Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton

Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium

Background The majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid progenitor species. While most cotton species are adapted to warm, semi-arid tropical and subtropical regions, and thus perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. One of the common biochemical responses of plants to cold temperatures is an increase in omega-3 fatty acids, which protects cellular function by maintaining membrane integrity. The purpose of our study was to identify and characterize the omega-3 fatty acid desaturase (FAD) gene family in G. hirsutum, with an emphasis on identifying omega-3 FADs involved in cold temperature adaptation. Results Eleven omega-3 FAD genes were identified in G. hirsutum, and characterization of the gene family in extant A and D diploid species (G. herbaceum and G. raimondii, respectively) allowed for unambiguous genome assignment of all homoeologs in tetraploid G. hirsutum. The omega-3 FAD family of cotton includes five distinct genes, two of which encode endoplasmic reticulum-type enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2, and FAD7/8-3). The FAD3-2 gene was duplicated in the A genome progenitor species after the evolutionary split from the D progenitor, but before the interspecific hybridization event that gave rise to modern tetraploid cotton. RNA-seq analysis revealed conserved, gene-specific expression patterns in various organs and cell types and semi-quantitative RT-PCR further revealed that FAD7/8-1 was specifically induced during cold temperature treatment of G. hirsutum seedlings. Conclusions The omega-3 FAD gene family in cotton was characterized at the genome-wide level in three species, showing relatively ancient establishment of the gene family prior to the split of A and D diploid progenitor species. The FAD genes are differentially expressed in various organs and cell types, including fiber, and expression of the FAD7/8-1 gene was induced by cold temperature. Collectively, these data define the genetic and functional genomic properties of this important gene family in cotton and provide a foundation for future efforts to improve cotton abiotic stress tolerance through molecular breeding approaches

Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton.This article is from G3 3 (2013): 1809, doi:10.1534/g3.113.007229. Posted with permission.</p

Dysophylla yatabeana Makino

原著和名: ミヅトラノヲ科名: シソ科 = Labiatae採集地: 三重県 北牟婁郡 海山町 船津 (太田沼付近) (紀伊 北牟婁郡 海山町 船津 (太田沼付近) )採集日: 1982/9/30採集者: 萩庭丈壽整理番号: JH031600国立科学博物館整理番号: TNS-VS-98160

The number of genes impacted by putative large gene conversion events based on copy number variants (by accession).

<p>The number of genes impacted by putative large gene conversion events based on copy number variants (by accession).</p

Effectiveness of mapping with GSNAP and categorization with PolyCat and PolyDog.

<p>PolyDog has higher categorization rates because it allows for genome-wide categorization, instead of relying on known homoeo-SNPs in regions present in both genomes. The percentage of trimmed reads successfully mapped from each species (AD₁-AD₇) to the A₂ reference (A) and the D₅ reference (B) is shown. For each reference, the percentage of mapped reads from each species (AD₁-AD₇) categorized to the A_T-genome by PolyCat, D_T-genome by PolyCat, or to the genome of the reference sequence by PolyDog is also shown.</p

Regions including 2 or more consecutive ancient gene conversion SNPs provided little SNP-based evidence for sequence conversion between genomes.

<p>Regions including 2 or more consecutive ancient gene conversion SNPs provided little SNP-based evidence for sequence conversion between genomes.</p

Homoeo-SNPs identified between the A- and D-genomes of the diploids and A_T- and D_T-genomes of the tetraploids.

<p>Homoeo-SNPs identified between the A- and D-genomes of the diploids and A_T- and D_T-genomes of the tetraploids.</p

Evidence for introgression of AD₂ material into AD₁ and <i>vice versa</i>.

<p>Introgression occurred in both directions and in both genomes.</p

Evolutionary relationships between accessions based on the A_T-genome.

<p>Most accessions are located according to expectation from previous studies and in agreement between the A_T- and D_T-genome based trees. Consensus bootstrap neighbor-joining trees were constructed (by PHYLIP) based on distance matrices representing SNPs between each pair of accessions. The root representing the point of connection to the diploid relatives. Individuals from AD₁ are colored blue, AD₂ colored green, and other tetraploid species colored red. Branch numbers indicate percent bootstrap support for that split. The A_T- and D_T-genome trees largely agreed in regard to the topology of the AD₂ clade, with the exception of the positioning of a sub-clade containing the 3 cultivars: Deltapine-340, Giza-7, and Phytogen-76. The AD₁ clade was similarly constructed in the A_T- and D_T-genome phylogenies, although the cultivars are so closely related to one another that their precise arrangements varied between trees.</p