Transcript Papaya X chromosome compared to monoecious

Rapid divergence and expansion of the papaya X chromosome
compared to its ancestral autosome
Andrea R. Gschwend1, Qingyi Yu2, Fanchang Zeng1, Robert VanBuren1, Rishi Aryal1, Jennifer Han1, Ray Ming1
1.
2.
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Texas AgriLife Research, Texas A&M University, Weslaco, Texas 78596, USA
Introduction:
It has long been thought that, while the hemizygous Y chromosome changes drastically over time, the X chromosome conserves the ancestral autosome content and
structure. To determine whether the X chromosome remains unchanged compared to its ancestral autosome, BAC sequences of Carica papaya and Vasconcellea
monoica were analyzed. Carica papaya is a trioecious tropical plant with very young sex chromosomes (2-3 my), the segregation of which results in male (XY), female
(XX), and hermaphrodite (XYh) individuals. Close relative Vasconcellea monoica, which diverged from a shared common ancestor with papaya 6.8-14.7 mya, is
monoecious, having separate male and female flowers on a single individual, with the lack of sexual dimorphism, signifying the absence of sex chromosomes. The
genome size of monoica is 626Mb compared to the 372Mb genome of papaya, signifying expansion in monoica since the divergence of these species. The retention
of the ancestral autosome in monoica and difference in sexual systems between closely related papaya and monoica allow for a unique opportunity to better
understand early X chromosome evolution.
Table 1. Summary of the repetitive element content of the papaya and monoica BACs.
Results:
The papaya X-specific region, overall, expanded 48%, where as the
monoica autosome expanded 62%. The autosomal expansion in
monoica is consistent with the larger monoica genome size and is largely
due to an increase of repetitive elements across the autosome. The
expansion of the papaya X-specific region is due to the lack of
recombination between the HSY and X regions of the sex chromosomes,
which, over time, allowed for the accelerated accumulation of repetitive
elements. The suppression of recombination also allowed for the
accumulation of autosomal genes and gene shuffling in the papaya sex
specific region. Though the X-specific region evolves slower then the Yspecific region, it is not as static as previously thought.
a)
papaya Xspecific BACs
monoica
corresponding
BACs
b)
papaya
autosomal
BAC
monoica
corresponding
BAC
45%
Retroelements
LINEs
LTR elements
DNA transposons
Unclassified
Total interspersed
repeats
56%
101.3 kb
2.56Mb
Figure 1. a) Expansion in the syntenic regions of 16 BACs and 2 contigs
found in the papaya X-specific region compared to its corresponding 11
monoica BACs. b) Expansion of the syntenic region of one monoica
autosomal BAC compared to its corresponding papaya autosomal BAC.
60.2%
Table 2. Gene density of the papaya
and monoica BACs
monoica
Papaya X
Sequence Gene Density
length (in kb) (per 100 Kb)
703
2.84
1,821
2.58
monoica
99
7.14
papaya
autosome
58
10.34
Conclusions:
5% 1.1 Mb
65.4%
Papaya X-specific
BACS (2,545 kb)
62%
72.8 kb
46.4%
0.9%
45.6%
0.1%
18.9%
monoica X
region BACS
(1,082 kb)
32.5%
1.4%
31.1%
1.1%
26.5%
papaya genome
(271,000 kb)
monoica autosome
BAC (102 kb)
42.2%
1.1%
41.1%
0.2%
8.7%
28.4%
7.8%
20.6%
0.7%
31.4%
51.2%
60.5%
Table 3. Gene content of the papaya and
monoica BACs
Total transcription units-SDR
Total pseudogenes-SDR
Paired
Vm-X-HSY
X-HSY paired
Vm-X or Vm-HSY
Vm-Specific
X-Specific
Total transcription units-Autosome
Paired
Vm-Specific
X-Specific
Total Genes
Vm
Cp X/A
20
47
5
9
33
10
23
0
10
13
7
6
6
1
0
*SDR-Sex determining region, HSY-hermaphrodite specific region of the Y chromosome
 The papaya X-specific region showed marked expansion compared to the ancestral
autosome in monoica. The monoica autosome expanded compared to the
corresponding autosomal BAC in papaya, consistent with genome size differences.
 The expansion of the papaya X-specific region is largely due to the increase of
repetitive elements, specifically LTR retrotransposons.
 The papaya sex specific regions gained a considerable number of genes compared
to the corresponding monoica region. The autosomal region of papaya and
monoica, had a greater gene density and the majority of genes and gene order
were conserved between the two species.
Acknowledgments:
This research was funded by the NSF Plant Genome Research Program (award number 0553417).