Aligned Myoglobin Sequences

5884 words (24 pages) Essay

23rd Sep 2019 Biology Reference this

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  1. DNA sequencing gel

Forward reaction DNA sequence (e value: 5e-44)

GCCGTTGTTGAGTCGCAACAAAAAGCCCCCACCTTTCGGTGGGGGCTTTCCGATTCAACTGACGCTGAATCTTTTGGAGACTTCAGCCTCAGCCGATGGCG

Reverse reaction DNA sequence (e value: 5e-44)

GGCATCCGTGAGCCCGTCGCTGGCTCCCTGATCTACGGCAACAACATCATCTCCGGTGCTGTTGTGCCCTCCTCGAACGCCATCGGCCTTCACTTCTATCC

The sequenced gene belongs to the psbA multigene family and codes for the D1 protein of photosystem II (PSII) in cyanobacteria such as Synechococcus WH7803. The D1 protein forms the core of the PSII’s reaction centre as a heterodimer with the D2 protein.  When light is absorbed, the heterodimer undergoes charge separation and the electrons get transferred from chlorophyll A via phaeophytin to the primary acceptor (quinone Qa) then to the secondary acceptor 9Qb), and the process results in the production of ATP. (Edelman and Kattoo 2008)

The primer site for the reverse reaction is closer to the C terminus than the primer for the forward reaction.

  1. Identifying ORFs, promoter regions and intron/exon boundaries

The protein encoded by the DNA sequence is myoglobin, which is a globular protein made of 153 amino acids and an embedded heme group. It is an oxygen-carrying molecule (like haemoglobin), found in the cardiac and skeletal muscle of most vertebrates, and can also be present in invertebrates and bacteria (Ferreras et al 2016). During periods of increased metabolic activity, myoglobin facilitates the transport of oxygen from red blood cells to mitochondria, and it can serve as a reservoir in anoxic conditions (e.g. the muscle tissues of diving birds and mammals are particularly abundant in myoglobin). (Ordway and Garry 2004)

AATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA

TCTATCTATAATTGACTTCAATCAAAATGTTCCAGATCAACTTAGGAGGT

GTTGTGAACATTTGAAGTGTGGTGAGAGGATGGGAGGTCTGGAATAATTT

GGTGATATGACGGTGAAGGGAGTATAAAAGGTCAGCTTTGAGGGGGGAAG

TCAGGTCAAGAAGAATTTTGTACAACATCACACAGGACATTTTACTACTC

TGCAGGTAAAAATTTTGTAATTGTTTAAATGTAATGAGGATAATAGGGTA

TAAGGACAGAGAATTGTCATTGTGGGAAATATTTTAACCCAAACCAATAT

AAGAAATAAAGCAGTTTTTAAGTGCCAAGGTTAGTATTGAAGAAATAAAA

AGGTATTTATAACCATGTAACAGCTCAAGAGCATCATCTGATTTCACTTC

ACATGAATTGTGCAGGGCTTCACCAAGGTTACAGTGCAGACTCAGTGAGG

GCAGCTGAGGTGATGAAGACGCCTCTTTCTAATAATGACTCACACTTGTT

CAGCAGTGACTGCACACAATGAAACGGTGGATGTGTACCTTGATATGATC

AGAGACCTTCTGTGCTTTTATTATATATTATATATACCTCCTCAGATAAT

GGCTGACTTTGACATGGTACTGAAGTGCTGGGGTCCAATGGAGGCGGACC

ACGCAACCCACGGGAGTCTGGTGCTGACCCGGTACTACCAGATTAAATGA

ATCTGCCCTCTGGTCAGGAGGTTTGCAGGGCTGTACAAAAGTTTTTTGAA

GGCACATTATTTTTCATTAAGTTCACATTAAATGTGAGGCCATGACAGTG

ATACATCAATATAGATTGATATAAATTAATTTACAAGTCAACAATCCATA

CAAATCATCATTTTTAAGATTTAGAATAAACATGTCTTTTGAAGTAAAAC

AGGCTGTTTTCCTAATGTATTTAATTTATTAGATTTTCTTTTATTTGTAT

AAAGAAGAATATATATGTTTTTTATATCTAAATGGGTCTAATAGTTGTTC

TAAACATAACTGAATCTGTTAGACTTTGTGATATCAGCAAATATTGTATT

GATGTCAAAGAATAAATATAGAATATATTATCATATTGTGATAAACTTGT

GATTTAAACCCCTTGTCCTCAGTTGTGAGTGTTATTTCAGGTGAACCCTC

ACATTTCCTTTTCCTCGCAGTTTATTCACAGAGCACCCAGAAACCCTAAA

GTTATTCCCCAAGTTTGCTGGCATCGCCCATGGGGACCTGGCCGGGGATG

CAGGTGTTTCTGCCCACGGTGCCACAGTGCTGAATAAACTGGGTGATCTG

CTGAAGGCCAGAGGCGCCCACGCTGCCCTCCTCAAACCTCTGTCCAGCAG

CCACGCCACCAAGCACAAGATCCCCATTATTAACTTCAAGGTGAGTTTGA

TTGACATGAGGGCAAGTTCGAACGTATCTAGACCATTGTGGTTTGATCTT

TCCTCCAACTTTTTGTGTCCTCCAACCTATTTTAAAGCATTTTTTGTGAT

TCTTGTTTTCAGCTGATTGCAGAGGTCATTGGTAAAGTCATGGAGGAGAA

GGCGGGACTGGATGCCGCCGGGCAGACTGCCCTGAGGAACGTGATGGCCA

TCATCATCACTGACATGGAGGCCGACTACAAAGAGCTGGGCTTCACTGAA

TGAAGATCAGATTCACAAAGTTTTGGCGACGACAGACAGGAAAATGTACC

ACATGCAAAAATAAAATGATAAAAATGGTCTGATTTTCTGTAAGCCTAAT

TAAATAATGTTTGCAATGAAATTAAATCAATCAATCAATCAATCAATCAA

TGTTTATTTATATAGCCCAATATCACAAATGTTACATTTGTCTCAGTGGT

CTTCACAGTGTGTACAGAATATCAGTATGACAATACGACACCCTCTGTCC

TTAGACCCTCACATCGTACAAGGAAAAACTTCCAAAGAAAACCCAGTTTA

AAGGGAAAAATGGGAGAAACCTCAGGGAGAGCAACAGAGGAGGGATCCCT

CTCCCCAGGACGGACAGACGTGCAATAGATGCCGTGTTGTTAAATTGAAA

AGATAAATACATTTGCAACATAGGTAGTCCCAATGTTTGGGAAATGCATG

TTGTTGTTATTAATAGGAAGATGAATCCCCCGAGGATATCCATCCCAGAA

CCTATGATCCCAGAACCACAGCCACGAATCCAGATTCCAGCGCTCCGCGA

ACCCAGAACCCGGACCGCGGGATTCTCCCTGAATCCGGATCCCAGCGTT

Alignment of splice sites:

Consensus  A/C A G G U

Intron1    C   C G G T

Exon1      C   A G T T

Intron2    A   A G G T

Exon2      C   A G C T

  1. Aligning sequences using ClustalX

gunnari         ATGGCTGACTTTGACATGGTGCTGAAGTGCTGGGGTCCAGTGGAGGCGGACCACGCAACC

spinosus        ATGGCTGACTTTGACATGGTACTGAAGTGCTGGGGTCCAATGGAGGCGGACCACGCAACC

                ******************** ****************** ********************

gunnari         CACGGGAGTCTGGTGCTGACCCGTTTATTCACAGAGCACCCAGAAACCTTGAAGTTATTC

spinosus        CACGGGAGTCTGGTGCTGACCCGTTTATTCACAGAGCACCCAGAAACCCTAAAGTTATTC

                ************************************************ * *********

gunnari         CCCAAGTTTGCCGGCATCGCCCATGGGGACCTGGCCGGGGATGCAGGTGTTTCTGCCCAC

spinosus        CCCAAGTTTGCTGGCATCGCCCATGGGGACCTGGCCGGGGATGCAGGTGTTTCTGCCCAC

                *********** ************************************************

gunnari         GGTGCCACAGTGCTGAATAAACTGGGCGATCTGCTGAAGGCCAGAGGCGCCCACGCTGCC

spinosus        GGTGCCACAGTGCTGAATAAACTGGGTGATCTGCTGAAGGCCAGAGGCGCCCACGCTGCC

                ************************** *********************************

gunnari         CTCCCCAAACCTCTGTCCAGCAGCCACGCCACGCCACCAAGCACAAGATCCCCATTATTA

spinosus        CTCCTCAAACCTCTGTCCAGCAGCCACG—–CCACCAAGCACAAGATCCCCATTATTA

                **** ***********************     ***************************

gunnari         ACTTCAAGCTGA————————————————

spinosus        ACTTCAAGCTGATTGCAGAGGTCATTGGTAAAGTCATGGAGGAGAAGGCGGGACTGGATG

                ************                                               

gunnari         ————————————————————

spinosus        CCGCCGGGCAGACTGCCCTGAGGAACGTGATGGCCATCATCATCACTGACATGGAGGCCG

gunnari         —————————–

spinosus        ACTACAAAGAGCTGGGCTTCACTGAATGA

Point mutations:

Position

C. gunnari codon

Amino acid

C. spinosus codon

Amino acid

21

GTG

Valine

GTA

Valine

40

GTG

Valine

ATG

Methionine

109 and 111

TTG

Leucine

CTA

Leucine

132

GCC

Alanine

GCT

Alanine

207

GGC

Glycine

GGT

Glycine

245

CCC

Proline

CTC

Leucine

Point mutations usually occur at the third nucleotide of a codon. One reason for this might be that a change in the third nucleotide rarely causes a change in the encoded amino acid. This is a silent change that will not lead to a mutant phenotype and can be passed on to daughter cells without being corrected.

Translation of C.gunnari sequence from position 241:

CTCCCCAAACCTCTGTCCAGCAGCCACGCCACGCCACCAAGCACAAGATCCCCATTATTAACTTCAAGCTGA

 L  P  K  P  L  S  S  S  H  A  T  P  P  S  T  R  S  P  L  L  T  S  S stop

                       264  269

C. spinosus would be AGCCACGCCACCAAGCACAAGATCCCCATTATTAACTTCAAGCTGA…

                      S  H  A  T  K  H  K  I  P  I  I  N  F  K  L

The CCACG sequence (positions 264-268 in C. spinosus) gets duplicated and the duplicate is inserted between nucleotides 268 and 269. This insertion moves the reading frame in the C. gunnari:

-          GCC to GCC: same amino acid (A) so not corrected

-          ACC to ACG: same amino acid (T) so not corrected

-          AAG to CCA: P instead of K, and then nonsense until reaching premature stop codon

  1. Aligned myoglobin sequences

icefish               FDMVLKCWGPMEADHATHGSLVLTRLFTEHPETLKLFPKFAGIAH-GDLAGDAGVSAHGA

tuna                  FDAVLKCWGPVEADYTTIGGLVLTRLFKEHPDTQKLFPKFAGIAQ-ADLAGNAAISAHGA

pufferfish            FDMVLKFWGPVEADYSAHGGMVLTRLFTENPETQQLFPKFVGIAQ-SELAGNAAVSAHGA

Cod                   YDLVLRCWGPVEADYNTHGGLVLTRLFTEHPDTQKLFPKLAGVG—ELAASVAVASHGA

carp                  AELVLKCWGGVEADFEGTGGEVLTRLFKQHPETQKLFPKFVGIAS-NELAGNAAVKAHGA

sealion               WQLVLNIWGKVEADLVGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKRSEDLKKHGK

dog                   WQLVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSEDLKKHGN

zebra                 WQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGT

horse                 WQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGT

tibetan-antelope      WQLVLNAWGKVEADVAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGN

humpbackwhale         WQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGN

minkewhale            WHLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGN

seiwhale              WQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGN

spermwhale            WQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGV

dolphin               WQLVLNVWGKVEADLAGHGQDVLIRLFKGHPETLEKFDKFKHLKTEADMKASEDLKKHGN

rabbit                WQLVLNVWGKVEADLAGHGQEVLIRLFHTHPETLEKFDKFKHLKSEDEMKASEDLKKHGN

human                 WQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGA

chimpanzee            WQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGA

gorilla               WQLVLNVWGKVEADISGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGA

Orangutan             WQLVLNVWGKVEADIPSHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGA

Rhesusmonkey          WQLVLNVWGKVEADIPSHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGV

woollymonkey          WQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKASEELKKHGV

aardvark              WQLVLNVWGKVEADIPGHGQDVLIRLFKGHPETLEKFDRFKHLKTEDEMKASEDLKKHGT

hedgehog              WQLVLNVWGKVEADIPGHGQEVLIRLFKDHPETLEKFDKFKHLKSEDEMKSSEDLKKHGT

pig                   WQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGN

otter                 WQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKGSEDLKKHGN

badger                WQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKGSEDLKKHGN

panda                 WQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKGSEDLKKHGN

kangaroo              WQLVLNIWGKVETDEGGHGKDVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGI

platypus              WQLVLKVWGKVEGDLPGHGQEVLIRLFKTHPETLEKFDKFKGLKTEDEMKASADLKKHGG

auklet                WQQVLSIWGKVESDLAGHGHQVLMRLFQDHPETLDRFEKFKGLKTPDQMKGSEDLKKHGV

Cormorant             WQQVLTIWGKVESDLPGHGHEVLMRLFRDHPETLDRFERFKGLKTPDQMKASEDLKKHGV

ostrich               WQQVLTIWGKVESDIAGHGHAILMRLFQDHPETLDRFEKFKGLTTPEQMKASEELKKHGV

chicken               WQQVLTIWGKVEADIAGHGHEVLMRLFHDHPETLDRFDKFKGLKTPDQMKGSEDLKKHGA

emperorpenguin        WQQVLTMWGKVESDLAGHGHAVLMRLFKSHPETMDRFDKFRGLKTPDEMRGSEDMKKHGV

iguana                WQKVIDIWGKVEPELPAHGQEVIIRLFQKHPETQEKFDKFKHLKSLDEMKSSEEIKKHGT

Lace_monitor          WKKVVDIWGKVEPDLPSHGQEVIIRMFQNHPETQDRFAKFKNLKTLDEMKNSEDLKKHGT

Loggerheadturtle      WNHVLGIWAKVEPDLSAHGQEVIIRLFQLHPETQERFAKFKNLTTIDALKSSEEVKKHGT

alligator             WKHVLDIWTKVESKLPEHGHEVIIRLLQEHPETQERFEKFKHMKTADEMKSSEKMKQHGN

shark                 WEKVNSVWSAVESDLTAIGQNILLRLFEQYPESQNHFPKFKNKS-LGELKDTADIKAQAD

                       . *   *  :* .    *  ::  ::   *:: . * ::        :     :  :.

icefish               TVLNKLGDLLKARGAHAALLKPLSSSHATKHKIPIINFKLIAEVIGKVMEEK–AGLDAA

tuna                  TVLKKLGELLKAKGSHASILKPMANSHATKHKIPINNFKLISEVLVKVMQEK–AGLDAG

pufferfish            TVLKKLGELLKAKGNHAAILQPLANSHATKHKIPIKNFKLIAEVIGKVMAEK–AGLDAA

Cod                   TVLKKLGELLKTRGDHAALLKPLATSHANVHKIPINNFKLITEVIAKHMAEK–AGLDAA

carp                  TVLKKLGELLKARGDHAAILKPLATTHANTHKIALNNFRLITEVLVKVMAEK–AGLDAG

sealion               TVLTALGGILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLQSKHPGDFGAD

dog                   TVLTALGGILKKKGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQSKHSGDFHAD

zebra                 VVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGAD

horse                 VVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGAD

tibetan-antelope      TVLTALGGILKKKGHHEAEVKHLAESHANKHKIPVKYLEFISDAIIHVLHAKHPSDFGAD

humpbackwhale         TVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPADFGAD

minkewhale            TVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPAEFGAD

seiwhale              TVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPGDFGAD

spermwhale            TVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGAD

dolphin               TVLTALGAILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPAEFGAD

rabbit                TVLTALGAILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISEAIIHVLHSKHPGDFGAD

human                 TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGAD

chimpanzee            TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLHSKHPGDFGAD

gorilla               TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGAD

Orangutan             TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISESIIQVLQSKHPGDFGAD

Rhesusmonkey          TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLELISESIIQVLQSKHPGDFGAD

woollymonkey          TVLTALGGILKKKGQHEAELKPLAQSHATKHKIPVKYLEFISDAIIHALQKKHPGDFGAD

aardvark              TVLTALGGILKKKGQHEAEIQPLAQSHATKHKIPVKYLEFISEAIIQVIQSKHSGDFGAD

hedgehog              TVLTALGGILKKKGQHEAQLAPLAQSHANKHKIPVKYLEFISEAIIQVLKSKHAGDFGAD

pig                   TVLTALGGILKKKGHHEAELTPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGAD

otter                 TVLTALGGILKKKGKHEAELKPLAQSHATKHKIPIKYLEFISEAIIQVLQSKHPGDFGAD

badger                TVLTALGGILKKKGHQEAELKPLAQSHATKHKIPVKYLEFISDAIAQVLQSKHPGNFAAE

panda                 TVFTALGGILKKKGQHEAELKPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGAD

kangaroo              TVLTALGNILKKKGHHEAELKPLAQSHATKHKIPVQFLEFISDAIIQVIQSKHAGNFGAD

platypus              TVLTALGNILKKKGQHEAELKPLAQSHATKHKISIKFLEYISEAIIHVLQSKHSADFGAD

auklet                TVLTQLGKILKQKGNHESELKPLAQTHATKHKIPVKYLEFISEAIMKVIAEKHAADFGGD

Cormorant             TVLTQLGKILKQKGNHESELKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHSADFGAD

ostrich               TVLTQLGKILKQKGKHEAELKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHSADFGAD

chicken               TVLTQLGKILKQKGNHESELKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHAADFGAD

emperorpenguin        TVLT-LGQILKKKGHHEAELKPLSQTHATKHKVPVKYLEFISEAIMKVIAQKHASNFGAD

iguana                TVLTALGKILKQKGHHDAELAPLAQSHATKHKIPVKYLEFICEVIVGVIAEKHSADFGSE

Lace_monitor          TVLTALGRILKQKGHHEAEIAPLAQTHANTHKIPIKYLEFICEVIVGVIAEKHSADFGAD

Loggerheadturtle      TVLTALGRILKQKNNHEQELKPLAESHATKHKIPVKYLEFICEIIVKVIAEKHPSDFGAD

alligator             TVFTALGNILKQKGNHAEVLKPLAKSHALEHKIPVKYLEFISEIIVKVIAEKYPADFGAD

shark                 TVLSALGNIVKKKGSHSQPVKALAATHITTHKIPPHYFTKITTIAVDVLSEMYPSEMNAQ

                      .*:. ** ::* :. :   :  :: :*   **:.   :  *       :     . : .

icefish               GQTALRNVMAIIITDMEADY

tuna                  GQTALRNVMGIIIADLEANY

pufferfish            GQQALRNIMATIIADIDATY

Cod                   GQEALRKVMSVVIADMDATY

carp                  GQSALRRVMDVVIGDIDTYY

sealion               THAAMKKALELFRNDIAAKY

dog                   TEAAMKKALELFRNDIAAKY

zebra                 AQGAMTKALELFRNDIAAKY

horse                 AQGAMTKALELFRNDIAAKY

tibetan-antelope      AQGAMSKALELFRNDMAAQY

humpbackwhale         AQAAMNKALELFRKDIAAKY

minkewhale            AQAAMNKALELFRKDIAAKY

seiwhale              AQAAMNKALELFRKDIAAKY

spermwhale            AQGAMNKALELFRKDIAAKY

dolphin               AQGAMNKALELFRKDIAAKY

rabbit                AQAAMSKALELFRNDIAAQY

human                 AQGAMNKALELFRKDMASNY

chimpanzee            AQGAMNKALELFRKDMASNY

gorilla               AQGAMNKALELFRKDMASNY

Orangutan             AQGAMNKALELFRKDMASNY

Rhesusmonkey          AQGAMNKALELFRNDMAAKY

woollymonkey          AQGAMKKALELFRNDMAAKY

aardvark              AQGAMSKALELFRNDIAAKY

hedgehog              AQGAMSKALELFRNDIAAKY

pig                   AQGAMSKALELFRNDMAAKY

otter                 AQGAMKRALELFRNDIAAKY

badger                AQGAMKKALELFRNDIAAKY

panda                 AQAAMRKALELFRNDIAAKY

kangaroo              AQAAMKKALELFRHDMAAKY

platypus              AQAAMGKALELFRNDMAAKY

auklet                SQAAMKKALELFRNDMASKY

Cormorant             SQAAMKKALELFRNDMASKY

ostrich               SQAAMKKALELFRNDMASKY

chicken               SQAAMKKALELFRNDMASKY

emperorpenguin        AQEAMKKALELFRNDMASKY

iguana                SQAAMRKALEVFRNDMASKY

Lace_monitor          SQEAMRKALELFRNDMASRY

Loggerheadturtle      SQAAMKKALELFRNDMASKY

alligator             SQAAMRKALELFRNDMASKY

shark                 VQAAFSGAFKIICSDIEKEY

                       . *:   :  .  *:   *

The above phylogram was generated from the myoglobin sequences of 40 different vertebrate species from the classes Chondrichthyes, Actinopterygii, Reptilia, Mammalia and Aves. Amphibia are not represented on the gene tree because their myoglobin gene was secondarily lost during their evolution (Hoffmann et al 2011).

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Shark myoglobin seems to be the most divergent compared to species from other classes, which is a faithful representation of the evolutionary history of cartilaginous fishes. We can group together the reptile, bird and mammal species in the gene tree based on their myoglobin sequences, which again corresponds well with the evolution of these taxa: they belong to the phylogenetic clade of Tetrapoda (Meyer and Zardoya 2003).

According to the most recent and accepted hypothesis, birds are part of the Sauropsida clade, together with reptiles (Meyer and Zardoya 2003). They are most closely related to the order Crocodilia, so on a phylogenetic tree, the bird species would be put close to the alligator. However, the myoglobin sequences from birds appear to be more related to mammals than to the reptiles. Testudines (like the loggerhead turtle) are the most ancient extant reptiles, so they would be closer to the root of the reptilian branch on the phylogenetic tree, followed by Lepidosauria (lizards, snakes and tuataras) and then Crocodilia (Meyer and Zardoya 2003). The turtle myoglobin, however, seems to be more similar to that of the alligator than to the myoglobin of the iguana or the lace monitor.

Diving vertebrates have to be able to hold their breath for long periods, so their myoglobin must be very effective in storing oxygen (Wright and Davies 2015). Among the bird species in the above gene tree, the emperor penguin’s myoglobin seems to stand out from the rest of the bird species – one for this could be that penguins spend prolonged periods under water. Among the mammals, Cetaceans form their own clade in the gene tree. Just like the penguins, the whales and dolphins need to have very effective myoglobin to serve as an oxygen store during periods of hypoxia, when they dive.

Resources

  1. DNA sequencing gel

Forward reaction DNA sequence (e value: 5e-44)

GCCGTTGTTGAGTCGCAACAAAAAGCCCCCACCTTTCGGTGGGGGCTTTCCGATTCAACTGACGCTGAATCTTTTGGAGACTTCAGCCTCAGCCGATGGCG

Reverse reaction DNA sequence (e value: 5e-44)

GGCATCCGTGAGCCCGTCGCTGGCTCCCTGATCTACGGCAACAACATCATCTCCGGTGCTGTTGTGCCCTCCTCGAACGCCATCGGCCTTCACTTCTATCC

The sequenced gene belongs to the psbA multigene family and codes for the D1 protein of photosystem II (PSII) in cyanobacteria such as Synechococcus WH7803. The D1 protein forms the core of the PSII’s reaction centre as a heterodimer with the D2 protein.  When light is absorbed, the heterodimer undergoes charge separation and the electrons get transferred from chlorophyll A via phaeophytin to the primary acceptor (quinone Qa) then to the secondary acceptor 9Qb), and the process results in the production of ATP. (Edelman and Kattoo 2008)

The primer site for the reverse reaction is closer to the C terminus than the primer for the forward reaction.

  1. Identifying ORFs, promoter regions and intron/exon boundaries

The protein encoded by the DNA sequence is myoglobin, which is a globular protein made of 153 amino acids and an embedded heme group. It is an oxygen-carrying molecule (like haemoglobin), found in the cardiac and skeletal muscle of most vertebrates, and can also be present in invertebrates and bacteria (Ferreras et al 2016). During periods of increased metabolic activity, myoglobin facilitates the transport of oxygen from red blood cells to mitochondria, and it can serve as a reservoir in anoxic conditions (e.g. the muscle tissues of diving birds and mammals are particularly abundant in myoglobin). (Ordway and Garry 2004)

AATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA

TCTATCTATAATTGACTTCAATCAAAATGTTCCAGATCAACTTAGGAGGT

GTTGTGAACATTTGAAGTGTGGTGAGAGGATGGGAGGTCTGGAATAATTT

GGTGATATGACGGTGAAGGGAGTATAAAAGGTCAGCTTTGAGGGGGGAAG

TCAGGTCAAGAAGAATTTTGTACAACATCACACAGGACATTTTACTACTC

TGCAGGTAAAAATTTTGTAATTGTTTAAATGTAATGAGGATAATAGGGTA

TAAGGACAGAGAATTGTCATTGTGGGAAATATTTTAACCCAAACCAATAT

AAGAAATAAAGCAGTTTTTAAGTGCCAAGGTTAGTATTGAAGAAATAAAA

AGGTATTTATAACCATGTAACAGCTCAAGAGCATCATCTGATTTCACTTC

ACATGAATTGTGCAGGGCTTCACCAAGGTTACAGTGCAGACTCAGTGAGG

GCAGCTGAGGTGATGAAGACGCCTCTTTCTAATAATGACTCACACTTGTT

CAGCAGTGACTGCACACAATGAAACGGTGGATGTGTACCTTGATATGATC

AGAGACCTTCTGTGCTTTTATTATATATTATATATACCTCCTCAGATAAT

GGCTGACTTTGACATGGTACTGAAGTGCTGGGGTCCAATGGAGGCGGACC

ACGCAACCCACGGGAGTCTGGTGCTGACCCGGTACTACCAGATTAAATGA

ATCTGCCCTCTGGTCAGGAGGTTTGCAGGGCTGTACAAAAGTTTTTTGAA

GGCACATTATTTTTCATTAAGTTCACATTAAATGTGAGGCCATGACAGTG

ATACATCAATATAGATTGATATAAATTAATTTACAAGTCAACAATCCATA

CAAATCATCATTTTTAAGATTTAGAATAAACATGTCTTTTGAAGTAAAAC

AGGCTGTTTTCCTAATGTATTTAATTTATTAGATTTTCTTTTATTTGTAT

AAAGAAGAATATATATGTTTTTTATATCTAAATGGGTCTAATAGTTGTTC

TAAACATAACTGAATCTGTTAGACTTTGTGATATCAGCAAATATTGTATT

GATGTCAAAGAATAAATATAGAATATATTATCATATTGTGATAAACTTGT

GATTTAAACCCCTTGTCCTCAGTTGTGAGTGTTATTTCAGGTGAACCCTC

ACATTTCCTTTTCCTCGCAGTTTATTCACAGAGCACCCAGAAACCCTAAA

GTTATTCCCCAAGTTTGCTGGCATCGCCCATGGGGACCTGGCCGGGGATG

CAGGTGTTTCTGCCCACGGTGCCACAGTGCTGAATAAACTGGGTGATCTG

CTGAAGGCCAGAGGCGCCCACGCTGCCCTCCTCAAACCTCTGTCCAGCAG

CCACGCCACCAAGCACAAGATCCCCATTATTAACTTCAAGGTGAGTTTGA

TTGACATGAGGGCAAGTTCGAACGTATCTAGACCATTGTGGTTTGATCTT

TCCTCCAACTTTTTGTGTCCTCCAACCTATTTTAAAGCATTTTTTGTGAT

TCTTGTTTTCAGCTGATTGCAGAGGTCATTGGTAAAGTCATGGAGGAGAA

GGCGGGACTGGATGCCGCCGGGCAGACTGCCCTGAGGAACGTGATGGCCA

TCATCATCACTGACATGGAGGCCGACTACAAAGAGCTGGGCTTCACTGAA

TGAAGATCAGATTCACAAAGTTTTGGCGACGACAGACAGGAAAATGTACC

ACATGCAAAAATAAAATGATAAAAATGGTCTGATTTTCTGTAAGCCTAAT

TAAATAATGTTTGCAATGAAATTAAATCAATCAATCAATCAATCAATCAA

TGTTTATTTATATAGCCCAATATCACAAATGTTACATTTGTCTCAGTGGT

CTTCACAGTGTGTACAGAATATCAGTATGACAATACGACACCCTCTGTCC

TTAGACCCTCACATCGTACAAGGAAAAACTTCCAAAGAAAACCCAGTTTA

AAGGGAAAAATGGGAGAAACCTCAGGGAGAGCAACAGAGGAGGGATCCCT

CTCCCCAGGACGGACAGACGTGCAATAGATGCCGTGTTGTTAAATTGAAA

AGATAAATACATTTGCAACATAGGTAGTCCCAATGTTTGGGAAATGCATG

TTGTTGTTATTAATAGGAAGATGAATCCCCCGAGGATATCCATCCCAGAA

CCTATGATCCCAGAACCACAGCCACGAATCCAGATTCCAGCGCTCCGCGA

ACCCAGAACCCGGACCGCGGGATTCTCCCTGAATCCGGATCCCAGCGTT

Alignment of splice sites:

Consensus  A/C A G G U

Intron1    C   C G G T

Exon1      C   A G T T

Intron2    A   A G G T

Exon2      C   A G C T

  1. Aligning sequences using ClustalX

gunnari         ATGGCTGACTTTGACATGGTGCTGAAGTGCTGGGGTCCAGTGGAGGCGGACCACGCAACC

spinosus        ATGGCTGACTTTGACATGGTACTGAAGTGCTGGGGTCCAATGGAGGCGGACCACGCAACC

                ******************** ****************** ********************

gunnari         CACGGGAGTCTGGTGCTGACCCGTTTATTCACAGAGCACCCAGAAACCTTGAAGTTATTC

spinosus        CACGGGAGTCTGGTGCTGACCCGTTTATTCACAGAGCACCCAGAAACCCTAAAGTTATTC

                ************************************************ * *********

gunnari         CCCAAGTTTGCCGGCATCGCCCATGGGGACCTGGCCGGGGATGCAGGTGTTTCTGCCCAC

spinosus        CCCAAGTTTGCTGGCATCGCCCATGGGGACCTGGCCGGGGATGCAGGTGTTTCTGCCCAC

                *********** ************************************************

gunnari         GGTGCCACAGTGCTGAATAAACTGGGCGATCTGCTGAAGGCCAGAGGCGCCCACGCTGCC

spinosus        GGTGCCACAGTGCTGAATAAACTGGGTGATCTGCTGAAGGCCAGAGGCGCCCACGCTGCC

                ************************** *********************************

gunnari         CTCCCCAAACCTCTGTCCAGCAGCCACGCCACGCCACCAAGCACAAGATCCCCATTATTA

spinosus        CTCCTCAAACCTCTGTCCAGCAGCCACG—–CCACCAAGCACAAGATCCCCATTATTA

                **** ***********************     ***************************

gunnari         ACTTCAAGCTGA————————————————

spinosus        ACTTCAAGCTGATTGCAGAGGTCATTGGTAAAGTCATGGAGGAGAAGGCGGGACTGGATG

                ************                                               

gunnari         ————————————————————

spinosus        CCGCCGGGCAGACTGCCCTGAGGAACGTGATGGCCATCATCATCACTGACATGGAGGCCG

gunnari         —————————–

spinosus        ACTACAAAGAGCTGGGCTTCACTGAATGA

Point mutations:

Position

C. gunnari codon

Amino acid

C. spinosus codon

Amino acid

21

GTG

Valine

GTA

Valine

40

GTG

Valine

ATG

Methionine

109 and 111

TTG

Leucine

CTA

Leucine

132

GCC

Alanine

GCT

Alanine

207

GGC

Glycine

GGT

Glycine

245

CCC

Proline

CTC

Leucine

Point mutations usually occur at the third nucleotide of a codon. One reason for this might be that a change in the third nucleotide rarely causes a change in the encoded amino acid. This is a silent change that will not lead to a mutant phenotype and can be passed on to daughter cells without being corrected.

Translation of C.gunnari sequence from position 241:

CTCCCCAAACCTCTGTCCAGCAGCCACGCCACGCCACCAAGCACAAGATCCCCATTATTAACTTCAAGCTGA

 L  P  K  P  L  S  S  S  H  A  T  P  P  S  T  R  S  P  L  L  T  S  S stop

                       264  269

C. spinosus would be AGCCACGCCACCAAGCACAAGATCCCCATTATTAACTTCAAGCTGA…

                      S  H  A  T  K  H  K  I  P  I  I  N  F  K  L

The CCACG sequence (positions 264-268 in C. spinosus) gets duplicated and the duplicate is inserted between nucleotides 268 and 269. This insertion moves the reading frame in the C. gunnari:

-          GCC to GCC: same amino acid (A) so not corrected

-          ACC to ACG: same amino acid (T) so not corrected

-          AAG to CCA: P instead of K, and then nonsense until reaching premature stop codon

  1. Aligned myoglobin sequences

icefish               FDMVLKCWGPMEADHATHGSLVLTRLFTEHPETLKLFPKFAGIAH-GDLAGDAGVSAHGA

tuna                  FDAVLKCWGPVEADYTTIGGLVLTRLFKEHPDTQKLFPKFAGIAQ-ADLAGNAAISAHGA

pufferfish            FDMVLKFWGPVEADYSAHGGMVLTRLFTENPETQQLFPKFVGIAQ-SELAGNAAVSAHGA

Cod                   YDLVLRCWGPVEADYNTHGGLVLTRLFTEHPDTQKLFPKLAGVG—ELAASVAVASHGA

carp                  AELVLKCWGGVEADFEGTGGEVLTRLFKQHPETQKLFPKFVGIAS-NELAGNAAVKAHGA

sealion               WQLVLNIWGKVEADLVGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKRSEDLKKHGK

dog                   WQLVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSEDLKKHGN

zebra                 WQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGT

horse                 WQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGT

tibetan-antelope      WQLVLNAWGKVEADVAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGN

humpbackwhale         WQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGN

minkewhale            WHLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGN

seiwhale              WQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGN

spermwhale            WQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGV

dolphin               WQLVLNVWGKVEADLAGHGQDVLIRLFKGHPETLEKFDKFKHLKTEADMKASEDLKKHGN

rabbit                WQLVLNVWGKVEADLAGHGQEVLIRLFHTHPETLEKFDKFKHLKSEDEMKASEDLKKHGN

human                 WQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGA

chimpanzee            WQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGA

gorilla               WQLVLNVWGKVEADISGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGA

Orangutan             WQLVLNVWGKVEADIPSHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGA

Rhesusmonkey          WQLVLNVWGKVEADIPSHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGV

woollymonkey          WQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKASEELKKHGV

aardvark              WQLVLNVWGKVEADIPGHGQDVLIRLFKGHPETLEKFDRFKHLKTEDEMKASEDLKKHGT

hedgehog              WQLVLNVWGKVEADIPGHGQEVLIRLFKDHPETLEKFDKFKHLKSEDEMKSSEDLKKHGT

pig                   WQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGN

otter                 WQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKGSEDLKKHGN

badger                WQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKGSEDLKKHGN

panda                 WQLVLNVWGKVEADLAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKGSEDLKKHGN

kangaroo              WQLVLNIWGKVETDEGGHGKDVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGI

platypus              WQLVLKVWGKVEGDLPGHGQEVLIRLFKTHPETLEKFDKFKGLKTEDEMKASADLKKHGG

auklet                WQQVLSIWGKVESDLAGHGHQVLMRLFQDHPETLDRFEKFKGLKTPDQMKGSEDLKKHGV

Cormorant             WQQVLTIWGKVESDLPGHGHEVLMRLFRDHPETLDRFERFKGLKTPDQMKASEDLKKHGV

ostrich               WQQVLTIWGKVESDIAGHGHAILMRLFQDHPETLDRFEKFKGLTTPEQMKASEELKKHGV

chicken               WQQVLTIWGKVEADIAGHGHEVLMRLFHDHPETLDRFDKFKGLKTPDQMKGSEDLKKHGA

emperorpenguin        WQQVLTMWGKVESDLAGHGHAVLMRLFKSHPETMDRFDKFRGLKTPDEMRGSEDMKKHGV

iguana                WQKVIDIWGKVEPELPAHGQEVIIRLFQKHPETQEKFDKFKHLKSLDEMKSSEEIKKHGT

Lace_monitor          WKKVVDIWGKVEPDLPSHGQEVIIRMFQNHPETQDRFAKFKNLKTLDEMKNSEDLKKHGT

Loggerheadturtle      WNHVLGIWAKVEPDLSAHGQEVIIRLFQLHPETQERFAKFKNLTTIDALKSSEEVKKHGT

alligator             WKHVLDIWTKVESKLPEHGHEVIIRLLQEHPETQERFEKFKHMKTADEMKSSEKMKQHGN

shark                 WEKVNSVWSAVESDLTAIGQNILLRLFEQYPESQNHFPKFKNKS-LGELKDTADIKAQAD

                       . *   *  :* .    *  ::  ::   *:: . * ::        :     :  :.

icefish               TVLNKLGDLLKARGAHAALLKPLSSSHATKHKIPIINFKLIAEVIGKVMEEK–AGLDAA

tuna                  TVLKKLGELLKAKGSHASILKPMANSHATKHKIPINNFKLISEVLVKVMQEK–AGLDAG

pufferfish            TVLKKLGELLKAKGNHAAILQPLANSHATKHKIPIKNFKLIAEVIGKVMAEK–AGLDAA

Cod                   TVLKKLGELLKTRGDHAALLKPLATSHANVHKIPINNFKLITEVIAKHMAEK–AGLDAA

carp                  TVLKKLGELLKARGDHAAILKPLATTHANTHKIALNNFRLITEVLVKVMAEK–AGLDAG

sealion               TVLTALGGILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLQSKHPGDFGAD

dog                   TVLTALGGILKKKGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQSKHSGDFHAD

zebra                 VVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGAD

horse                 VVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGAD

tibetan-antelope      TVLTALGGILKKKGHHEAEVKHLAESHANKHKIPVKYLEFISDAIIHVLHAKHPSDFGAD

humpbackwhale         TVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPADFGAD

minkewhale            TVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPAEFGAD

seiwhale              TVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPGDFGAD

spermwhale            TVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGAD

dolphin               TVLTALGAILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPAEFGAD

rabbit                TVLTALGAILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISEAIIHVLHSKHPGDFGAD

human                 TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGAD

chimpanzee            TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLHSKHPGDFGAD

gorilla               TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGAD

Orangutan             TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISESIIQVLQSKHPGDFGAD

Rhesusmonkey          TVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLELISESIIQVLQSKHPGDFGAD

woollymonkey          TVLTALGGILKKKGQHEAELKPLAQSHATKHKIPVKYLEFISDAIIHALQKKHPGDFGAD

aardvark              TVLTALGGILKKKGQHEAEIQPLAQSHATKHKIPVKYLEFISEAIIQVIQSKHSGDFGAD

hedgehog              TVLTALGGILKKKGQHEAQLAPLAQSHANKHKIPVKYLEFISEAIIQVLKSKHAGDFGAD

pig                   TVLTALGGILKKKGHHEAELTPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGAD

otter                 TVLTALGGILKKKGKHEAELKPLAQSHATKHKIPIKYLEFISEAIIQVLQSKHPGDFGAD

badger                TVLTALGGILKKKGHQEAELKPLAQSHATKHKIPVKYLEFISDAIAQVLQSKHPGNFAAE

panda                 TVFTALGGILKKKGQHEAELKPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGAD

kangaroo              TVLTALGNILKKKGHHEAELKPLAQSHATKHKIPVQFLEFISDAIIQVIQSKHAGNFGAD

platypus              TVLTALGNILKKKGQHEAELKPLAQSHATKHKISIKFLEYISEAIIHVLQSKHSADFGAD

auklet                TVLTQLGKILKQKGNHESELKPLAQTHATKHKIPVKYLEFISEAIMKVIAEKHAADFGGD

Cormorant             TVLTQLGKILKQKGNHESELKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHSADFGAD

ostrich               TVLTQLGKILKQKGKHEAELKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHSADFGAD

chicken               TVLTQLGKILKQKGNHESELKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHAADFGAD

emperorpenguin        TVLT-LGQILKKKGHHEAELKPLSQTHATKHKVPVKYLEFISEAIMKVIAQKHASNFGAD

iguana                TVLTALGKILKQKGHHDAELAPLAQSHATKHKIPVKYLEFICEVIVGVIAEKHSADFGSE

Lace_monitor          TVLTALGRILKQKGHHEAEIAPLAQTHANTHKIPIKYLEFICEVIVGVIAEKHSADFGAD

Loggerheadturtle      TVLTALGRILKQKNNHEQELKPLAESHATKHKIPVKYLEFICEIIVKVIAEKHPSDFGAD

alligator             TVFTALGNILKQKGNHAEVLKPLAKSHALEHKIPVKYLEFISEIIVKVIAEKYPADFGAD

shark                 TVLSALGNIVKKKGSHSQPVKALAATHITTHKIPPHYFTKITTIAVDVLSEMYPSEMNAQ

                      .*:. ** ::* :. :   :  :: :*   **:.   :  *       :     . : .

icefish               GQTALRNVMAIIITDMEADY

tuna                  GQTALRNVMGIIIADLEANY

pufferfish            GQQALRNIMATIIADIDATY

Cod                   GQEALRKVMSVVIADMDATY

carp                  GQSALRRVMDVVIGDIDTYY

sealion               THAAMKKALELFRNDIAAKY

dog                   TEAAMKKALELFRNDIAAKY

zebra                 AQGAMTKALELFRNDIAAKY

horse                 AQGAMTKALELFRNDIAAKY

tibetan-antelope      AQGAMSKALELFRNDMAAQY

humpbackwhale         AQAAMNKALELFRKDIAAKY

minkewhale            AQAAMNKALELFRKDIAAKY

seiwhale              AQAAMNKALELFRKDIAAKY

spermwhale            AQGAMNKALELFRKDIAAKY

dolphin               AQGAMNKALELFRKDIAAKY

rabbit                AQAAMSKALELFRNDIAAQY

human                 AQGAMNKALELFRKDMASNY

chimpanzee            AQGAMNKALELFRKDMASNY

gorilla               AQGAMNKALELFRKDMASNY

Orangutan             AQGAMNKALELFRKDMASNY

Rhesusmonkey          AQGAMNKALELFRNDMAAKY

woollymonkey          AQGAMKKALELFRNDMAAKY

aardvark              AQGAMSKALELFRNDIAAKY

hedgehog              AQGAMSKALELFRNDIAAKY

pig                   AQGAMSKALELFRNDMAAKY

otter                 AQGAMKRALELFRNDIAAKY

badger                AQGAMKKALELFRNDIAAKY

panda                 AQAAMRKALELFRNDIAAKY

kangaroo              AQAAMKKALELFRHDMAAKY

platypus              AQAAMGKALELFRNDMAAKY

auklet                SQAAMKKALELFRNDMASKY

Cormorant             SQAAMKKALELFRNDMASKY

ostrich               SQAAMKKALELFRNDMASKY

chicken               SQAAMKKALELFRNDMASKY

emperorpenguin        AQEAMKKALELFRNDMASKY

iguana                SQAAMRKALEVFRNDMASKY

Lace_monitor          SQEAMRKALELFRNDMASRY

Loggerheadturtle      SQAAMKKALELFRNDMASKY

alligator             SQAAMRKALELFRNDMASKY

shark                 VQAAFSGAFKIICSDIEKEY

                       . *:   :  .  *:   *

The above phylogram was generated from the myoglobin sequences of 40 different vertebrate species from the classes Chondrichthyes, Actinopterygii, Reptilia, Mammalia and Aves. Amphibia are not represented on the gene tree because their myoglobin gene was secondarily lost during their evolution (Hoffmann et al 2011).

Shark myoglobin seems to be the most divergent compared to species from other classes, which is a faithful representation of the evolutionary history of cartilaginous fishes. We can group together the reptile, bird and mammal species in the gene tree based on their myoglobin sequences, which again corresponds well with the evolution of these taxa: they belong to the phylogenetic clade of Tetrapoda (Meyer and Zardoya 2003).

According to the most recent and accepted hypothesis, birds are part of the Sauropsida clade, together with reptiles (Meyer and Zardoya 2003). They are most closely related to the order Crocodilia, so on a phylogenetic tree, the bird species would be put close to the alligator. However, the myoglobin sequences from birds appear to be more related to mammals than to the reptiles. Testudines (like the loggerhead turtle) are the most ancient extant reptiles, so they would be closer to the root of the reptilian branch on the phylogenetic tree, followed by Lepidosauria (lizards, snakes and tuataras) and then Crocodilia (Meyer and Zardoya 2003). The turtle myoglobin, however, seems to be more similar to that of the alligator than to the myoglobin of the iguana or the lace monitor.

Diving vertebrates have to be able to hold their breath for long periods, so their myoglobin must be very effective in storing oxygen (Wright and Davies 2015). Among the bird species in the above gene tree, the emperor penguin’s myoglobin seems to stand out from the rest of the bird species – one for this could be that penguins spend prolonged periods under water. Among the mammals, Cetaceans form their own clade in the gene tree. Just like the penguins, the whales and dolphins need to have very effective myoglobin to serve as an oxygen store during periods of hypoxia, when they dive.

Resources

  • Edelman, M. and Mattoo, A.K. (2008) D1-protein dynamics in photosystem II: the lingering enigma. Photosynthesis Research. 98(1-3) pp. 609-620
  • Ferreras, J.M., Ragucce, S., Citores, L., Iglesias, R., Pedone, P.V. and Di Maro, A. (2016) Insight into the phylogenetic relationship and structural features of vertebrate myoglobin family. International Journal of Biological Macromolecules. 93(A) pp. 1041-1050
  • Hoffmann F.G., Opazo, J.C. and Storz J.F. (2011) Differential Loss and Retention of Cytoglobin, Myoglobin, and Globin-E during the Radiation of Vertebrates. Genome Biology and Evolution. 3(1) pp. 588-600
  • Meyer, A. and Zardoya, R. (2003) Recent advances in the (molecular)phylogeny of vertebrates. Annual Review of Ecology, Evolution, and Systematics. 34(1) pp. 311-338
  • Ordway, G.A. and Garry, D.J. (2004) Myoglobin: an essential hemoprotein in striated muscle. Journal of Experimental Biology. 207(20) pp. 3441-3446
  • Wright, T.J. and Davis, R.W. (2015) Myoglobin oxygen affinity in aquatic and terrestrial birds and mammals. Journal of Experimental Biology. 218(14) pp. 2180-2189

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