrast, even access to an initial draft quality genome (see below for definitions) opens a wide range of opportunities that are simply not available without that reference genome assembly. Although a complete discussion of the impact of genome sequencing and assembly is beyond the scope of this short paper, the goal of this review is to summarize the most common and highest impact contributions that whole genome sequencing and assembly has had on comparative and evolutionary biology.
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Affiliation(s)
- Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Lewis J, van der Burg K, Mazo-Vargas A, Reed R. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis -Regulatory Evolution in Lepidoptera. Cell Rep 2016; 16:2855-2863. [DOI: 10.1016/j.celrep.2016.08.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/14/2016] [Accepted: 08/12/2016] [Indexed: 12/11/2022] Open
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Iwata M, Otaki JM. Focusing on butterfly eyespot focus: uncoupling of white spots from eyespot bodies in nymphalid butterflies. SPRINGERPLUS 2016; 5:1287. [PMID: 27547662 PMCID: PMC4977239 DOI: 10.1186/s40064-016-2969-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/29/2016] [Indexed: 01/23/2023]
Abstract
BACKGROUND Developmental studies on butterfly wing color patterns often focus on eyespots. A typical eyespot (such as that of Bicyclus anynana) has a few concentric rings of dark and light colors and a white spot (called a focus) at the center. The prospective eyespot center during the early pupal stage is known to act as an organizing center. It has often been assumed, according to gradient models for positional information, that a white spot in adult wings corresponds to an organizing center and that the size of the white spot indicates how active that organizing center was. However, there is no supporting evidence for these assumptions. To evaluate the feasibility of these assumptions in nymphalid butterflies, we studied the unique color patterns of Calisto tasajera (Nymphalidae, Satyrinae), which have not been analyzed before in the literature. RESULTS In the anterior forewing, one white spot was located at the center of an eyespot, but another white spot associated with either no or only a small eyespot was present in the adjacent compartment. The anterior hindwing contained two adjacent white spots not associated with eyespots, one of which showed a sparse pattern. The posterior hindwing contained two adjacent pear-shaped eyespots, and the white spots were located at the proximal side or even outside the eyespot bodies. The successive white spots within a single compartment along the midline in the posterior hindwing showed a possible trajectory of a positional determination process for the white spots. Several cases of focus-less eyespots in other nymphalid butterflies were also presented. CONCLUSIONS These results argue for the uncoupling of white spots from eyespot bodies, suggesting that an eyespot organizing center does not necessarily differentiate into a white spot and that a prospective white spot does not necessarily signify organizing activity for an eyespot. Incorporation of these results in future models for butterfly wing color pattern formation is encouraged.
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Affiliation(s)
- Masaki Iwata
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan
| | - Joji M Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan
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