Supplementary Materials for

Similar documents
Visual pigments. Neuroscience, Biochemistry Dr. Mamoun Ahram Third year, 2015

Visual pigments. Neuroscience, Biochemistry Dr. Mamoun Ahram Third year, 2019

C3020 Molecular Evolution. Exercises #3: Phylogenetics

Supplementary Materials for

Section III. Biochemical and Physiological Adaptations

Adaptation in the Neural Code of the Retina

Sensory Systems (con t)

Sensory Processing II Chapter 13

Sensory Processing II

SUPPLEMENTARY INFORMATION

Life in an unusual intracellular niche a bacterial symbiont infecting the nucleus of amoebae

Introduction to CNS neurobiology: focus on retina

SENSORY PROCESSES PROVIDE INFORMATION ON ANIMALS EXTERNAL ENVIRONMENT AND INTERNAL STATUS 34.4

Lecture 6: Non-Cortical Visual Pathways MCP 9.013/7.68, 03

Comparative Genomics II

Nature Neuroscience: doi: /nn.2662

Fig. S1. Proliferation and cell cycle exit are affected by the med mutation. (A,B) M-phase nuclei are visualized by a-ph3 labeling in wild-type (A)

Vertebrate Photoreceptors

Proteorhodopsin phototrophy in the ocean

SUPPLEMENTARY INFORMATION

OPTO 5320 VISION SCIENCE I

Supplementary Information Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes

Many of the slides that I ll use have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks!

Lecture 07, 13 Sept 2005 Chapters 12 and 13. Vertebrate Physiology ECOL 437 (aka MCB 437, VetSci 437) University of Arizona Fall 2005

Spatial Vision: Primary Visual Cortex (Chapter 3, part 1)


Supplementary Materials for

Elements of Bioinformatics 14F01 TP5 -Phylogenetic analysis

15 Grossberg Network 1

Supplementary Materials for

Modeling signal transduction. Phototransduction from frogs to flies

Supplementary Information for Discovery and characterization of indel and point mutations

The Eukaryotic Genome and Its Expression. The Eukaryotic Genome and Its Expression. A. The Eukaryotic Genome. Lecture Series 11

Visit to BPRC. Data is crucial! Case study: Evolution of AIRE protein 6/7/13

SUPPLEMENTARY INFORMATION

Supplemental Information. Inferring Cell-State Transition. Dynamics from Lineage Trees. and Endpoint Single-Cell Measurements

Identify the structure labelled 1.

Comparative Bioinformatics Midterm II Fall 2004

Inferring phylogeny. Constructing phylogenetic trees. Tõnu Margus. Bioinformatics MTAT

Bioinformatics tools for phylogeny and visualization. Yanbin Yin

Fine structure of the retina of black bass, Micropterus salmoides (Centrarchidae, Teleostei)

Supplementary Materials for

What is the central dogma of biology?

Illegitimate translation causes unexpected gene expression from on-target out-of-frame alleles

Supplementary Figure 1: Mechanism of Lbx2 action on the Wnt/ -catenin signalling pathway. (a) The Wnt/ -catenin signalling pathway and its

Phylogenetic relationship among S. castellii, S. cerevisiae and C. glabrata.

Do Neurons Process Information Efficiently?

Supplemental Information

Structural Studies of the Flexible Filamentous Plant Viruses

In order to confirm the contribution of diffusion to the FRAP recovery curves of

Figure S1. Programmed cell death in the AB lineage occurs in temporally distinct

Fig. S1. Expression pattern of moody-gal4 in third instar. Maximum projection illustrating a dissected moody-gal4>ngfp L3 larva stained for Repo

BINF6201/8201. Molecular phylogenetic methods

Supplementary Fig. 1. Infection of three C. elegans strains used for spatially restricted enzymatic tagging. Animals infected with N.

1 ATGGGTCTC 2 ATGAGTCTC

METHODS FOR DETERMINING PHYLOGENY. In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task.

Introduction to Bioinformatics

Role of Mitochondrial Remodeling in Programmed Cell Death in

Session 5: Phylogenomics

Axon Guidance. Multiple decision points along a growing axon s trajectory Different types of axon guidance cues:

Visual System. Anatomy of the Visual System. Advanced article

POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics

Perception of colour, form, depth and movement; organization of associative visual fields. Seminar Prof Maja Valić

Bioinformatics: Investigating Molecular/Biochemical Evidence for Evolution

Supplementary Figure 1. Phenotype of the HI strain.

Theory of colour measurement Contemporary wool dyeing and finishing

Macroevolution Part I: Phylogenies

LIST of SUPPLEMENTARY MATERIALS

Evolution by duplication

Nature Genetics: doi: /ng Supplementary Figure 1. The phenotypes of PI , BR121, and Harosoy under short-day conditions.

concentration ( mol l -1 )

Anatomy of a tree. clade is group of organisms with a shared ancestor. a monophyletic group shares a single common ancestor = tapirs-rhinos-horses

SUPPLEMENTARY INFORMATION

Supplementary Materials for

Sensors. Sensory Physiology. Transduction. Types of Environmental Stimuli. Chemoreception. Taste Buds (Contact Chemoreceptors)

Estimating Evolutionary Trees. Phylogenetic Methods

Phylogenetics - Orthology, phylogenetic experimental design and phylogeny reconstruction. Lesser Tenrec (Echinops telfairi)

Supplementary Figure 1

08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega

Supplementary Figure 1. Markedly decreased numbers of marginal zone B cells in DOCK8 mutant mice Supplementary Figure 2.

Description: Supplementary Figures, Supplementary Methods, and Supplementary References

Fig. 16. Majority rule consensus tree depicting phylogenetic relationships inferred among 74 species of heterokont algae. Note that A.

SUPPLEMENTARY INFORMATION

Phylogenetic analyses. Kirsi Kostamo

3/8/ Complex adaptations. 2. often a novel trait

Supplementary Figure 1. Characterization of the single-photon quantum light source based on spontaneous parametric down-conversion (SPDC).

Phylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline

GEP Annotation Report

Supplementary Materials for

A Three-dimensional Physiologically Realistic Model of the Retina

Evolution of Dim-Light and Color Vision Pigments

Genome-wide analysis of the MYB transcription factor superfamily in soybean

Supplementary Figures

thebiotutor.com A2 Biology Unit 5 Responses, Nervous System & Muscles

reconciling trees Stefanie Hartmann postdoc, Todd Vision s lab University of North Carolina the data

COMP 546. Lecture 21. Cochlea to brain, Source Localization. Tues. April 3, 2018

UoN, CAS, DBSC BIOL102 lecture notes by: Dr. Mustafa A. Mansi. The Phylogenetic Systematics (Phylogeny and Systematics)

EST1 Homology Domain. 100 aa. hest1a / SMG6 PIN TPR TPR. Est1-like DBD? hest1b / SMG5. TPR-like TPR. a helical. hest1c / SMG7.

Cells. Steven McLoon Department of Neuroscience University of Minnesota

1. Understand the methods for analyzing population structure in genomes

Transcription:

advances.sciencemag.org/cgi/content/full/3/11/eaao4709/dc1 Supplementary Materials for Pushing the limits of photoreception in twilight conditions: The rod-like cone retina of the deep-sea pearlsides Fanny de Busserolles, Fabio Cortesi, Jon Vidar Helvik, Wayne I. L. Davies, Rachel M. Templin, Robert K. P. Sullivan, Craig T. Michell, Jessica K. Mountford, Shaun P. Collin, Xabier Irigoien, Stein Kaartvedt, Justin Marshall The PDF file includes: Published 8 November 2017, Sci. Adv. 3, eaao4709 (2017) DOI: 10.1126/sciadv.aao4709 fig. S1. Gene coding region (CDS) inferred vertebrate opsin gene phylogeny. fig. S2. Reconstruction of amino acid changes at known key spectral tuning sites of pearlside opsins. fig. S3. Vertebrate Gα transducin gene phylogeny. fig. S4. Vertebrate arrestin gene phylogeny. fig. S5. rh2 opsin gene conversion phylogeny. fig. S6. Topographic distribution of rod-like cone photoreceptors in three individuals of M. muelleri. fig. S7. Topographic distribution of ganglion cells (excluding amacrine cells and glial cells) in three individuals of M. muelleri. fig. S8. Expression of rh2 and rh1 opsin genes from sectional RNA in situ hybridization analyses of the eye of M. muelleri. fig. S9. Location of the true rod photoreceptors and their distribution across the retina in M. muelleri. fig. S10. Manual approach to extract genes from back-mapped reads. table S1. Summary of transcriptomes, GenBank accession numbers, opsin mapping (including base pair coverage), and proportional opsin gene expression. table S2. Summary of transcriptomes, GenBank accession numbers, transducin mapping (including base pair coverage), and proportional transducin gene expression. table S3. Summary of transcriptomes, GenBank accession numbers, arrestin mapping (including base pair coverage), and proportional arrestin gene expression.

table S4. Single-gene GenBank accession numbers of gene sequences produced during this study. table S5. Summary of the stereology parameters used for the analysis of the rodlike cone photoreceptors and ganglion cell distribution along with the quantitative results obtained using the optical fractionator methods in six retinas of M. muelleri. Legends for movies S1 and S2 Other Supplementary Material for this manuscript includes the following: (available at advances.sciencemag.org/cgi/content/full/3/11/eaao4709/dc1) movie S1 (.mp4 format). 3D reconstruction of the two photoreceptor types in M. muelleri. movie S2 (.mp4 format). Close-up 3D reconstruction of the nucleus and synaptic terminal of the two photoreceptor types in M. muelleri.

Supplementary Materials fig. S1. Gene coding region (CDS) inferred vertebrate opsin gene phylogeny. The pearlside retinal transcriptomes (n = 5 per species) contained three opsin genes (one rod opsin and two cone

opsins) (darker coloured boxes). Note that the rh2 cone opsins cluster as sisters within pearlside species suggesting two separate duplication events. However, as shown in fig. S5, gene conversion affecting the rh2 CDS is the cause of this pattern and the duplication is therefore likely to have occurred ancestrally. Vertebrate ancient (va) opsin gene sequences from five fish and one reptile species were used as outgroups to reconstruct the phylogenetic relationship. Node numbers depict Bayesian posterior probabilities. GenBank Accession Numbers are depicted after the species names, pearlside specific accession numbers are given in table S4.

bovine aa # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 M. muelleri rh2-1 M - N G T E G D N F Y I P M S N A S G L V R S P Y E Y P Q Y Y L G E K W Q F Y L L A A Y M V F L I S M. muelleri rh2-2 M - N G T E G D N F Y I P M S N A S G L V R S P Y E Y P Q Y Y L G E K W Q F Y L L A A Y M V F L I S M. mucronatus rh2-1 M - N G T E G E N F Y I P M S N A S G L V R S P F E Y P Q Y Y L G E K W Q F Y L L A V Y M L F L I F M. mucronatus rh2-2 M - N G T E G D N F Y I P M S N A S G L V R S P F E Y P Q Y Y L G E K W Q F Y L L A F Y M L F L I F S. analis rh2 M E N G T E G K N F Y I P M N N R S G L V R S P Y E Y P Q Y Y L A D P I L Y K F Q A A Y M L F L M F M. muelleri rh1 M - N G T E G P Y F Y V P M S N A T G V V R S P Y E Y P Q Y Y L V N P V A F F V L G A Y M F F L I L M. mucronatus rh1 M - N G T E G P Y F Y I P M S N A T G V V R S P Y E Y P Q Y Y L V N P A A F F V L G A Y M F F L I L bovine aa # 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 M. muelleri rh2-1 T G L P L N G L T L V V T A Q N K K L Q Q P L N F I L V N L A V A G L I M V C F G F T I T F V T A M M. muelleri rh2-2 T G L P L N G L T L V V T A Q N K K L Q Q P L N F I L V N L A V A G L I M V C F G F T I T F V T A M M. mucronatus rh2-1 T G L P L N G L T L I V T F Q N K K L Q Q P L N F I L V N L A V A G M I M V C F G F T I T F C T A M M. mucronatus rh2-2 T G L P L N G L T L I V T A Q N K K L Q Q P L N F I L V N L A I A G M I M V C F G F T I T F C T A M S. analis rh2 T G G P I N I L T L V V T A Q N K K L R Q P L N F I L V N L A L A G A I M V F G G F V I T F Y T S M M. muelleri rh1 T V F P I N F L T L Y V T I E H K K L R T A L N Y V L L N L A V A N L F M V T G G F T T T L Y S S M M. mucronatus rh1 T C F P I N F L T L Y V T I E H K K L R T A L N Y V L L N L A V A N L F M V V G G F T T T L Y T S M bovine aa # 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 M. muelleri rh2-1 N G Y F V F G P M G C A I E G F M A T L G G Q I S L W S L V V L A V E R Y I V V C K P M G S F K F G M. muelleri rh2-2 N G Y F V F G P M G C A I E G F M A T L G G Q I S L W S L V V L A V E R Y I V V C K P M G S F K F G M. mucronatus rh2-1 S G Y F I F G A M G C A I E G F M A T L G G Q I S L W S L V V L A V E R Y I V V C K P M G S F K F A M. mucronatus rh2-2 S G Y F I F G P M G C A I E G F M A T L G G Q I S L W S L V V L A V E R Y I V V C K P M G S F K F A S. analis rh2 N G Y F L L G P T S C A V E G F M A T L G G Q I S L W S L V V L A V E R Y I V V C K P M G S F K F S M. muelleri rh1 H G Y F V L G R S G C I I E G F C A T H G G Q V A L W S L V V L A I E R Y L V V C K P I A N F R F G M. mucronatus rh1 A G Y F V L G R T G C I I E G F C A T H G G Q V A L W S L V V L A I E R Y L V V C K P I A N F R F G bovine aa # 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 M. muelleri rh2-1 N S H A T I G V V F T W V M A I A C A A P P L F G W S R Y L P E G L Q C S C G P D Y Y T L N P K C N M. muelleri rh2-2 N S H A T I G V V F T W V M A V A C A A P P L F G W S R Y L P E G L Q C S C G P D Y Y T L N P K C N M. mucronatus rh2-1 N S H A T A G V V F T W I M A L A C A A P P L L G W S R Y L P E G L Q C S C G P D Y Y T L N P K C N M. mucronatus rh2-2 N S H A T A G V V F T W I M A M A C A A P P L L G W S R Y L P E G L Q C S C G P D Y Y T L N P K C N S. analis rh2 A T H A G I G C G I T W F M A M A C A A P P L V G W S R Y L P E G L Q C S C G P D Y Y T M A P G Y N M. muelleri rh1 E N H A I M G L V F S W V M A F S C S L P P L F G W S R Y I P E G M Q C S C G I D Y Y T R A E G F N M. mucronatus rh1 E N H A I M G L V F S W V M A S S C S V P P L F G W S R Y I P E G M Q C S C G I D Y Y T R A E G F N bovine aa # 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 M. muelleri rh2-1 N E S Y V M Y M F S C H F M V P V C T I F F T Y G S L V L T V K A A A A S Q Q E S E S T Q K A E R E M. muelleri rh2-2 N E S Y V M Y M F S C H F M V P V C T I F F T Y G S L V L T V K A A A A S Q Q E S E S T Q K A E R E M. mucronatus rh2-1 N E S Y V M Y M F S C H F C V P L F T I F F T Y G S L V L T V K A A A A S Q Q E S E S T Q K A E R E M. mucronatus rh2-2 N E S Y V M Y M F S C H F C V P L F T I F F T Y G S L V L T V K A A A A S Q Q E S E S T Q K A E R E S. analis rh2 N E S Y V I Y M F T C H F C F P V F T I F F T Y G S L V L T V K A A A A Q Q Q E S E S T Q K A E R E M. muelleri rh1 N E S F V I Y M F V V H F T I P L T I I T F C Y G R L L C A V K E A A A A Q Q E S E T T Q R A E K E M. mucronatus rh1 N E S F V I Y M F I V H F T I P L L I I L F C Y G R L L C A V K E A A A A Q Q E S E T T Q R A E R E bovine aa # 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 M. muelleri rh2-1 V T R M C V L M V C G F L M A W T P Y A S Y A A W I F V N K G V S F S P Q S M A I P A F F A K S A S M. muelleri rh2-2 V T R M C V L M V C G F L M A W T P Y A S Y A A W I F V N K G V S F S P Q S M A I P A F F A K S A S M. mucronatus rh2-1 V T R M C I L M V F G F L L S W L P Y A S Y A A F I F M N K G I A F T P Q S M A V P A F F A K S G A M. mucronatus rh2-2 V T R M C I L M V F G F L L S W L P Y A S Y A A F I F M N K G I A F T P Q S M A V P A F F A K S G A S. analis rh2 V T R M C V L M V L G F L T A W V P Y A S L A A W I F F N K G A A F S A V G M A V P A F F A K S A S M. muelleri rh1 V S R M V V L M V M S Y M V S W M P Y A A V A W Y I F C N Q G T E F G P L F M A V P A F F A K S S A M. mucronatus rh1 V S R M V I L M V M S Y M V S W S P Y A S V A W Y I F C N Q G T E F G P L F M A V P A F F A K S S A bovine aa # 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 - - - - 334 335 336 337 338 339 340 341 342 343 344 345 M. muelleri rh2-1 I V N P V I Y V V L N K Q F R N C M M A T L - - G M A P A G D D E S S S - - V S S S S K T E V S S V M. muelleri rh2-2 I V N P V I Y V V L N K Q F R N C M M A T L - - G M A P A G D D E S S S - - V S S S S K T E V S S V M. mucronatus rh2-1 I I N P M I Y V V M N K Q F R T C M L A T L - - G M A A A G D D E S S S - - V S S S S K T E V S S V M. mucronatus rh2-2 I I N P M I Y V V M N K Q F R T C M L A T L - - G M A A A G D D E S S S - - V S S S S K T E V S S V S. analis rh2 L T N P V I Y V L L N K Q F R N C M L T T I - - G M G G M V D D E S S A S G S S S S S K T E V S S V M. muelleri rh1 L Y N P V I Y I C M N K Q F R M C M I T T L F C G K N P F E D M E G D S - - T T S A S K T E A S S V M. mucronatus rh1 L Y N P V I Y I C M N K Q F R T C M I T T L F C G K N P F E D M E G D S - - T T S A S K T E A S S V bovine aa # - - - - - - - - 346 347 348 muelleri rh2-1 - - - - - - - - S P A M. Key spectral tuning sites (20, 23 ) M. muelleri rh2-2 - - - - - - - - S P A RH2 amino acid changes within Maurolicus species M. mucronatus rh2-1 - - - - - - - - S P A RH2 amino acid change between Maurolicus species and S. analis at key spectral tuning sites M. mucronatus rh2-2 - - - - - - - - S P A Retinal binding pocket site in bovine rhodopsin S. analis rh2 - - - - - - - - S Q G Q122 in cones and deeps-sea fish rods M. muelleri rh1 S S S S T S S V G P A P189 in cones, I189 in rods M. mucronatus rh1 - S S S T S S V A P A Transmembrane region fig. S2. Reconstruction of amino acid changes at known key spectral tuning sites of pearlside opsins. rh2 paralogs in both species showed very few amino acid differences (marked in yellow). Accession number for S. analis is EF517406.

fig. S3. Vertebrate Gα transducin gene phylogeny. The pearlside retinal transcriptomes (n = 5 M. mucronatus; n = 4 M. muelleri) contained three alpha transducin genes (one rod transducin and two cone transducin). Mammalian taste transducing alpha subunit (gnat3) was used as outgroup to reconstruct the phylogenetic relationship. Node numbers depict Bayesian posterior probabilities. GenBank Accession Numbers are depicted after the species names, pearlside specific accession numbers are given in table S4.

fig. S4. Vertebrate arrestin gene phylogeny. The pearlside retinal transcriptomes (n = 5 M. mucronatus; n = 4 M. muelleri) contained four arrestin genes (two rod arrestins and two cone arrestins). The arrestin of the ascidian Ciona intestinalis (ciarr) was used as an outgroup sequence to reconstruct the phylogenetic relationship. Node numbers depict Bayesian posterior probabilities. GenBank accession numbers are depicted after the species names, pearlside specific Accession Numbers are given in table S4.

fig. S5. rh2 opsin gene conversion phylogeny. Using the information contained in the 3 - untranslated regions (3 -UTRs) and the last 50 bp of exon 5 revealed the ancestral origin of the duplicated pearlside rh2 genes, and shows that gene conversion affecting the gene coding sequences (CDS) within pearlside species may have maintained an almost identical function of these gene products (also see Fig. 3, and fig. S2).

fig. S6. Topographic distribution of rod-like cone photoreceptors in three individuals of M. muelleri. (A to C) individuals S2004, S2005, S3001, respectively (refer to table S5). The black lines represent iso-density contours, and values are expressed in densities x 10 4 cells/mm 2. The arrows indicate the orientation of the retina. N = nasal, V = ventral. Scale bar = 1 mm. (D and E) wholemount view of the photoreceptors in a high-density (D) and low-density (E) area. Scale bar 10 µm.

fig. S7. Topographic distribution of ganglion cells (excluding amacrine cells and glial cells) in three individuals of M. muelleri. (A to C) individuals S2005, S2006, S3002, respectively (refer to table S5). The black lines represent iso-density contours, and values are expressed in densities x 10 3 cells/mm 2. The arrows indicate the orientation of the retina. N = nasal, V = ventral. Scale bars = 1 mm. (D and E) light micrographs of the Nissl-stained ganglion cells in a low-density (D) and highdensity (E) area. gc = ganglion cell, ac = amacrine cell, g = glial cell. Scale bars = 25 µm.

fig. S8. Expression of rh2 and rh1 opsin genes from sectional RNA in situ hybridization analyses of the eye of M. muelleri. (A to D) rh2 labeling and (E to H) rh1 labeling. (D and E) show the entire retina labelled with either rh2 (D) or rh1 (E). (A to C) higher magnification images of the black boxes in (D) from top to bottom, respectively. (F-H) higher magnification images of the black boxes in (E) from top to bottom, respectively. Note that while rh2 was labelled everywhere in the retina, rh1 labelled cells (arrowheads in F-H) were very sparse and nearly exclusively found in the retinal margins of the retina. Scale bars = 100 µm (A to C, F to H), 1 mm (D, E).

fig. S9. Location of the true rod photoreceptors and their distribution across the retina in M. muelleri. (A) Rod photoreceptors labeled with anti-rhodopsin antibody and (B) distribution of the true rods across the retina (B). Each dot on the map in (B) represent one labeled cell. The black arrows indicate the orientation of the retina. N = nasal, V = ventral. Scale bars (A) = 1 µm, (B) = 1 mm.

reference sequence allele 4 allele 3 allele 2 allele 1 fig. S10. Manual approach to extract genes from back-mapped reads. Using a heterozygous individual to map unassembled reads against a reference sequence reveals a polymorphic site with four distinct single polynucleotide polymorphism (SNP) combinations (alleles) i.e. two gene copies (copy 1 = alleles 1 and 3; copy two = alleles 2 and 4). The copy specific SNPs in combination with the paired-end information were then used to manually reconstruct sequences by moving from SNP to SNP along the reference sequence.

table S1. Summary of transcriptomes, GenBank accession numbers, opsin mapping (including base pair coverage), and proportional opsin gene expression. Sub-mapping refers to the re-mapping of rh2 specific reads against the 3 -UTR alone. rh1 = rod opsin, rh2 = rhodopsin-like 2. Reads refer to number of Paired End fragments. RNA sequencing Mapping Relative expression % Transcriptome Rod Cones rod vs cone cones Species SRA GenBank Acc. No. Tot. raw reads rh1 rh2-1 Sub- rh2-2 Mapping No. reads x Cov. No. reads x Cov. No. reads No. reads x Cov. Sub- Mapping No. reads rh1 vs rh2 rh2-1 vs rh2-2 SRX3161870 61,531,936 25,906 2,141 1,679,058 110,026 114,204 1,039,146 68,051 46,022 1.19 98.81 70.73 29.27 SRX3161890 63,301,844 30,203 2,495 1,790,792 117,523 141,412 1,117,667 73,251 60,728 1.29 98.71 69.39 30.61 Maurolicus muelleri (Norwegian Fjord) SRX3161913 59,332,288 23,925 1,978 1,829,472 119,782 125,890 1,081,219 70,851 49,770 1.03 98.97 71.12 28.88 SRX3161914 56,544,348 22,186 1,833 1,634,751 106,811 125,222 1,075,381 70,314 52,246 1.02 98.98 69.98 30.02 SRX3161915 30,078,936 14,338 1,185 1,714,183 112,330 155,174 1,070,155 70,092 69,258 0.65 99.35 68.57 31.43 Mean 54,157,870 23,312 1,926 1,729,651 113,294 132,380 1,076,714 70,512 55,605 1.04 98.96 69.96 30.04 Standard error 6,124,761 2,611 216 35,712 2,384 7,158 12,557 833 4,182 0.11 0.46 SRX3162896 58,396,072 2,543 210 620,146 40,479 97,712 556,608 35,969 79,530 0.27 99.73 56.08 43.92 SRX3162897 27,499,520 1,108 92 141,425 9,243 34,686 124,889 8,072 29,580 0.53 99.47 54.93 45.07 Maurolicus mucronatus (Red Sea) SRX3162898 75,574,170 4,196 347 1,004,880 65,569 158,530 961,288 62,110 110,360 0.27 99.73 59.89 40.11 SRX3162899 74,036,026 1,202 100 378,127 24,708 91,572 327,565 21,167 67,130 0.22 99.78 58.64 41.36 SRX3162900 73,718,678 4,022 333 1,001,589 65,325 140,128 919,289 59,407 110,722 0.27 99.73 56.81 43.19 Mean 61,844,893 2,614 216 629,233 41,065 104,526 577,928 37,345 79,464 0.31 99.69 57.27 42.73 Standard error SRA, short-read archive 9,136,746 662 55 170,419 11,112 21,536 163,076 10,537 15,120 0.06 0.89

table S2. Summary of transcriptomes, GenBank accession numbers, transducin mapping (including base pair coverage), and proportional transducin gene expression. gnat1 = G protein subunit alpha transducin 1, gnat2 = G protein subunit alpha transducin 2. Reads refer to number of Paired End fragments. RNA sequencing Mapping Relative expression % Transcriptome Rod Cones rod vs cone cones Species SRA GenBank Acc. No. Tot. reads Filtered gnat1 gnat2-1 gnat2-2 N 0 reads x Cov. N 0 reads x Cov. N 0 reads x Cov. gnat1 vs gnat2 gnat2-1 vs gnat2-2 Maurolicus muelleri (Norwegian Fjord) SRX3161870 61,531,936 1,470 124 198,451 16,781 36,551 3,133 0.62 99.38 84.26 15.74 SRX3161890 63,301,844 1,762 149 225,756 19,090 44,018 3,773 0.65 99.35 83.49 16.51 SRX3161913 59,332,288 1,642 139 217,747 18,411 41,438 3,551 0.63 99.37 83.82 16.18 SRX3161914 56,544,348 1,504 127 258,728 21,878 42,270 3,624 0.50 99.50 85.79 14.21 Maurolicus mucronatus (Red Sea) Mean 60,177,604 1,595 135 225,171 19,040 41,069 3,520 0.60 99.40 84.34 15.66 Standard error 1,458,029 67 6 12,568 1,063 1,599 137 0.03 0.51 SRX3162896 58,396,072 276 23 103,533 8,736 12,730 1,087 0.24 99.76 88.93 11.07 SRX3162897 27,499,520 140 12 15,672 1,325 2,122 183 0.78 99.22 87.88 12.12 SRX3162898 75,574,170 557 47 182,230 15,375 23,277 1,987 0.27 99.73 88.55 11.45 SRX3162899 74,036,026 144 12 47,880 4,040 5,424 465 0.27 99.73 89.68 10.32 SRX3162900 73,718,678 552 46 174,743 14,745 22,143 1,888 0.28 99.72 88.64 11.36 Mean 61,844,893 334 28 104,812 8,844 13,139 1,122 0.37 99.63 88.74 11.26 Standard error 9,136,746 93 8 33,221 2,803 4,271 364 0.10 0.29 SRA, short-read archive

table S3. Summary of transcriptomes, GenBank accession numbers, arrestin mapping (including base pair coverage), and proportional arrestin gene expression. sag = s-antigen visual arrestin, arr3 = arrestin 3. Reads refer to number of Paired End fragments. RNA sequencing Mapping Relative expression % Transcriptome Rod Cones rod vs cone cones Species Maurolicus muelleri (Norwegian Fjord) SRA GenBank Acc. No. Tot. raw reads saga arr3a arr3b N 0 reads x Cov. N 0 reads x Cov. N 0 reads x Cov. saga vs arr3 arr3a vs arr3b SRX3161870 61,531,936 630 48 7667 624 21517 1754 1.98 98.02 26.22 73.78 SRX3161890 63,301,844 530 41 9537 776 37966 3096 1.04 98.96 20.03 79.97 SRX3161913 59,332,288 560 43 8676 708 24195 1974 1.57 98.43 26.38 73.62 SRX3161914 56,544,348 488 37 9154 745 27764 2264 1.22 98.78 24.75 75.25 Maurolicus mucronatus (Red Sea) Mean 60,177,604 72 6 8759 713 27861 2272 1.45 98.55 24.34 75.66 Standard error 1,458,029 552 42 404 33 3603 294 0.21 1.48 SRX3162896 58,396,072 106 8 1816 146 18624 1511 0.49 99.51 8.83 91.17 SRX3162897 27,499,520 40 3 254 21 3124 254 1.11 98.89 7.54 92.46 SRX3162898 75,574,170 148 11 3118 252 32265 2617 0.39 99.61 8.77 91.23 SRX3162899 74,036,026 22 2 808 66 8174 664 0.23 99.77 8.97 91.03 SRX3162900 73,718,678 146 11 3498 283 30220 2452 0.40 99.60 10.34 89.66 Mean 61,844,893 92 7 1899 153 18481 1500 0.52 99.48 8.89 91.11 Standard error 9,136,746 26 2 630 51 5787 469 0.15 0.44 SRA, short-read archive

table S4. Single-gene GenBank accession numbers of gene sequences produced during this study. rh1 = rod opsin, rh2 = rhodopsin-like 2, gnat1 = G protein subunit alpha transducin 1, gnat2 = G protein subunit alpha transducin 2, sag = s-antigen visual arrestin, arr3 = arrestin 3. Species GenBank accession no. Photoreceptor Gene (length bp) Maurolicus muelleri MF805834 rod rh1 (1077) MF805835 cone rh2-1 (1365)* MF805836 cone rh2-2 (1365)* MF805831 rod gnat1 (1053) MF805832 cone gnat2-1 (1053) MF805833 cone gnat2-2 (1038) MF805837 rod (outer segment) x saga (1176) MF805838 rod (synapses) x sagb-v1 (isoform) (1176) MF805839 rod (synapses) x sagb-v2 (isoform) (1194) MF805840 rod (synapses) x sagb-v3 (isoform) (1161) MF805829 cone arr3a (1095) MF805830 cone arr3b (1092) Maurolicus mucronatus MF805824 rod rh1 (1074) MF805825 cone rh2-1 (1368)* MF805826 cone rh2-2 (1380)* MF805821 rod gnat1 (1053) MF805822 cone gnat2-1 (1053) MF805823 cone gnat2-2 (1041) MF805827 rod (outer segment) x saga (1179) MF805828 rod (synapses) x sagb (1176) MF805819 cone arr3a (1104) MF805820 cone arr3b (1095) x sag expression localization according to (16). * length includes CDS and 3 -UTR (all other genes only CDS).

table S5. Summary of the stereology parameters used for the analysis of the rod-like cone photoreceptors and ganglion cell distribution along with the quantitative results obtained using the optical fractionator methods in six retinas of M. muelleri. CE = Schaeffer coefficient of error, Ø = diameter, SRP = spatial resolving power, PR = photoreceptors, GC = ganglion cells. Indiv Lens Ø, mm Cell type Counting frame size (µm) Grid size (µm) CE Total cells (n) Peak density (cells/ mm 2 ) S2004L 2.1 PR 40 x 40 420 x 420 0.039 1,699,724 118,750 S2005L* 2.0 PR 40 x 40 390 x 390 0.042 1,576,991 130,000 S3001R 2.1 PR 40 x 40 400 x 400 0.040 1,610,500 116,875 S2005R* 2.0 GC 80 x 80 400 x 400 0.049 145,950 18,750 S2006R 1.9 GC 80 x 80 380 x 380 0.050 144,918 17,969 S3002R 2.2 GC 80 x 80 450 x 450 0.051 178,248 19,531 * Same individual with the two eyes analyzed (left eye for PR and right eye for GC). Supplementary movies movie S1. 3D reconstruction of the two photoreceptor types in M. muelleri. movie S2. Close-up 3D reconstruction of the nucleus and synaptic terminal of the two photoreceptor types in M. muelleri.

2024 © sciencedocbox.com Privacy Policy | Terms of Service | Feedback