scholarly journals ebony affects pigmentation divergence and cuticular hydrocarbons in Drosophila americana and D. novamexicana

2020 ◽  
Author(s):  
Abigail M. Lamb ◽  
Zinan Wang ◽  
Patricia Simmer ◽  
Henry Chung ◽  
Patricia J. Wittkopp
Keyword(s):  
Genome Editing ◽  
Cuticular Hydrocarbon ◽  
Phenotypic Evolution ◽  
Body Color ◽  
Light Yellow ◽  
Yellow Body ◽  
Virilis Group ◽  
Trait Locus ◽  
Brown Body ◽  
Null Mutants

1AbstractDrosophila pigmentation has been a fruitful model system for understanding the genetic and developmental mechanisms underlying phenotypic evolution. For example, prior work has shown that divergence of the tan gene contributes to pigmentation differences between two members of the virilis group: Drosophila novamexicana, which has a light yellow body color, and D. americana, which has a dark brown body color. Quantitative trait locus (QTL) mapping and expression analysis has suggested that divergence of the ebony gene might also contribute to pigmentation differences between these two species. Here, we directly test this hypothesis by using CRISPR/Cas9 genome editing to generate ebony null mutants in D. americana and D. novamexicana and then using reciprocal hemizygosity testing to compare the effects of each species’ ebony allele on pigmentation. We find that divergence of ebony does indeed contribute to the pigmentation divergence between species, with effects on both the overall body color as well as a difference in pigmentation along the dorsal abdominal midline. Motivated by recent work in D. melanogaster, we also used the ebony null mutants to test for effects of ebony on cuticular hydrocarbon (CHC) profiles. We found that ebony affects CHC abundance in both species, but does not contribute to qualitative differences in the CHC profiles between these two species. Additional transgenic resources for working with D. americana and D. novamexicana, such as white mutants of both species and yellow mutants in D. novamexicana, were generated in the course of this work and are also described. Taken together, this study advances our understanding of loci contributing to phenotypic divergence and illustrates how the latest genome editing tools can be used for functional testing in non-model species.

scholarly journals Genetic basis of body color and spotting pattern in redheaded pine sawfly larvae (Neodiprion lecontei)

2017 ◽  
Author(s):  
Catherine R. Linnen ◽  
Claire T. O’Quin ◽  
Taylor Shackleford ◽  
Connor R. Sears ◽  
Carita Lindstedt
Keyword(s):  
Genetic Basis ◽  
Developmental Stages ◽  
Color Variation ◽  
Body Color ◽  
Sawfly Larvae ◽  
Pine Sawfly ◽  
Neodiprion Lecontei ◽  
Yellow Body ◽  
In The Wild ◽  
Trait Locus

ABSTRACTPigmentation has emerged as a premier model for understanding the genetic basis of phenotypic evolution, and a growing catalog of color loci is starting to reveal biases in the mutations, genes, and genetic architectures underlying color variation in the wild. However, existing studies have sampled a limited subset of taxa, color traits, and developmental stages. To expand our sample of color loci, we performed quantitative trait locus (QTL) mapping analyses on two types of larval pigmentation traits that vary among populations of the redheaded pine sawfly (Neodiprion lecontei): carotenoid-based yellow body color and melanin-based spotting pattern. For both traits, our QTL models explained a substantial proportion of phenotypic variation and suggested a genetic architecture that is neither monogenic nor highly polygenic. Additionally, we used our linkage map to anchor the current N. lecontei genome assembly. With these data, we identified promising candidate genes underlying: (1) a loss of yellow pigmentation in Mid-Atlantic/northeastern populations (Cameo2 and apoLTP-II/I), and (2) a pronounced reduction in black spotting in Great-Lakes populations (yellow, TH, Dat). Several of these genes also contribute to color variation in other wild and domesticated taxa. Overall, our findings are consistent with the hypothesis that predictable genes of large-effect contribute to color evolution in nature.

scholarly journals Three new species of the fangblenny genus Meiacanthus from Indonesia, with color photographs and comments on other species (Teleostei: Blenniidae: Nemophini)

Zootaxa ◽  
2011 ◽  
Vol 3046 (1) ◽  
pp. 39 ◽  
Author(s):  
William F. SMITH-VANIZ ◽  
GERALD R. ALLEN
Keyword(s):  
New Species ◽  
Undescribed Species ◽  
Body Color ◽  
Caudal Fin ◽  
Black Stripe ◽  
Dorsal Fin ◽  
Yellow Body ◽  
Deep Water Species ◽  
Three New Species ◽  
Water Species

Three new species of fangblennies are described from Indonesia. Meiacanthus abruptus is described based on two specimens, 31.4–36.6 mm SL, from Komodo Island and color photographs of others from Bali. The combination of a white or yellow body color and a single dark mid-lateral stripe that is bluntly rounded at its terminus on the caudal-fin base distinguishes it from other single striped species. This new species closely resembles the allopatric M. vicinus, which has the mid-lateral stripe extending farther onto the caudal fin and tapering to a point. Meiacanthus erdmanni is described from the only known specimen, 35.8 mm SL, photographed and collected in 65–70 m in Cenderawasih Bay, western New Guinea. One of the deepest known species of Meiacanthus, it has two dark mid-lateral stripes and differs from other doublestriped species in having a series of dark blotches on the base of the dorsal fin and only 24 segmented dorsal-fin rays. Meiacanthus cyanopterus, another deep-water species, is described from seven specimens, 19.8–45.3 mm SL, collected in 40–65 m at three sites in Alor Strait. In life this species has a dorsal fin with a blue-violet stripe bordered above by a wide black stripe. An identification key is provided for all the striped species of Meiacanthus, including at least one additional undescribed species previously confused with M. abditus. Color photographs of other Meiacanthus species and some new distributional records are also given.

scholarly journals An efficient genome editing strategy to generate putative null mutants in Caenorhabditis elegans using CRISPR/Cas9

2018 ◽  
Author(s):  
Han Wang ◽  
Heenam Park ◽  
Jonathan Liu ◽  
Paul W. Sternberg
Keyword(s):  
Dna Repair ◽  
Caenorhabditis Elegans ◽  
Genome Editing ◽  
Gene Function ◽  
Unique Sequence ◽  
Target Site ◽  
Null Alleles ◽  
Wild Type ◽  
C Elegans ◽  
Null Mutants

AbstractNull mutants are essential for analyzing gene function. Here, we describe a simple and efficient method to generate Caenorhabditis elegans null mutants using CRISPR/Cas9 and short single stranded DNA oligo repair templates to insert a universal 43-nucleotide-long stop knock-in (STOP-IN) cassette into the early exons of target genes. This cassette has stop codons in all three reading frames and leads to frameshifts, which will generate putative null mutations regardless of the reading frame of the insertion position in exons. The STOP-IN cassette also contains an exogenous Cas9 target site that allows further genome editing and provides a unique sequence that simplifies the identification of successful insertion events via PCR. As a proof of concept, we inserted the STOP-IN cassette right at a Cas9 target site in aex-2 to generate new putative null alleles by injecting preassembled Cas9 ribonucleoprotein and a short synthetic single stranded DNA repair template containing the STOP-IN cassette and two 35-nucleotide-long homology arms identical to the sequences flanking the Cas9 cut site. We showed that these new aex-2 alleles phenocopied an existing loss-of-function allele of aex-2. We further showed that the new aex-2 null alleles could be reverted back to the wild-type sequence by targeting exogenous Cas9 cut site included in the STOP-IN cassette and providing a single stranded wild-type DNA repair oligo. We applied our STOP-IN method to generate new putative null mutants for additional 20 genes, including three pharyngeal muscle-specific genes (clik-1, clik-2, and clik-3), and reported a high insertion rate (46%) based on the animals we screened. We showed that null mutations of clik-2 cause recessive lethality with a severe pumping defect and clik-3 null mutants have a mild pumping defect, while clik-1 is dispensable for pumping. We expect that the knock-in method using the STOP-IN cassette will facilitate the generation of new null mutants to understand gene function in C. elegans and other genetic model organisms.SummaryWe report a simple and efficient CRISPR/Cas9 genome editing strategy to generate putative null C. elegans mutants by inserting a small universal stop knock-in (STOP-IN) cassette with stop codons in three frames and frameshifts. The strategy is cloning-free, with the mixture consisting of preassembled Cas9 ribonucleoprotein and single stranded repair DNA oligos directly injected into gonads of adult C. elegans. The universal STOP-IN cassette also contains a unique sequence that simplifies detection of successful knock-in events via PCR and an exogenous Cas9 target sequence that allows further genome editing.

scholarly journals Ectodysplasin signalling genes and phenotypic evolution in sculpins ( Cottus )

2015 ◽  
Vol 282 (1815) ◽  
pp. 20150746 ◽  
Author(s):  
Jie Cheng ◽  
Fritz Sedlazek ◽  
Janine Altmüller ◽  
Arne W. Nolte
Keyword(s):  
Body Shape ◽  
Morphological Evolution ◽  
Genomic Region ◽  
Phenotypic Evolution ◽  
Natural Hybrid ◽  
Microevolutionary Change ◽  
Trait Locus ◽  
Locus Mapping ◽  
Edar Gene

Despite their deeply conserved function among vertebrates, ectodysplasin (Eda) signalling genes are involved in microevolutionary change in humans and sticklebacks. If such a dual role is common, Eda signalling genes constitute hotspots for morphological evolution. Variation in sculpin ( Cottus ) skin prickling and body shape resembles patterns caused by variation in Eda signalling in sticklebacks. We mapped Eda signalling genes and performed quantitative trait locus mapping in crosses between Cottus rhenanus and Cottus perifretum . A genomic region containing the Eda receptor (Edar) was strongly associated with prickling and contributed to shape. The expression of Edar in developing prickles and skeletal elements in Cottus was confirmed by in situ hybridization. Coding sequence changes between Edar alleles in C. rhenanus and C. perifretum exceeded sequence differentiation in other vertebrates. However, it is likely that additional genetic elements besides coding changes affect the phenotypic variation. Although the phenotype in a natural hybrid lineage between C. rhenanus and C. perifretum resembles C. perifretum , the respective coding Edar alleles are not fully fixed (88.6%). Hence, our results support an involvement of Eda signalling in microevolutionary changes, but imply that the Edar gene is affected by multiple evolutionary processes that vary among freshwater sculpins.

scholarly journals CRISPR-Cas9 targeted disruption of the yellow ortholog in the housefly identifies the brown body locus

2017 ◽  
Author(s):  
Svenia D. Heinze ◽  
Tea Kohlbrenner ◽  
Domenica Ippolito ◽  
Angela Meccariello ◽  
Alexa Burger ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genome Editing ◽  
Musca Domestica ◽  
Open Reading Frame ◽  
Targeted Disruption ◽  
Gene Encoding ◽  
Reading Frame ◽  
Molecular Identity ◽  
Brown Body ◽  
Body Locus

ABSTRACTThe classic brown body (bwb) mutation in the housefly Musca domestica impairs normal melanization of the adult cuticle. In Drosophila melanogaster, a reminiscent pigmentation defect results from mutations in the yellow gene encoding dopachrome conversion enzyme (DCE). Here, we demonstrate that the bwb locus structurally and functionally represents the yellow ortholog of Musca domestica, MdY. In bwb Musca strains, we identified two mutant MdY alleles that contain lesions predicted to result in premature truncation of the MdY open reading frame. We targeted wildtype MdY by CRISPR-Cas9 RNPs and generated new mutant alleles that fail to complement existing MdY alleles, genetically confirming that MdY is the bwb locus. We further found evidence for Cas9-mediated interchromosomal recombination between wildtype and mutant bwb alleles. Our work resolves the molecular identity of the classic bwb mutation in Musca domestica and establishes the feasibility of Cas9-mediated genome editing in the Musca model.

INHIBITION OF YELLOW BODY COLOR IN THE HONEY BEE: Apis mellifera L.

1962 ◽  
Vol 53 (4) ◽  
pp. 171-173 ◽  
Author(s):  
HARRY H. LAIDLAW ◽  
M. A. EL-BANBY
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Body Color ◽  
Yellow Body

scholarly journals Six new species of aglajid opisthobranch mollusks from the tropical Indo-Pacific

Zootaxa ◽  
2011 ◽  
Vol 2751 (1) ◽  
pp. 1 ◽  
Author(s):  
TERRENCE GOSLINER
Keyword(s):  
New Species ◽  
Red Sea ◽  
Black Body ◽  
Ventral Surface ◽  
The Philippines ◽  
Marshall Islands ◽  
Posterior Lobe ◽  
Body Color ◽  
Yellow Body ◽  
Apical Papilla

Six new species of aglajid opisthobranchs are described from various localities in the tropical Indo-Pacific. Philinopsis falciphallus n. sp., found from the Marshall Islands to the Red Sea, is distinguished by its reddish body color, a distinct black or maroon longitudinal line on the foot, a posterior projection on the posterior shield and a penis with a chitinous, sickle-shaped spine and numerous smaller spines. Philinopsis coronata n. sp., known only from the Philippines, is similar to P. falciphallus but dominated by yellow body color and a ventral surface of the foot with yellow and maroon spots. It has a trumpet-shaped penis with a crown of rounded tubercles on the apex and anterior and posterior zones of penial spines. Philinopsis ctenophoraphaga n. sp. is found from the Philippines, Indonesia and the Red Sea. It feeds on platyctene ctenophores, including Coeloplana meteroris. It can be distinguished by its elongate posterior lobe of the headshield, reddish color with white spots, thinly muscularized buccal mass and simple, unarmed penis. Chelidonura mandroroa n. sp. is characterized by its black body with orange patches lined by yellow. It has a simple penis with a cuticularized apical papilla. This species has been found from Japan, Taiwan, the Philippines, Indonesia, Madagascar and Kenya. Chelidonura alisonae n. sp. is apparently restricted to the central and eastern Pacific of the Hawai’ian Islands, Johnston Island, the Marianas Islands and Easter Island. It is similar in coloration to C. hirundinina, but has orange lines on the dorsal and lateral shields and has a broad right posterior lobe rather than an acutely pointed one. The penis is simple and unarmed. Odontoglaja mosaica n. sp., found from the Indian Ocean of Madagascar and South Africa, differs from O. guamensis by possessing a reticulate pattern on the notum rather than a pattern of brown spots. It also has a shorter penial papilla that is bifurcate rather than undivided one.

scholarly journals Testing Natural Selection vs. Genetic Drift in Phenotypic Evolution Using Quantitative Trait Locus Data

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2099-2104 ◽  
Author(s):  
H Allen Orr
Keyword(s):  
Quantitative Trait Locus ◽  
Natural Selection ◽  
Genetic Drift ◽  
Quantitative Trait ◽  
Null Hypothesis ◽  
Sign Test ◽  
Phenotypic Evolution ◽  
Phenotypic Difference ◽  
Quantitative Trait Locus Data ◽  
Trait Locus

Abstract Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the “high line” with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed.

Pomacentrus bangladeshius, a new species of damselfish (Perciformes, Pomacentridae) from Saint Martin’s Island, Bangladesh

Zootaxa ◽  
2020 ◽  
Vol 4860 (3) ◽  
pp. 413-424
Author(s):  
KAZI AHSAN HABIB ◽  
MD JAYEDUL ISLAM ◽  
NAJMUN NAHAR ◽  
AMIT KUMER NEOGI
Keyword(s):  
New Species ◽  
Body Color ◽  
Gill Rakers ◽  
Body Depth ◽  
Dorsal Fin ◽  
Fin Rays ◽  
Brown Body ◽  
A New Species ◽  
Yellow Iris ◽  
Pectoral Fin Rays

A new species of damselfish, Pomacentrus bangladeshius, is described from 3 specimens, 67–77 mm standard length (SL), collected from Saint Martin’s Island, Bangladesh. The new species is distinguished from congeners in having the following combination of characters: XIV, 13 dorsal-fin elements; II, 14 anal-fin elements; 19 pectoral-fin rays; 18–19 lateral-line scales; 17–19 gill rakers on first arch; body depth 1.68–1.88 (1.88) in SL; snout 4.17–4.60 (4.17) in head length; head 2.91–3.09 (3.08) in SL; a prominent notch present between preorbital and suborbital; olive to dark brown body color, dark brown premaxilla, and yellow iris with a narrow bronze eye ring. The new species inhabits shallow reef flats around rock and coral outcrops. Phylogenetic analysis also shows the clear divergence of P. bangladeshius from other genetically closely related congeneric species retrieved from GenBank and that it represents a separate lineage. 

scholarly journals An Efficient Genome Editing Strategy To Generate Putative Null Mutants in Caenorhabditis elegans Using CRISPR/Cas9

2018 ◽  
Vol 8 (11) ◽  
pp. 3607-3616 ◽  
Author(s):  
Han Wang ◽  
Heenam Park ◽  
Jonathan Liu ◽  
Paul W. Sternberg
Keyword(s):  
Caenorhabditis Elegans ◽  
Genome Editing ◽  
Null Mutants
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