Ibm Pc And Clones By Govindarajulu Pdf 209
Karmen Mcarthun
Copyright: 2018 Tennessen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: Reads from whole-genome sequencing (Bioproject Accession PRJNA402067) have been uploaded to NCBI SRA (accession numbers listed in S1 Table). The reconstructed W haplotype is in S3 Data. Other aligned sequences are in S1, S2, and S4 Data. Additional data are included in the Supporting Information files.
Abbreviations: BAC, bacterial artificial chromosome; CGRB, Center for Genome Research and Biocomputing; CUGI, Clemson University Genomics Institute; Fvb, diploid reference genome assembly informed by F. vesca ssp. bracteata; GPCL, Genomics and Proteomics Core Laboratories; IFC, Integrated Fluidic Circuit; Mb, megabase; Mya, million years ago; QTL, quantitative trait locus; SDR, sex-determining region
Turnovers of SDRs are likely to be quite common in plants, in which genetic control of sex appears to be poorly conserved [28,29]. Flowering plant SDRs may be diverse because dioecy (separate males and females) has evolved repeatedly from hermaphroditism (combined male and female function) and many sex chromosomes are relatively young and homomorphic [28,29,30]. Additionally, approximately one-third of flowering plant species are estimated to have a recent polyploid ancestry [31]. These whole-genome duplications provide a larger substrate for potential sex-determining genes or rearrangements [32]. Yet despite the potential of dioecious plants for yielding evolutionary insights, there are few systems with mapped SDRs [28,29] or known causal genes [33,34], although long-standing theory predicts that two linked genes, one controlling male function and one controlling female function, are involved [1,35]. Moreover, even when observed, the pattern and mechanism of turnovers remain entirely unexplored.
To assess and annotate the SDR, we assembled the shared female-specific sequence, generating three contigs totaling 13 kb in length. These contigs were ordered and oriented into a unified W-specific haplotype, the SDR cassette (Fig 2), by using highly similar autosomal and Z chromosome sequences as scaffolds. Specifically, most (10.4 kb) of the SDR cassette could be aligned (98% similarity) to Z chromosome bacterial artificial chromosomes (BACs) obtained from F. virginiana ssp. virginiana, originating from the maternal linkage cross parent at the fine-mapped SDR location from that cross (S4 and S5 Figs). Most of this sequence (8.6 kb) could also be aligned (93% similarity) to the diploid (F. vesca) reference genome at the fine-mapped location of Fvb6 position 1 Mb. A 1.2 kb segment of the SDR cassette was not homologous to Fvb6 but instead showed 99% similarity to Fvb7 position 18 Mb. Therefore, the W-specific SDR cassette is relatively short and shows homology to multiple sections of the genome.
In classic two-gene SDR models, one gene affects male function and another female function [35]. Previous quantitative trait locus (QTL) mapping has shown that the Fragaria SDR affects both male and female function [36,39,40] and shows differential recombination rates in ZZ versus ZW individuals [39]. However, we cannot yet conclude that there are two functional, non-recombining genes because a single master regulator could also perform both roles [33] and additional modifiers of female function could have evolved. Moreover, in addition to the two genes, there is the diagnostic deletion and two repetitive unassembled gaps within the SDR (Fig 2), which, though apparently noncoding, could also be functional motifs. Regardless, what is striking here is that an SDR cassette (W-specific) is shared across females from different taxa and populations where it occurs at multiple genomic locations (Fig 1B).
Top: there are seven predicted genes in the longest haplotype (S3 Table), including two shared by all females (GMEW and RPP0W, Fig 2). Middle: all three clades (α, β, and γ) share the SDR cassette, suggesting that it is the oldest and that Fvb6 position 1 Mb is the original SDR position. Clades β and γ also share the flanking sections, suggesting a translocation to Fvb6 position 13 Mb. Only clade γ possesses the outer section, consistent with a second translocation to Fvb6 position 37 Mb unique to this clade. At either ends of the flanking sequences, terminal inverted repeats (blue nucleotides) are adjacent to target-site duplications (TA dinucleotide), a pattern consistent with transposon-mediated movement of this section. Bottom: inferred size and composition of the hemizygous W-specific insertion in each of the three clades, α, β, and γ. Z chromosome composition is inferred from the Fvb reference genome and Z-specific sequence obtained from BACs of a maternal F. virginiana ssp. virginiana linkage cross parent in clade α (S4 Fig). BAC, bacterial artificial chromosome; Fvb, diploid reference genome assembly informed by F. vesca ssp. bracteata; Mb, megabase; SDR, sex-determining region.
Using the full W-specific haplotype in F. chiloensis as the reference, we characterized in detail the sequence neighboring the SDR cassette in each of the three phylogenetic clades (Fig 4). We did not assemble complete haplotypes for each clade independent of the F. chiloensis W haplotype assembly because the α clade had few female-specific 31-mers and the β clade had only three females and therefore we lacked the power to eliminate false-positive female-specific 31-mers. Instead, we identified portions of the assembled haplotype within clades that we could infer to be female specific using the following two parallel methods: alignment of female-specific 31-mers to the haplotype, and sites on the haplotype at which paired reads aligned on either side in females only (S7 Fig). These analyses revealed that distinct portions of the W haplotype were female specific in each clade (S7 Fig and S4 Table). In particular, in the α clade, only the SDR cassette is female specific. In contrast, the β clade shows female-specific sequence in both the SDR cassette and flanking sections, and the γ clade shows female-specific sequence in all three sections. The two females lacking the diagnostic deletion also did not possess any female-specific read pairs, further confirming that the SDR cassette is absent in these individuals and suggesting other mechanism(s) of male sterility [51].
A 2 kb portion of the downstream flanking section shows homology to Fvb4 position 21 Mb, which could be a souvenir from another prior SDR location or an independent translocation of sequence into the SDR in the β and γ ancestor; such events are commonly seen in sex chromosomes [2]. The proposed translocations must have occurred rapidly because octoploid Fragaria originated only approximately 1 million years ago (Mya) [46,66] and the aligned 2.7 kb portions of the SDR cassettes (Fig 2 and S2 Data) show >99% sequence similarity. This conjecture is also supported by incomplete lineage sorting of the SDR in F. virginiana (Fig 3), resulting in SDR polymorphism among females of this species. In contrast, F. chiloensis, which is monophyletic and is derived from F. virginiana ssp. platypetala [46], is apparently fixed for the derived SDR γ clade. All three SDR clades are found within F. virginiana ssp. platypetala (Fig 3), whose phylogenetic position [46,67] and geographic range (S2 Fig) lie between F. virginiana ssp. virginiana and F. chiloensis.
Although the mechanism of translocation of sex-determining sequence remains unknown, a striking sequence pattern suggests transposon-mediated movement. Specifically, we observe a 25 bp sequence that is inverted and repeated at the very distal ends of the flanking sections, where sequence homologous to Fvb6 13 Mb meets sequence homologous to Fvb6 37 Mb (Fig 4). On the distal end of each segment, we observe the dinucleotide motif TA. Pairs of terminal inverted repeats of 10 bp or more in length, adjacent to short duplications, are hallmarks of Class 2 transposable elements [68,69]. Therefore, this sequence signature is consistent with the hypothesis that a mobile element transported the 23 kb of SDR cassette and flanking sequence from the β clade location at Fvb6 13 Mb to the γ clade location at Fvb6 37 Mb. Terminal inverted repeats also occur in foldback elements, which can cause chromosomal rearrangement via ectopic recombination [70], and this mechanism could also facilitate movement of the SDR among homoeologs of Fvb6. We do not see terminal inverted repeats at the border between the SDR cassette and the flanking sequence, but this may have been lost, perhaps explaining why adjacent sequence was then also moved during the second translocation. Most transposable elements are under 23 kb in size, and we see no evidence of either an intact transposase, a Helitron transposon, or any known plant repetitive sequences other than stretches of dinucleotide repeats under 50 bp. Therefore, although the full W-specific haplotype remains incompletely assembled and could harbor a transposase (Fig 4), we hypothesize that the SDR movements do not involve a classic, active transposon but rather are relatively rare events that leverage active transposases that may be encoded elsewhere, as with miniature inverted-repeat transposable elements [68,69].
Consistent with the scenario of relatively few SDR movements, no female appears to have more than a single SDR cassette. Although we cannot assemble paralogous autosomal sequence due to high similarity among subgenomes, we can identify autosomal read pairs that align to the W haplotype but are spaced too far apart (>1 kb) to have originated in the SDR. The nonadjacent sections of the W haplotype where these paired reads align must therefore be contiguous in autosomes as they are in Fvb, though not in the SDR (S7 Fig and S4 Table). Coverage depth for these reads does not differ between males and females (Student t test, p > 0.1), and in females, coverage is 8-fold higher than for W-specific read pairs, suggesting that these reads originate from autosomal or pseudoautosomal regions on all four subgenomes. Therefore, there is no evidence that any autosomal homoeolog possesses an insertion representing a degraded or partial SDR. After an SDR translocation event, there would have been little or no co-occurrence of two SDR cassettes in the same female because the SDRs would occur on distinct subgenomes that segregate separately. Once separated, two SDR cassettes can never rejoin the same genome because two female plants cannot mate. Therefore, it appears that the former sex chromosomes, which have reverted to autosomes due to SDR turnover events, are descended from Z chromosomes and not W chromosomes (Fig 5).
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