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Species Resource name RRC ID Author Title Journal Published Volume Pages Pubmed ID DOI
Medaka   Qurt (MT828), hi-medaka (MT835)   35677   Ogino Y, Kuraku S, Ishibashi H, Miyakawa H, Sumiya E, Miyagawa S, Matsubara H, Yamada G, Baker ME, Iguchi T.   Neofunctionalization of Androgen Receptor by Gain-of-Function Mutations in Teleost Fish Lineage.   Mol. Biol. Evol.   2015 -10 -29   33(1)   228-44   26507457   10.1093/molbev/msv218  
Algae   NIES-3581   37141   Kamikawa R, Tanifuji G, Ishikawa SA, Ishii K, Matsuno Y, Onodera NT, Ishida K, Hashimoto T, Miyashita H, Mayama S, Inagaki Y.   Proposal of a Twin Arginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes. [Corrected].   Mol. Biol. Evol.   2015 -6 -7   32(10)   2598-604   26048548   10.1093/molbev/msv134  
C.intestinalis / (O.japonicus)   Wild C. int   31334   Satou Y, Hirayama K, Mita K, Fujie M, Chiba S, Yoshida R, Endo T, Sasakura Y, Inaba K, Satoh N.   Sustained heterozygosity across a self-incompatibility locus in an inbred ascidian.   Mol. Biol. Evol.   2014 -9 -23   32(1)   81-90   25234703   10.1093/molbev/msu268  
C.intestinalis / (O.japonicus)   Wild C. int   31335   Sakamaki K, Shimizu K, Iwata H, Imai K, Satou Y, Funayama N, Nozaki M, Yajima M, Nishimura O, Higuchi M, Chiba K, Yoshimoto M, Kimura H, Gracey AY, Shimizu T, Tomii K, Gotoh O, Akasaka K, Sawasaki T, Miller DJ.   The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution.   Mol. Biol. Evol.   2014 -9 -11   31(12)   3282-301   25205508   10.1093/molbev/msu260  
Drosophila   10045R-4   31984   Gloss AD, Vassão DG, Hailey AL, Nelson Dittrich AC, Schramm K, Reichelt M, Rast TJ, Weichsel A, Cravens MG, Gershenzon J, Montfort WR, Whiteman NK.   Evolution in an ancient detoxification pathway is coupled with a transition to herbivory in the drosophilidae.   Mol. Biol. Evol.   2014 -6 -30   31(9)   2441-56   24974374   10.1093/molbev/msu201  
Drosophila     35977   Nozawa M, Fukuda N, Ikeo K, Gojobori T.   Tissue- and stage-dependent dosage compensation on the neo-X chromosome in Drosophila pseudoobscura.   Mol. Biol. Evol.   2013 -12 -7   31(3)   614-24   24307686   10.1093/molbev/mst239  
Algae   NIES-722,NIES-866,NIES-1710,NIES-1712,NIES-1859,...   38098   Hiraide R, Kawai-Toyooka H, Hamaji T, Matsuzaki R, Kawafune K, Abe J, Sekimoto H, Umen J, Nozaki H.   The evolution of male-female sexual dimorphism predates the gender-based divergence of the mating locus gene MAT3/RB.   Mol. Biol. Evol.   2013 -2 -1   30(5)   1038-40   23364323   10.1093/molbev/mst018  
Algae   NIES-1363   30400   Smith DR, Hamaji T, Olson BJ, Durand PM, Ferris P, Michod RE, Featherston J, Nozaki H, Keeling PJ.   Organelle genome complexity scales positively with organism size in volvocine green algae.   Mol. Biol. Evol.   2013 -1 -10   30(4)   793-7   23300255   10.1093/molbev/mst002  
Algae   NIES-2170,NIES-484,NIES-1332,NIES-296,NIES-547   28754   Miyagishima SY, Suzuki K, Okazaki K, Kabeya Y.   Expression of the nucleus-encoded chloroplast division genes and proteins regulated by the algal cell cycle.   Mol. Biol. Evol.   2012 -4 -12   29(10)   2957-70   22490821   10.1093/molbev/mss102  
Rice, Information   W1943, W0106, Oryzabase   15409   Yang CC, Kawahara Y, Mizuno H, Wu J, Matsumoto T, Itoh T.   Independent domestication of Asian rice followed by gene flow from japonica to indica.   Mol. Biol. Evol.   2012 -2 -10   29(5)   1471-9   22319137   10.1093/molbev/msr315  
Silkworms     16053   Osanai-Futahashi M, Fujiwara H.   Coevolution of telomeric repeats and telomeric repeat-specific non-LTR retrotransposons in insects.   Mol. Biol. Evol.   2011 -6 -7   28(11)   2983-6   21642634   10.1093/molbev/msr135  
Information, Drosophila   Infomation of DME1-001M04 and DME1-007E02 (Drosophi...   15378   Méndez-Lago M, Bergman CM, de Pablos B, Tracey A, Whitehead SL, Villasante A.   A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome.   Mol. Biol. Evol.   2011 -2 -8   28(7)   1967-71   21297157   10.1093/molbev/msr034  
Prokaryotes E. coli   ?   35406   Huvet M, Toni T, Sheng X, Thorne T, Jovanovic G, Engl C, Buck M, Pinney JW, Stumpf MP.   The evolution of the phage shock protein response system: interplay between protein function, genomic organization, and system function.   Mol. Biol. Evol.   2010 -11 -10   28(3)   1141-55   21059793   10.1093/molbev/msq301  
GAIN     10943   Sugawara T, Go Y, Udono T, Morimura N, Tomonaga M, Hirai H, Imai H.   Diversification of bitter taste receptor gene family in western chimpanzees.   Mol. Biol. Evol.   2010 -10 -22   28(2)   921-31   20961961   10.1093/molbev/msq279  
GAIN     10945   Ohshima K, Igarashi K.   Inference for the initial stage of domain shuffling: tracing the evolutionary fate of the PIPSL retrogene in hominoids.   Mol. Biol. Evol.   2010 -6 -8   27(11)   2522-33   20525901   10.1093/molbev/msq138  
Algae   NIES-2672   28419   McDonald SM, Plant JN, Worden AZ.   The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of micromonas.   Mol. Biol. Evol.   2010 -5 -12   27(10)   2268-83   20457585   10.1093/molbev/msq113  
Algae   NIES-397,NIES-398   28044   Smith DR, Lee RW.   Low nucleotide diversity for the expanded organelle and nuclear genomes of Volvox carteri supports the mutational-hazard hypothesis.   Mol. Biol. Evol.   2010 -5 -1   27(10)   2244-56   20430860   10.1093/molbev/msq110  
C.intestinalis / (O.japonicus)   Wild C. int   12184   Sakai T, Aoyama M, Kusakabe T, Tsuda M, Satake H.   Functional diversity of signaling pathways through G protein-coupled receptor heterodimerization with a species-specific orphan receptor subtype.   Mol. Biol. Evol.   2009 -12 -23   27(5)   1097-106   20026483   10.1093/molbev/msp319  
Algae   NIES-2541   27004   Hoshina R, Imamura N.   Phylogenetically close group I introns with different positions among Paramecium bursaria photobionts imply a primitive stage of intron diversification.   Mol. Biol. Evol.   2009 -3 -13   26(6)   1309-19   19279084   10.1093/molbev/msp044  
Algae   NIES-101,NIES-98,NIES-89,NIES-102,NIES-298   21245   Cadel-Six S, Dauga C, Castets AM, Rippka R, Bouchier C, Tandeau de Marsac N, Welker M.   Halogenase genes in nonribosomal peptide synthetase gene clusters of Microcystis (cyanobacteria): sporadic distribution and evolution.   Mol. Biol. Evol.   2008 -7 -11   25(9)   2031-41   18614525   10.1093/molbev/msn150  
Tropical clawed frog     2522   Hikosaka A, Kobayashi T, Saito Y, Kawahara A.   Evolution of the Xenopus piggyBac transposon family TxpB: domesticated and untamed strategies of transposon subfamilies.   Mol. Biol. Evol.   2007 -10 -16   24(12)   2648-56   17934208   10.1093/molbev/msm191  
Prokaryotes E. coli   pMCL200   3346   Fujita MK, Boore JL, Moritz C.   Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae).   Mol. Biol. Evol.   2007 -10 -9   24(12)   2775-86   17921488   10.1093/molbev/msm212  
Algae   NIES-547   26432   Nozaki H, Iseki M, Hasegawa M, Misawa K, Nakada T, Sasaki N, Watanabe M.   Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes.   Mol. Biol. Evol.   2007 -5 -10   24(8)   1592-5   17488739   10.1093/molbev/msm091  
Information   E.coli   1827   Homma K, Fukuchi S, Nakamura Y, Gojobori T, Nishikawa K.   Gene cluster analysis method identifies horizontally transferred genes with high reliability and indicates that they provide the main mechanism of operon gain in 8 species of gamma-Proteobacteria.   Mol. Biol. Evol.   2006 -12 -23   24(3)   805-13   17185745   10.1093/molbev/msl206  
Algae   NIES-955,NIES-936,NIES-1333,NIES-1335   20376   Kim E, Simpson AG, Graham LE.   Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes.   Mol. Biol. Evol.   2006 -9 -20   23(12)   2455-66   16982820   10.1093/molbev/msl120  
Silkworms   ?   3457   Kojima KK, Kuma K, Toh H, Fujiwara H.   Identification of rDNA-specific non-LTR retrotransposons in Cnidaria.   Mol. Biol. Evol.   2006 -7 -28   23(10)   1984-93   16870681   10.1093/molbev/msl067  
Medaka   MT67, IB178   2855   Koga A, Iida A, Hori H, Shimada A, Shima A.   Vertebrate DNA transposon as a natural mutator: the medaka fish Tol2 element contributes to genetic variation without recognizable traces.   Mol. Biol. Evol.   2006 -5 -5   23(7)   1414-9   16672286   10.1093/molbev/msl003  
Algae   NIES-296   20353   Nedelcu AM, Borza T, Lee RW.   A land plant-specific multigene family in the unicellular Mesostigma argues for its close relationship to Streptophyta.   Mol. Biol. Evol.   2006 -2 -16   23(5)   1011-5   16476689   10.1093/molbev/msj108  
Drosophila     11574   Nozawa M, Kumagai M, Aotsuka T, Tamura K, SMBE Tri-National Young Investigators.   Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Unusual evolution of interspersed repeat sequences in the Drosophila ananassae subgroup.   Mol. Biol. Evol.   2006 -2 -10   23(5)   981-7   16467489   10.1093/molbev/msj105  
Information   E.coli   1711   Fang G, Rocha E, Danchin A.   How essential are nonessential genes?   Mol. Biol. Evol.   2005 -7 -15   22(11)   2147-56   16014871   10.1093/molbev/msi211  
Silkworms   Database   3357   Kojima KK, Fujiwara H.   Long-term inheritance of the 28S rDNA-specific retrotransposon R2.   Mol. Biol. Evol.   2005 -7 -15   22(11)   2157-65   16014872   10.1093/molbev/msi210  
Information   NBRP   1774   Kojima KK, Fujiwara H.   Long-term inheritance of the 28S rDNA-specific retrotransposon R2.   Mol. Biol. Evol.   2005 -7 -15   22(11)   2157-65   16014872   10.1093/molbev/msi210  
Pathogenic microorganisms   P. vivax?   1175   Jongwutiwes S, Putaporntip C, Iwasaki T, Ferreira MU, Kanbara H, Hughes AL.   Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax.   Mol. Biol. Evol.   2005 -5 -20   22(8)   1733-9   15901839   10.1093/molbev/msi168  
Zebrafish   ?   12086   Kijimoto T, Watanabe M, Fujimura K, Nakazawa M, Murakami Y, Kuratani S, Kohara Y, Gojobori T, Okada N.   cimp1, a novel astacin family metalloproteinase gene from East African cichlids, is differentially expressed between species during growth.   Mol. Biol. Evol.   2005 -4 -29   22(8)   1649-60   15858202   10.1093/molbev/msi159  
Human and Animal Cells   COS-1   1518   Chinen A, Matsumoto Y, Kawamura S.   Reconstitution of ancestral green visual pigments of zebrafish and molecular mechanism of their spectral differentiation.   Mol. Biol. Evol.   2005 -1 -14   22(4)   1001-10   15647516   10.1093/molbev/msi086  
Information   E.coli   1670   Rocha EP, Danchin A.   An analysis of determinants of amino acids substitution rates in bacterial proteins.   Mol. Biol. Evol.   2003 -11 -5   21(1)   108-16   14595100   10.1093/molbev/msh004  
Silkworms   Silkbase ?   526   Kojima KK, Fujiwara H.   Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets.   Mol. Biol. Evol.   2003 -9 -2   21(2)   207-17   12949131   10.1093/molbev/msg235  
Silkworms   Silkbase   494   Kojima KK, Fujiwara H.   Evolution of target specificity in R1 clade non-LTR retrotransposons.   Mol. Biol. Evol.   2003 -3 -20   20(3)   351-61   12644555    
Rice   Wild rice   659   Cheng C, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E.   Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs.   Mol. Biol. Evol.   2003 -1 -10   20(1)   67-75   12519908    
Wheat   -   682   Matsuoka Y, Yamazaki Y, Ogihara Y, Tsunewaki K.   Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals.   Mol. Biol. Evol.   2002 -11 -26   19(12)   2084-91   12446800    
Silkworms   ?   441   Yukuhiro K, Sezutsu H, Itoh M, Shimizu K, Banno Y.   Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the wild mulberry silkmoth, Bombyx mandarina, and its close relative, the domesticated silkmoth, Bombyx mori.   Mol. Biol. Evol.   2002 -7 -26   19(8)   1385-9   12140251    
Drosophila     277   Inomata N, Yamazaki T.   Nucleotide variation of the duplicated amylase genes in Drosophila kikkawai.   Mol. Biol. Evol.   2002 -4 -19   19(5)   678-88   11961101    
Algae   NIES-296   20169   Turmel M, Otis C, Lemieux C.   The complete mitochondrial DNA sequence of Mesostigma viride identifies this green alga as the earliest green plant divergence and predicts a highly compact mitochondrial genome in the ancestor of all green plants.   Mol. Biol. Evol.   2001 -12 -26   19(1)   24-38   11752187    
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