Phylogeny, Duplication, and Intraspecific Variation of Adh Sequences in New World Diploid Cottons (Gossypium L., Malvaceae)

Small, Randall L.; Wendel, Jonathan F.

doi:10.1006/mpev.1999.0750

Cited by 65 publications

(83 citation statements)

References 53 publications

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“…G. arboreum are Old World cultivated cotton species and G. hirsutum are New World cultivated cotton species, whereas G. raimondii is wild and cannot produce spinnable fiber. Studies have shown that the expression of duplicated genes in tetraploid species at the transcriptional level may have three fates: (1) silencing of one of the duplicated copies (Wendel 2000;Adams et al 2003); (2) molecular interactions mediated by concerted evolutionary processes leading to a rapid sequence conversion of homologous loci, homology-specific sequence elimination, and extensive genomic rearrangements (Wendel et al 1995;Adams et al 2003); or (3) independent evolution of the duplicated copies in allopolyploids (Cronn et al 1999;Small and Wendel 2000).…”

Section: Discussionmentioning

confidence: 99%

A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium

Guo¹,

Cai²,

et al. 2007

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The mapping of functional genes plays an important role in studies of genome structure, function, and evolution, as well as allowing gene cloning and marker-assisted selection to improve agriculturally important traits. Simple sequence repeats (SSRs) developed from expressed sequence tags (ESTs), EST-SSR (eSSR), can be employed as putative functional marker loci to easily tag corresponding functional genes. In this paper, 2218 eSSRs, 1554 from G. raimondii-derived and 754 from G. hirsutum-derived ESTs, were developed and used to screen polymorphisms to enhance our backbone genetic map in allotetraploid cotton. Of the 1554 G. raimondii-derived eSSRs, 744 eSSRs were able to successfully amplify polymorphisms between our two mapping parents, TM-1 and Hai7124, presenting a polymorphic rate of 47.9%. However, only a 23.9% (159/754) polymorphic rate was produced from G. hirsutum-derived eSSRs. No relationship was observed between the level of polymorphism, motif type, and tissue origin, but the polymorphism appeared to be correlated with repeat type. After integrating these new eSSRs, our enhanced genetic map consists of 1790 loci in 26 linkage groups and covers 3425.8 cM with an average intermarker distance of 1.91 cM. This microsatellite-based, gene-rich linkage map contains 71.96% functional marker loci, of which 87.11% are eSSR loci. There were 132 duplicated loci bridging 13 homeologous At/Dt chromosome pairs. Two reciprocal translocations after polyploidization between A2 and A3, and between A4 and A5, chromosomes were further confirmed. A functional analysis of 975 ESTs producing 1122 eSSR loci tagged in the map revealed that 60% had clear BLASTX hits (,1e À10 ) to the Uniprot database and that 475 were associated mainly with genes belonging to the three major gene ontology categories of biological process, cellular component, and molecular function; many of the ESTs were associated with two or more category functions. The results presented here will provide new insights for future investigations of functional and evolutionary genomics, especially those associated with cotton fiber improvement.

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Section: Discussionmentioning

confidence: 99%

A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium

Guo¹,

Cai²,

et al. 2007

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“…Considerable accumulated evidence supports the monophyly of the six subsections of American cottons (Fryxell 1971;Wendel and Percival 1990;Wendel and Albert 1992;Cronn et al 1996;Seelanan et al 1997;Small and Wendel 2000a). Genetic divergence between species in different subsections is high relative to the divergence within species of a subsection (Wendel and Percival 1990;Cronn et al 1996;Seelanan et al 1997;Small and Wendel 2000a).…”

Section: Plant Materialsmentioning

confidence: 99%

“…This conclusion was initially dismissed as a potential artifact of African introgression (Cronn et al 1996). Nevertheless, subsequent studies of American cottons using unlinked, lowcopy nuclear genes AdhA (Small and Wendel 2000a) and FAD-2-1 (Liu et al 2001) resolved G. gossypioides identically as 5S rDNA, suggesting that this phylogenetic resolution is unlikely to be entirely due to introgressive hybridization.…”

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confidence: 99%

“…In addition, experimental triploids derived from interploidal crosses between New World species (including G. gossypioides) and AD-genome allotetraploids reveal chromosome pairing only with D-genome homoeologues (Menzel and Brown 1954;Endrizzi et al 1985). Despite this uncomplicated cartographic and cytogenetic description, molecular evolutionary studies of G. gossypioides based on chloroplast DNA (cpDNA; Wendel and Albert 1992), nuclear ribosomal sequences (Wendel et al 1995;Cronn et al 1996) and low copy genes (Small and Wendel 2000a;Liu et al 2001) have yielded three radically different interpretations for the evolutionary history of this species. The first, based upon chloroplast DNA restriction site variation (Wendel and Albert 1992; Fig.…”

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confidence: 99%

“…Hypotheses initially derived from cpDNA restriction site analysis (Wendel and Albert 1992) were tested by examining 7.3 kb of sequence information from four chloroplast regions (ndhF, matK, rpl16 intron, trnT-trnL spacer). To evaluate the phylogenetic signal from the nuclear genome, we sampled six low-copy nuclear genes (CesA1, AdhC, CesA1b, A1341, G1121, and G1262; 5.5 kb) to obtain multiple inde- (Wendel et al 1995), 5S rDNA (Cronn et al 1996), AdhA (Small and Wendel 2000a), and FAD-2-1 (Liu et al 2001), this evaluation of the affinity of G. gossypioides to New World cottons includes about 16.4 kb of sequence information per taxon. Results from this survey show that cpDNA, nuclear ITS, and lowcopy nuclear DNA continue to exhibit significantly different patterns of sequence evolution, reflecting their different evolutionary trajectories.…”

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Cryptic Repeated Genomic Recombination During Speciation in Gossypium Gossypioides

Cronn

Small

Haselkorn

et al. 2003

Evol

Self Cite

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The Mexican cotton Gossypium gossypioides is a perplexing entity, with conflicting morphological, cytogenetic, and molecular evidence of its phylogenetic affinity to other American cottons. We reevaluated the evolutionary history of this enigmatic species using 16.4 kb of DNA sequence. Phylogenetic analyses show that chloroplast DNA (7.3 kb), nuclear ribosomal internal transcribed spacers (ITS; 0.69 kb), and unique nuclear genes (8.4 kb) yield conflicting resolutions for G. gossypioides. Eight low-copy nuclear genes provide a nearly unanimous resolution of G. gossypioides as the basalmost American diploid cotton, whereas cpDNA sequences resolve G. gossypioides deeply nested within the American diploid clade sister to Peruvian G. raimondii, and ITS places G. gossypioides in an African (rather than an American) clade. These data, in conjunction with previous evidence from the repetitive fraction of the genome, implicate a complex history for G. gossypioides possibly involving temporally separated introgression events from genetically divergent cottons that are presently restricted to different hemispheres. Based on repetitive nuclear DNA, it appears that G. gossypioides experienced nuclear introgression from an African species shortly after divergence from the remainder of the American assemblage. More recently, hybridization with a Mexican species may have resulted in cpDNA introgression, and possibly a second round of cryptic nuclear introgression. Gossypium gossypioides provides a striking example of the previously unsuspected chimeric nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events. KeywordsGossypium gossypioides, hybridization, introgression, phylogenetic incongruence, speciation RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted. Abstract. The Mexican cotton Gossypium gossypioides is a perplexing entity, with conflicting morphological, cytogenetic, and molecular evidence of its phylogenetic affinity to other American cottons. We reevaluated the evolutionary history of this enigmatic species using 16.4 kb of DNA sequence. Phylogenetic analyses show that chloroplast DNA (7.3 kb), nuclear ribosomal internal transcribed spacers (ITS; 0.69 kb), and unique nuclear genes (8.4 kb) yield conflicting resolutions for G. gossypioides. Eight low-copy nuclear genes provide a nearly unanimous resolution of G. gossypioides as the basalmost American diploid cotton, whereas cpDNA sequences resolve G. gossypioides deeply nested within the American diploid clade sister to Peruvian G. raimondii, and ITS places G. gossypioides in an African (rather than an American) clade. These data, in conjunction with previous evidence from the repetitive fraction of the genome, implicate a complex history for G. gossypioides possibly involving temporally separated introgression events from genetically divergent cottons that are presently r...

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Evolution and Natural History of the Cotton Genus

Wendel

Brubaker²,

Álvarez³

et al. 2009

Genetics and Genomics of Cotton

166

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Phylogeny, Duplication, and Intraspecific Variation of Adh Sequences in New World Diploid Cottons (Gossypium L., Malvaceae)

Cited by 65 publications

References 53 publications

A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium

A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium

Cryptic Repeated Genomic Recombination During Speciation in Gossypium Gossypioides

Evolution and Natural History of the Cotton Genus

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