Browsing by Author "Joshi P"

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    On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae)
    (BioMed Central, 2009) Tate JA; Joshi P; Soltis KA; Soltis P; Soltis D
    Background: Polyploidy (whole-genome duplication) is an important speciation mechanism,particularly in plants. Gene loss, silencing, and the formation of novel gene complexes are some ofthe consequences that the new polyploid genome may experience. Despite the recurrent natureof polyploidy, little is known about the genomic outcome of independent polyploidization events.Here, we analyze the fate of genes duplicated by polyploidy (homoeologs) in multiple individualsfrom ten natural populations of Tragopogon miscellus (Asteraceae), all of which formedindependently from T. dubius and T. pratensis less than 80 years ago.Results: Of the 13 loci analyzed in 84 T. miscellus individuals, 11 showed loss of at least one parentalhomoeolog in the young allopolyploids. Two loci were retained in duplicate for all polyploidindividuals included in this study. Nearly half (48%) of the individuals examined lost a homoeologof at least one locus, with several individuals showing loss at more than one locus. Patterns of losswere stochastic among individuals from the independently formed populations, except that the T.dubius copy was lost twice as often as T. pratensis.Conclusion: This study represents the most extensive survey of the fate of genes duplicated byallopolyploidy in individuals from natural populations. Our results indicate that the road to genomedownsizing and ultimate genetic diploidization may occur quickly through homoeolog loss, but withsome genes consistently maintained as duplicates. Other genes consistently show evidence ofhomoeolog loss, suggesting repetitive aspects to polyploid genome evolution.
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    Polyploidy on islands - concerted evolution and gene loss amid chromosomal stasis
    (Oxford University Press on behalf of the Annals of Botany Company, 2023-01-01) Joshi P; Ansari H; Dickson R; Ellison NW; Skema C; Tate JA
    BACKGROUND AND AIMS: Polyploidy is an important process that often generates genomic diversity within lineages, but it can also cause changes that result in loss of genomic material. Island lineages, while often polyploid, typically show chromosomal stasis but have not been investigated in detail regarding smaller-scale gene loss. Our aim was to investigate post-polyploidization genome dynamics in a chromosomally stable lineage of Malvaceae endemic to New Zealand. METHODS: We determined chromosome numbers and used fluorescence in situ hybridization to localize 18S and 5S rDNA. Gene sequencing of 18S rDNA, the internal transcribed spacers (ITS) with intervening 5.8S rDNA, and a low-copy nuclear gene, GBSSI-1, was undertaken to determine if gene loss occurred in the New Zealand lineage following polyploidy. KEY RESULTS: The chromosome number for all species investigated was 2nā€…=ā€…42, with the first published report for the monotypic Australian genus Asterotrichion. The five species investigated all had two 5S rDNA signals localized interstitially on the long arm of one of the largest chromosome pairs. All species, except Plagianthus regius, had two 18S rDNA signals localized proximally on the short arm of one of the smallest chromosome pairs. Plagianthus regius had two additional 18S rDNA signals on a separate chromosome, giving a total of four. Sequencing of nuclear ribosomal 18S rDNA and the ITS cistron indicated loss of historical ribosomal repeats. Phylogenetic analysis of a low-copy nuclear gene, GBSSI-1, indicated that some lineages maintained three copies of the locus, while others have lost one or two copies. CONCLUSIONS: Although island endemic lineages show chromosomal stasis, with no additional changes in chromosome number, they may undergo smaller-scale processes of gene loss and concerted evolution ultimately leading to further genome restructuring and downsizing.
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    Role of chromosomes in systematics, evolution and phylogenies
    (Australasian Systematic Botany Society, 30/09/2015) Joshi P