Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes

Álvarez, Inés; Cronn, Richard; Wendel, Jonathan F.

doi:10.1007/s00606-004-0294-0

Cited by 36 publications

(46 citation statements)

References 34 publications

(84 reference statements)

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“…Among the 56 372 genes in the cotton assembly, an average of 47.5% were expressed in leaf tissue (Table 1). Notably, percentages were similar among the two D-genome diploids, as expected from their high genetic similarity (499% nucleotide identity in exons) (Alvarez et al, 2005). We also mapped the reads from D 5 onto the recently released D 5 -genome draft sequence to compare mapping efficiency; this resulted in 75% of reads mapping onto the 13 scaffolds of the draft assembly (Supplementary Table S2).…”

Section: Mapping Efficiency Of Rna-seq Datamentioning

confidence: 93%

Homoeolog expression bias and expression level dominance in allopolyploid cotton

2012

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Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the reconciliation of two or more sets of diverged genomes and regulatory interactions. In this study, we explored gene expression patterns in interspecific hybrid F 1 , and synthetic and natural allopolyploid cotton using RNA-Seq reads from leaf transcriptomes. We determined how the extent and direction of expression level dominance (total level of expression for both homoeologs) and homoeolog expression bias (relative contribution of homoeologs to the transcriptome) changed from hybridization through evolution at the polyploid level and following cotton domestication. Genome-wide expression level dominance was biased toward the A-genome in the diploid hybrid and natural allopolyploids, whereas the direction was reversed in the synthetic allopolyploid. This biased expression level dominance was mainly caused by up-or downregulation of the homoeolog from the 'non-dominant' parent. Extensive alterations in homoeolog expression bias and expression level dominance accompany the initial merger of two diverged diploid genomes, suggesting a combination of regulatory (cis or trans) and epigenetic interactions that may arise and propagate through the transcriptome network. The extent of homoeolog expression bias and expression level dominance increases over time, from genome merger through evolution at the polyploid level. Higher rates of transgressive and novel gene expression patterns as well as homoeolog silencing were observed in natural allopolyploids than in F 1 hybrid and synthetic allopolyploid cottons. These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection.

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Section: Mapping Efficiency Of Rna-seq Datamentioning

confidence: 93%

Homoeolog expression bias and expression level dominance in allopolyploid cotton

2012

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“…With respect to the D-genome half, the American diploid cottons (subgenus Houzingenia Fryxell) are a monophyletic group of 13 species located primarily in southwest Mexico and extending north into Arizona. Phylogenetic relationships among the species have been evaluated (Alvarez et al 2005), and previous research has identified Gossypium raimondii (D5) as the closest living relative of the paternal ancestor to all polyploid species using non-nuclear molecular methods and other evidence (Endrizzi et al 1985;Wendel and Cronn 2003). In the present study, we used sequence data from an intergenic region to explicitly test the relationship of D-genome species to all allopolyploids.…”

Section: Phylogenetic Inferences Of Monophylymentioning

confidence: 99%

Assessing the monophyly of polyploid Gossypium species

et al. 2012

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The origin and monophyly of the polyploid cotton (Gossypium) species has been largely accepted, despite the lack of explicit phylogenetic evidence. Recent studies in other polyploid systems have demonstrated that multiple origins for polyploid species are much more common than once thought, raising the possibility that Gossypium polyploids also had multiple origins, as postulated by some authors. To test the monophyly of polyploid cotton, we sequenced a 2.8-kb intergenic region from all diploid species belonging to the genome groups from which the polyploid originates. The resulting phylogenetic analyses strongly support a single origin of polyploid cotton involving a D-genome ancestor related to Gossypium raimondii and an A-genome ancestor that was sister to both extant A-genome species.

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“…The anticipated value of SNPs for analysis of candidate gene evolution and their eVects on complex traits have stimulated large scale SNP characterization and marker mapping in rice (Feltus et al 2004), wheat (Mochida et al 2003;Somers et al 2003;Zhang et al 2003;Caldwell et al 2004), maize (Ching et al 2002;Batley et al 2003), soybean Kim et al 2005), and barley (Kanazin et al 2002;Bundock et al 2003;Bundock and Henry 2004). Most cotton sequence variation analyses have been conWned to a single gene family or DNA fragments for phylogenetic analysis (Small et al 1998;Small and Wendel 2000;Cronn et al 2002;Alvarez et al 2005). Candidate gene-based association mapping using SNP markers has emerged as a powerful tool to determine the role of genes in complex traits (Glazier et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton

Saha

Jenkins

et al. 2007

Mol Genet Genomics

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The knowledge of biological significance associated with DNA markers is very limited in cotton. SNPs are potential functional marker to tag genes of biological importance. Plant expansins are a group of extracellular proteins that directly modify the mechanical properties of cell walls, enable turgor-driven cell extension, and likely affect length and quality of cotton fibers. Here, we report the expression profiles of EXPANSIN transcripts during fiber elongation and the discovery of SNP markers, assess the SNP characteristics, and localize six EXPANSIN A genes to chromosomes. Transcriptome profiling of cotton fiber oligonucleotide microarrays revealed that seven EXPANSIN transcripts were differentially expressed when there was parallel polar elongation during morphogenesis at early stage of fiber development, suggesting that major and minor isoforms perform discrete functions during polar elongation and lateral expansion. Ancestral and homoeologous relationships of the six EXPANSIN A genes were revealed by phylogenetic grouping and comparison to extant A- and D-genome relatives of contemporary AD-genome cottons. The average rate of SNP per nucleotide was 2.35% (one SNP per 43 bp), with 1.74 and 3.99% occurring in coding and noncoding regions, respectively, in the selected genotypes. An unequal evolutionary rate of the EXPANSIN A genes at the subgenome level of tetraploid cotton was recorded. Chromosomal locations for each of the six EXPANSIN A genes were established by gene-specific SNP markers. Results revealed a strategy for discovering SNP markers in a polyploidy species like cotton. These markers could be useful to associate candidate genes with the complex fiber traits in MAS.

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Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes

Cited by 36 publications

References 34 publications

Homoeolog expression bias and expression level dominance in allopolyploid cotton

Homoeolog expression bias and expression level dominance in allopolyploid cotton

Assessing the monophyly of polyploid Gossypium species

Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton

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