Introduction to kudu and oryx issues
Comparison of amino acid sequences
Comparison of nucleic acid sequences
DNA and protein sequences of kudu, oryx, sheep, and cow
References
It seems that three individual animals of this species have been sequenced with three different resulting sequences, called here A, B, and C. Sequence A was published by Poidinger M, Kirkwood J, Almond JW in Arch Virol 131 (1-2): 193-199 (1993) but never submitted to Genbank. That article also contained DNA and protein sequences for the Arabian oryx, Oryx leucoryx, that are also missing from Genbank. Sequences B and C were never published but submitted directly to the databases, by Martin,T.C., Hughes,S.L., Hughes,K.J. and Dawson,M. of the Central Veterinary Laboratory, Surrey, in August, 1993.
Sequence A is that of a zoo kudu that died of TSE (as is the oryx sequence). Neither pathology nor genealogy is clear for sequences B and C. As seen below, considerable polymorphic differences in the repeat region are reported. While it is hard to believe that each of three kudus would have a different sequence, an extra octapeptide repeat is also found in cow and human. Kudu subspecies, distinct African populations, or in-bred zoo animals could also figure in. Almond notes that cDNA from a diploid animal might just pick up a haplotype, i.e., these kudus could have more in common than it appears. There are also many opportunities for errors with repeated DNA, from initial amplification, to the reading of gels, to recording of data, to copying, editing, or transmissal of sequence text, as happened with primate sequences.
Closely related species (with BSE involvement but no sequence data) include the lesser kudu, Tragelaphus imberbis, with its reduced chromosome count of 38 with X and Y chromosomes showing autosomal fusions; nyala (Tragelaphus angasi); the eland (Taurotragus oryx) which hybridizes with greater kudu; gemsbok (Oryx gazella); Arabian oryx (Oryx leucoryx); and scimitar-horned oryx (Oryx dammah).
In classical taxonomy, both kudu and oryx placed in Eukaryotae; Mitochondrial; Metazoa; Chordata; Vertebrata; Eutheria; Artiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Tragelaphus. This would make them more closely related to bovine than to ovine, inconsistent with prion sequence data, considered in isolation, for the oryx.
Inter-kudu differences: sequence A compared to sequence B 40 50 60 70 80 SRYPGQGSPGGNRYPPQEGGDWGQPHGGGWGQPHVGGWGQ ...............S.G..G.............G..... Differences relative to sheep Sequence A: A E D V T G S M E Arch Virol Sequence B: A S T G S M E Martin et al Sequence C: A S WGQPHGGG T G S M E Martin et al
162 170 180 210 220 261 270 CCTCAAGAAGGGGGTGACTGG CAGCCTCATGTAGGTGGC CCACATGGTGGTGGAGGG T....G.G........G.... ....C....G......T ..G..............C P Q E G G D W Q P H V G G P H G G G G 250 260 270 280 290 300 GGAGGTGGCTGGGGTCAGCCCCATGGTGGTGGTTGGGGACAGCCACATGGTGGTGGAGGC -----...T.......................C...........G............... G G G W G Q P H G G G W G Q P H G G G G 162 170 180 TCTCAGGGAGGGGGTGGCTGG C....A.A........A.... S Q G G G G WWhere did the extra repeat come from in Sequence C? This can be determined at the DNA level by looking at third codon micro-heterogeneity under a maximum parsimony assumption. The result is: R1 R1 R2 R3 R4 consistent with a DNA slippage model for the genetic origin of repeats in this region. Comparison of amino acid and nucleotide sequences A, B, C in the repeat region
Sequence A | Sequence C | Sequence B |
---|---|---|
RYP | RYP | RYP |
PQEGGDWGQ | SQGGGGWGQ | SQGGGGWGQ |
PHGGG.WGQ | PHGGG.WGQ | PHGGG.WGQ |
PHVGG.WGQ | PHGGG.WGQ | PHGGG.WGQ |
PHGGG.WGQ | PHGGG.WGQ | PHGGG.WGQ |
PHGGGGWGQ | PHGGG.WGQ | PHGGGGWGQ |
- | PHGGGGWGQ | - |
GGTHG | GGTHG | GGTHG |
cgctatcca | cgctatcca | cgctatcca |
cctcaagaagggggtgactggggtcag | tctcagggagggggtggctggggtcag | tctcagggagggggtggctggggtcag |
ccccatggaggtggctggggccag | ccccatggaggtggctggggccag | ccccatggaggtggctggggccag |
cctcatgtaggtggctggggtcag | ccccatggaggcggctggggccag | ccccatggaggtggttggggtcag |
ccccatggtggtggctggggacag | cctcatggaggtggctggggtcag | ccccatggtggtggctggggacag |
ccacatggtggtggagggtggggt | ccccatggtggtggttggggacag | ccgcatggtggtggaggctggggtcaag |
caaggtggtacccacggt | ccacatggtggtggaggctggggt | gtggtacccacggtc |
- | caaggtggtacccacggt | - |
Tragelaphus streptsiceros greater kudu 257aa; 771bp Sequence A Artiodactyla; Ruminantia; Pecora; Bovoidea Bovidae; Bovinae; Tragelaphus. ACCESSION 398938; PID g398938; EMBL: locus TSPRIP,X74771; 04-OCT-1994; Martin TC et al. MVKSHIGSWILVLFVAMWSDVALCKKRPKPGGGWNTGGSRYPGQGSPGGNRYP PQEGGDWGQPHGGGWGQPHVGGWGQPHGGGWGQPHGGGGWGQGGTHGQW NKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGSDYEDRYYRENMYRY PNQVYYRPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKMMERVVEQMCI TQYQRESEAYYQRGASVILFSSPPVILLISFLIFLIVG 1 atggtgaaaa gccacatagg cagttggatc ctggtcctct ttgtggccat gtggagtgac 61 gtggccctct gcaagaagcg accaaaacct ggaggaggat ggaacactgg ggggagccga 121 tacccgggac agggcagtcc tggaggcaac cgctatccac ctcaagaagg gggtgactgg 181 ggtcagcccc atggaggtgg ctggggccag cctcatgtag gtggctgggg tcagccccat 241 ggtggtggct ggggacagcc acatggtggt ggagggtggg gtcaaggtgg tacccacggt 301 cagtggaaca agcccagtaa gccaaaaacc aacatgaaac atgtggcagg agctgctgca 361 gcgggagcag tggtaggggg ccttggtggc tacatgctgg gaagtgccat gagcaggcct 421 cttatacatt ttggcagtga ctatgaggac cgttactatc gtgaaaacat gtaccgttac 481 cccaaccaag tgtactacag gccagtggat cagtatagta accagaacaa ctttgtgcat 541 gactgtgtca acatcacagt caagcagcac acagtcacca ccaccaccaa gggggagaac 601 ttcaccgaaa ctgacatcaa gatgatggag cgagtggtgg agcaaatgtg catcacccag 661 taccagagag aatccgaggc ttattaccaa cgaggggcaa gtgtcatcct cttctcttcc 721 cctcctgtga tcctcctcat ctctttcctc atttttctca tagtaggata g
Tragelaphus streptsiceros greater kudu 257 aa; 771bp Sequence B Artiodactyla; Ruminantia; Pecora; Bovoidea Bovidae; Bovinae; Tragelaphus. Poidinger M, Kirkwood J, Almond W in Arch Virol 131 (1-2): 193-199 (1993): not submitted MVKSHIGSWILVLFVAMWSDVALCKKRPKPGGGWNTGGSRYPGQGSPGGNRYP SQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGTHGQW NKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGSDYEDRYYRENMYRY PNQVYYRPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKMMERVVEQMCI TQYQRESEAYYQRGASVILFSSPPVILLISFLIFLIVG 1 atgg tgaaaagcca cataggcagt tggatcctgg 35 tCctctttgt ggccatgtgg agtgacgtgg Ccctctgcaa gaagcgacca aaacctggAg 95 gaggatggaa cactgggggg agccgatacc cgggacaggg cagtcctgga ggcaaccgct 155 atccaTctca gggagggggt ggctggggtc agccccatgg aggtggctgg ggccaGccCc 215 atggaggtgg Ttggggtcag ccccatggtg gtggctgggg acagccGcat ggtggtggag 275 gctggggtca aggtggtaCc cacGgtcagt ggaacaagcc cagtaagcca aaaaccaaca 335 tgaaAcatgt ggcaggagct gctgcagcGg gagcagtggt agggggcctt ggtggctaca 395 tgctgggaag tgccatgagc aggcctctta tacattttgg caGtgactat gaggaccgtt 455 actatcgtga aaacatgtac cgttacccca accaagtgta ctacagGcca gtggatcAgt 515 atagtaacca gaacaacttt gtgcatgact gtgtcaacat cacagtcaag caGcacacag 575 tcaccaccac caccaagggg gagaacttca ccgaaactga catcaagatG atggagcgag 635 tggtggagca aatgtgcatc acccagtacc agagagaatc cGaggcttat taccaaCgAg 695 gggcaagtgt CatcctcttC tcttcccctc ctgtgatcct cctcatctct ttcctcattt 755 ttctcatagt aggatag
Tragelaphus streptsiceros greater kudu 265 aa; 795bp Sequence C Artiodactyla; Ruminantia; Pecora; Bovoidea Bovidae; Bovinae; Tragelaphus. PID g730409; embl X74759, gi: 400491; SWISSPROT: PRP2_TRAST, P40243; updated: Feb 1995; Martin TC et al. MVKSHIGSWI LVLFVAMWSD VALCKKRPKP GGGWNTGGSR YPGQGSPGGN RYPSQGGGGW GQPHGGGWGQ PHGGGWGQPH GGGWGQPHGG GWGQPHGGGG WGQGGTHGQW NKPSKPKTNM KHVAGAAAAG AVVGGLGGYM LGSAMSRPLI HFGSDYEDRY YRENMYRYPN QVYYRPVDQY SNQNNFVHDC VNITVKQHTV TTTTKGENFT ETDIKMMERV VEQMCITQYQ RESEAYYQRG ASVILFSSPP VILLISFLIF LIVG 1 atggtgaaaa gccacatagg cagttggatc ctggtcctct ttgtggccat gtggagtgac 61 gtggccctct gcaagaagcg accaaaacct ggaggaggat ggaacactgg ggggagccga 121 tacccgggac agggcagtcc tggaggcaac cgctatccat ctcagggagg gggtggctgg 181 ggtcagcccc atggaggtgg ctggggccag ccccatggag gcggctgggg ccagcctcat 241 ggaggtggct ggggtcagcc ccatggtggt ggttggggac agccacatgg tggtggaggc 301 tggggtcaag gtggtaccca cggtcagtgg aacaagccca gtaagccaaa aaccaacatg 361 aaacatgtgg caggagctgc tgcagcggga gcagtggtag ggggccttgg tggctacatg 421 ctgggaagtg ccatgagcag gcctcttata cattttggca gtgactatga ggaccgttac 481 tatcgtgaaa acatgtaccg ttaccccaac caagtgtact acaggccagt ggatcagtat 541 agtaaccaga acaactttgt gcatgactgt gtcaacatca cagtcaagca gcacacagtc 601 accaccacca ccaaggggga gaacttcacc gaaactgaca tcaagatgat ggagcgagtg 661 gtggagcaaa tgtgcatcac ccagtaccag agagaatccg aggcttatta ccaacgaggg 721 gcaagtgtca tcctcttctc ttcccctcct gtgatcctcc tcatctcttt cctcattttt 781 ctcatagtag gatag
Oryx leucoryx Arabian oryx 257 aa;771bp Artiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Oryx. Poidinger M, Kirkwood J, Almond W in Arch Virol 131 (1-2): 193-199 (1993): not submitted MVKSHIGSWILVLFVAMWSDVGLCKKRPKPGGGWNTGGSRYPGQGSPGGNRYP PQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGTHSQWNKPS KPKTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYR YPNQVYYRPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERV VEQMCITQYQRESQAYYQRGASVILFSSPPVILLISFLIFLIVG atgg tgaaaagcca cataggcagt tggatcctgg ttctctttgt ggccatgtgg agtgacgtgg gcctctgcaa gaagcgacca aaacctggTg gaggatggaa cactgggggA agccgatacc cgggacaggg cagtcctgga ggcaaccgct atccacctca gggagggggt ggctggggtc agccccatgg aggtggctgg ggccaacctc atggaggtgg ctggggtcag ccccatggtg gtggctgggg acagccacat ggtggtggag gctggggtca aggtggtaCc cacagtcagt ggaacaagcc cagtaagcca aaaaccaaca tgaagcatgt ggcaggagct gctgcagctg gagcagtggt agggggcctt ggAggctaca tgctgggaag Cgccatgagc aggcctctta tacattttgg caatgactat gaggaccgtt actaCcgtga aaacatgtac cgttacccca accaagtgta ctacagacca gtggatcAgt atagtaacca gaacaacttt gtgcatgact gtgtcaacat cacagtcaag caacacacag tcaccaccac caccaagggg gagaacttca ccgaaactga catcaagatC atggagcgag tggtggagca aatgtgcatc acccagtacc agagagaatc ccaggcttat taccaaagAg gggcaagtgt gatcctcttC tcttcccctc ctgtgatcct cctcatctct ttcctcattt ttctcatagt aggatag
Ovis aries Sheep gene 257 aa;771bp Artiodactyla; Ruminantia; Pecora; Bovoidea Bovidae; Caprinae; Ovis. MVKSHIGSWILVLFVAMWSDVGLCKKRPKPGGGWNTGGSRYPGQ GSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGSHSQW NKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRY PNQVYYRPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCI TQYQRESQAYYQRGASVILFSSPPVILLISFLIFLIVG 747 atgg tgaaaagcca cataggcagt tggatcctgg 781 ttctctttgt ggccatgtgg agtgacgtgg gcctctgcaa gaagcgacca aaacctggcg 841 gaggatggaa cactgggggg agccgatacc cgggacaggg cagtcctgga ggcaaccgct 901 atccacctca gggagggggt ggctggggtc agccccatgg aggtggctgg ggccaacctc 961 atggaggtgg ctggggtcag ccccatggtg gtggctgggg acagccacat ggtggtggag 1021 gctggggtca aggtggtagc cacagtcagt ggaacaagcc cagtaagcca aaaaccaaca 1081 tgaagcatgt ggcaggagct gctgcagctg gagcagtggt agggggcctt ggtggctaca 1141 tgctgggaag tgccatgagc aggcctctta tacattttgg caatgactat gaggaccgtt 1201 actatcgtga aaacatgtac cgttacccca accaagtgta ctacagacca gtggatcagt 1261 atagtaacca gaacaacttt gtgcatgact gtgtcaacat cacagtcaag caacacacag 1321 tcaccaccac caccaagggg gagaacttca ccgaaactga catcaagata atggagcgag 1381 tggtggagca aatgtgcatc acccagtacc agagagaatc ccaggcttat taccaaaggg 1441 gggcaagtgt gatcctcttt tcttcccctc ctgtgatcct cctcatctct ttcctcattt 1501 ttctcatagt aggatag
Bos taurus bovine 257 aa;771bp Artiodactyla; Ruminantia; Pecora; Bovoidea Bovidae; Bovinae; Bos. MVKSHIGSWILVLFVAMWSDVGLCKKRPKPGGGWNTGGSRYPGQ GSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGSHSQW NKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMHRY PNQVYYRPVDQYSNQNNFVHDCVNITVKEHTVTTTTKGENFTETDIKMMERVVEQMCI TQYQRESQAYYQRGASVILFSSPPVILLISFLIFLIVG 1 atggtgaaaa gccacatagg cagttggatc ctggttctct ttgtggccat gtggagtgac 61 gtgggcctct gcaagaagcg accaaaacct ggcggaggat ggaacactgg ggggagccga 121 tacccgggac agggcagtcc tggaggcaac cgctatccac ctcagggagg gggtggctgg 181 ggtcagcccc atggaggtgg ctggggccag cctcatggag gtggctgggg tcagccccat 241 ggtggtggct ggggacagcc acatggtggt ggaggctggg gtcaaggtgg tagccacagt 301 cagtggaaca aacccagtaa gccaaaaacc aacatgaagc atgtggcagg agctgctgca 361 gctggagcag tggtaggggg ccttggtggc tacatgctgg gaagtgccat gagcaggcct 421 cttatacatt ttggcaatga ctatgaggac cgttactatc gtgaaaacat gcaccgttac 481 cccaaccaag tgtactacag gccagtggat cagtatagta accagaacaa ctttgtgcat 541 gactgtgtca acatcacagt caaggaacac acagtcacca ccaccaccaa gggggagaac 601 ttcaccgaaa ctgacatcaa gatgatggag cgagtggtgg agcaaatgtg cattacccag 661 taccagagag aatcccaggc ttattaccaa cgaggggcaa gtgtgatcct cttctcttcc 721 cctcctgtga tcctcctcat ctctttcctc atttttctca tagtaggata g
Vet Rec 135 (13): 296-303 (Sep 24 1994) Kirkwood JK, Cunningham AASince 1986, scrapie-like spongiform encephalopathy has been diagnosed in 19 captive wild animals of eight species at or from eight zoological collections in the British Isles. The affected animals have comprised members of the family Bovidae: one nyala (Tragelaphus angasi), four eland (Taurotragus oryx), and six greater kudu (Tragelaphus strepsiceros), one gemsbok (Oryx gazella), one Arabian oryx (Oryx leucoryx), and one scimitar-horned oryx (Oryx dammah), and members of the family Felidae: four cheetah (Acinonyx jubatus) and one puma (Felis concolor). In addition, three cases of a spongiform encephalopathy of unknown aetiology have been reported in ostriches (Struthio camellus) from two zoos in north west Germany. Three features suggest that some of these cases may have been caused by the agent of bovine spongiform encephalopathy (BSE). First, they have been temporally and geographically coincident with the BSE epidemic. Secondly, in all the ungulates for which details are available, it is possible that either the affected animal itself, or the herd into which it was born or moved, had been exposed to proprietary feeds containing ruminant-derived protein or other potentially contaminated material, and all the carnivores had been fed parts of cattle carcases judged unfit for human consumption. Thirdly, the pathological results of inoculating mice with a homogenate of fixed brain tissue from the nyala and from one greater kudu were similar to the results of inoculating mice with BSE brain tissue.
Kirkwood JK, Cunningham AA, Wells GA, Wilesmith JW, Barnett JE Vet Rec 133 (15): 360-364 (Oct 9 1993)A small herd of greater kudu, derived from three individuals, has been maintained at the Zoological Society of London since 1970. Spongiform encephalopathy has been diagnosed in five out of eight of the animals born in this herd since 1987. With the possible exception of the first confirmed case, none of these is thought to have been exposed to feeds containing ruminant-derived protein. The pattern of incidence suggests that greater kudu are very susceptible to the disease and that natural lateral transmission may have occurred among them.
Vet Rec 127 (17): 418-420 (Oct 27 1990) Kirkwood JK, Wells GA, Wilesmith JW, Cunningham AA, Jackson SIClinical, pathological and epidemiological details of scrapie-like encephalopathies are described in an arabian oryx and a greater kudu. Clinical signs included ataxia and loss of condition with a short, progressive clinical course (22 and three days, respectively). Histopathological examination of the brains revealed spongiform encephalopathy characteristic of that observed in scrapie and bovine spongiform encephalopathy (BSE). It seems probable that these cases have a common aetiology with BSE. Scrapie-like spongiform encephalopathies have now been described in five species of exotic artiodactyls in Britain indicating a, hitherto inapparent, wider range of ruminant species as natural hosts for these diseases. See also:
Acta Neuropathol (Berl) 84 (5): 559-569 (1992) Jeffrey M, Scott JR, Williams A, Fraser H
J Reprod Fertil 46 (1): 13-16 (Jan 1976) Jorge W, Butler S, Benirschke KAn accidental mating between a male eland and a female kudu produced an animal with primarily eland phenotypic characteristics. Despite pronounced male behaviour the animal was azoospermic. Histological examination of the testis showed complete lack of germ cells. Chromosome studies with analysis of Giemsa bands showed that the parental karyotypes differed by two reciprocal translocations and one pericentric inversion, involving chromosomes 1 and 3, 5 and 11, and 9 respectively. All other chromosomes had identical banding patterns.
Cytogenet Cell Genet 26 (2-4): 85-92 (1980) Benirschke K, Ruedi D, Muller H, Kumamoto AT, Wagner KL, Downes HSThe chromosome set of the lesser kudu, Tragelaphus imberbis, consists of 38 elements in both sexes. In contrast to most other members of the bovid subfamily Tragelaphinae, both the X and the Y chromosomes are compound, having fused with identical autosomes from ancestors presumed to have higher chromosome numbers. From a comparison of the unusual sex chromosomal rearrangements that have occurred in this family, a hypothetical lineage has been derived. This family tree and the details of various banding studies in the lesser kudu are described.
Vet Rec 130 (17): 365-367 (Apr 25 1992) Kirkwood JK, Wells GA, Cunningham AA, Jackson SI, Scott AC, Dawson M, Wilesmith JWA 19-month-old greater kudu (Tragelaphus strepsiceros), whose dam had died 15 months earlier with spongiform encephalopathy, required euthanasia after developing severe ataxia and depression with an apparently sudden onset. No macroscopic abnormalities were detected on post mortem examination but a scrapie-like spongiform encephalomyelopathy was apparent on histopathological examination of brain and segments of spinal cord. Negative stain electron microscopy of proteinase K-treated detergent extracts of tissue from the brain stem revealed the presence of scrapie associated fibrils, and a 25 to 28 kDa band comparable with that identified as abnormal PrP (prion protein) from the brains of domestic cattle with spongiform encephalopathy was detected using rabbit antiserum raised against mouse PrP. The animal was born nine months after the statutory ban on the inclusion of ruminant-derived protein in ruminant feeds and, as no other possible sources of the disease were apparent, it appears likely that the infection was acquired from the dam.