The complex polyploid genome architecture of sugarcane.

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Mapping the distribution of the telomeric sequence (T2AG3)n in the Macropodoidea (Marsupialia) by fluorescence in situ hybridization. II. The ancestral 2n = 22 macropodid karyotype.

In marsupial karyotypes with little heterochromatin, the telomeric sequence (T(2)AG(3))(n), is involved in chromosome rearrangements. Here we compare the distribution of the (T(2)AG(3))(n) sequence in chromosomes recently derived by fusions and other rearrangements (7-0.5 MYBP) with its distribution in chromosomes derived earlier (24-9 MYBP). We have previously shown that the (T(2)AG(3))(n) sequence is consistently retained during chromosome rearrangements that are recent (7-0.5 MYBP). We suggest that in less recent rearrangements (24-9 MYBP) the pattern observed is initial retention followed by loss or amplification. We also suggest that the presence of interstitial (T(2)AG(3))(n) sequence is related to the evolutionary status of single chromosomes rather than entire karyotypes.

Centromere dynamics and chromosome evolution in marsupials.

The eukaryotic centromere poses an interesting evolutionary paradox: it is a chromatin entity indispensable to precise chromosome segregation in all eukaryotes, yet the DNA at the heart of the centromere is remarkably variable. Its important role of spindle attachment to the kinetochore during meiosis and mitosis notwithstanding, recent studies implicate the centromere as an active player in chromosome evolution and the divergence of species. This is exemplified by centromeric involvement in translocations, fusions, inversions, and centric shifts. Often species are defined karyotypically simply by the position of the centromere on certain chromosomes. Little is known about how the centromere, either as a functioning unit of chromatin or as a specific block of repetitive DNA sequences, acts in the creation of these types of chromosome rearrangements in an evolutionary context. Macropodine marsupials (kangaroos and wallabies) offer unique insights into current theories expositing centromere emergence during karyotypic diversification and speciation.

Mapping the distribution of the telomeric sequence (T2AG3)n in the 2n = 14 ancestral marsupial complement and in the macropodines (Marsupialia: Macropodidae) by fluorescence in situ hybridization.

In this study we test the theory that the presence of the conserved vertebrate telomeric sequence (T(2)AG(3))(n) at the centromeres of Australian marsupial 2n = 14 complements is evidence that these karyotypes are recently derived, which is contrary to the generally held view that the 2n = 14 karyotype is ancestral for Australasian and American marsupials. Here we compare the distribution of the (T(2)AG(3))( n ) sequence and constitutive heterochromatin in the presumed ancestral 2n = 14 complement and in complements with known rearrangements. We found that where there were moderate to large amounts of constitutive heterochromatin, the distribution of the (T(2)AG(3))(n) sequence reflected its presence as a native component of satellite DNA rather than its involvement in past rearrangements. The presence of centromeric heterochromatin in all Australian 2n = 14 complements therefore suggests that centromeric sites of the (T(2)AG(3))(n) sequence do not represent evidence for recent rearrangements.

Mapping the distribution of the telomeric sequence (T2AG3)n in rock-wallabies, Petrogale (Marsupialia: Macropodidae), by fluorescence in situ hybridization. I. The penicillata complex.

The eight Petrogale (rock-wallaby) species of the penicillata complex have a variable rate of karyotypic evolution, with species differing from the ancestral karyotype by two to six rearrangements. The distribution of the predominant vertebrate telomeric sequence (T2AG3)n was examined by fluorescence in situ hybridization (FISH) to determine if this sequence is retained during centric fusion events or is involved in other rearrangements. In all submetacentric chromosomes derived by centric fusions, the telomeric sequence was identified at or near the centromere, indicating that the (T2AG3)n sequence is consistently retained. In two acrocentric chromosomes, derived by centromeric transpositions from submetacentric fusion chromosomes, an interstitial signal was observed at the presumed site of the fusion. This represents the identification of a novel mechanism by which the (T2AG3)n sequence may become interstitial. Other interstitial telomeric signals were identified just below the centromere of chromosome 1 and interstitially on chromosome 4 in all eight species of the penicillata complex. These may be related to, respectively, the formation of euchromatic short arms on chromosome 1 and a more ancient rearrangement of chromosome 4 within marsupials.

Mapping the distribution of the telomeric sequence (T2AG3)n in the Macropodoidea (Marsupialia), by fluorescence in situ hybridization. I. The swamp wallaby, Wallabia bicolor.

Thylogale spp. (pademelons) retain the plesiomorphic (ancestral) 2n = 22 karyotype for the marsupial family Macropodidae (kangaroos and wallabies). The swamp wallaby, Wallabia bicolor, has the most derived macropodid karyotype with the lowest chromosome number (2n = 10 female, 11 male), and a multiple sex chromosome system (XX female, XY1Y2 male). All but one of the W. bicolor chromosomes are fusion chromosomes. Two of these chromosomes, the X chromosome and chromosome 1, are composed of three plesiomorphic Thylogale-like chromosomes. The distribution of the vertebrate telomeric sequence (T2AG3)n was examined by fluorescence in situ hybridization (FISH) in both species and a 'map' of non-telomeric (T2AG3)n sites on W. bicolor chromosomes relative to Thylogale chromosomes was constructed. (T2AG3)n signals were observed at six fusion sites in the four fusions chromosomes examined, indicating that the (T2AG3)n sequence is consistently retained during fusions. The distribution of the interstitial signals on the long arm of chromosome 1 of W. bicolor and the X chromosome suggests how a combination of inversions, fusions and centromeric transpositions have resulted in interstitial telomeric sequence.

Mapping the distribution of the telomeric sequence (T(2)AG(3))(n) in rock wallabies, Petrogale (Marsupialia: Macropodidae), by fluorescence in situ hybridization. ii. the lateralis complex.

The distribution of the conserved vertebrate telomeric sequence (T(2)AG(3))(n) was examined by fluorescence in situ hybridization in the six Petrogale (rock wallabies) taxa of the lateralis complex. As expected, the (T(2)AG(3))(n) sequence was located at the termini of all chromosomes in all taxa. However, the sequence was also present at several nontelomeric (viz., interstitial and centromeric) sites. The signals identified were associated with either ancient rearrangements involved with the formation of the 2n = 22 plesiomorphic macropodine karyotype or more recent rearrangements associated with karyotypes derived from the 2n = 22 karyotype. Interstitial (T(2)AG(3))(n) signals identified on chromosomes 3 and 4 in all six species of the lateralis complex and a large centromeric signal identified on chromosome 7 in the five subspecies/races of P. lateralis appear to be related to the more ancient rearrangements. Subsequent chromosome evolution has seen these signals retained, lost, or amplified in different Petrogale lineages. Within the lateralis complex, in two submetacentric chromosome derived by recent centric fusions, the telomeric sequence was identified at or near the centromere, indicating its retention during the fusion process. In the two taxa where chromosome 3 was rearranged via a recent centromeric transposition to become an acrocentric chromosome, the telomeric signal was located interstitially.