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Supernumerary chromosomes that appear in addition to the standard chromosome set exist in many plant, animal and fungal species (Jones & Rees, 1982). These extra chromosomes have been termed B chromosomes (Bs) while the standard chromosomes are called A chromosomes (As). In most cases Bs do not confer any advantage to the host and can even be detrimental if they exceed a certain number. For instance, rye (Secale cereale) plants are sterile when they harbor eight Bs (Rees & Ayonoadu, 1973). Bs do not follow Mendelian inheritance; instead, they often accumulate by a ‘drive’ mechanism (reviewed in Jones, 1991; Jones & Houben, 2003).
Characterization of sequences residing on Bs might shed light on their origin and evolution. Until recently, few sequence data for Bs were available. Early attempts to elucidate the DNA composition of Bs were mainly based on comparative studies of 0B versus +B genomic DNA (Rimpau & Flavell, 1975; Timmis et al., 1975; Sandery et al., 1990; Wilkes et al., 1995). Later, microdissection (Houben et al., 2001a) and flow-sorting (Martis et al., 2012) allowed reliable isolation of B-derived DNA. Bs of many species contain sequences that originated from one or more As (Houben et al., 2001b; Page et al., 2001; Cheng & Lin, 2003; Bugrov et al., 2007; Martis et al., 2012). Even sequences considered as B-specific are also present on As but at low copy number, indicating an intraspecific origin of the B.
As selfish entities, Bs take a distinct path of evolution, and their sequence composition may differ from that of the As. Because Bs are not under selective pressure, mobile elements and other repeats may easily spread and amplify, as in Bs of maize (Zea mays) (Lamb et al., 2007), Brachycome dichromosomatica (Houben et al., 2001b) and Plantago (Dhar et al., 2002). Bs replicating later than As have been shown in the black rat Rattus rattus (Raman & Sharma, 1974), the fox Vulpes fulvus (Świtoński et al., 1987), the fish Astyanax scabripinnis (Maistro et al., 1992) and the frog Gastrotheca espeletia (Schmid et al., 2002), although heterochromatic micro-Bs of B. dichromosomatica replicate during the entire S-phase (Marschner et al., 2007).
The non-Mendelian accumulation of the rye B by nondisjunction requires factors located at the end of its long arm and at the extended pericentromere (Müntzing, 1948; Håkanson, 1959; Endo et al., 2008; Banaei-Moghaddam et al., 2012). Two B-specific repeat families, E3900 (Blunden et al., 1993) and D1100 (Sandery et al., 1990), reside in the long-arm terminal nondisjunction control region. Both sequences, although heterochromatic, are associated with the euchromatin-specific histone mark H3K4me3 (Carchilan et al., 2007) and transcribe nonconding RNA in anthers, which might be involved in the nondisjunction process.
Rye Bs of c. 560 Mbp (Martis et al., 2012) have been found in accessions from many parts of the world. They are probably of monophyletic origin and similar to those of Secale segetale and Secale ancestrale (Niwa & Sakamoto, 1995). However, no Bs are known from older rye species such as Secale strictum or Secale sylvestre. Thus, the origin of the rye B might be linked to the divergence of the S. cereale clade from S. strictum (Martis et al., 2012).
Employing next-generation sequencing, we determined the DNA composition of flow-sorted rye Bs and As (Martis et al., 2012). The age of rye Bs was estimated to be c. 1.1–1.3 million yr. Thus, the rye B originated during or shortly after the radiation of the genus Secale (1.7 million yr ago). We proposed that rye Bs are descended from rearrangements of chromosomes 3RS and 7R, with subsequent accumulation of repeats and genic fragments from other A chromosomal regions, as well as insertions of organellar DNA (Martis et al., 2012).
Because of the dispensable nature of the Bs, their non-Mendelian inheritance, and their origin from As, one might assume that the B followed a different evolutionary pathway from the As, this being reflected in differences in their high-copy DNA constitution. Here we provide insight into the composition and distribution of rye B-located high-copy sequences and show that Bs contain a similar proportion of repeats to As, but differ substantially in repeat composition. Although the overall mobile element content is similar, we found a massive accumulation of B-enriched repeats, mostly in the nondisjunction control region at the terminal part of the long arm, which is transcriptionally active and very late replicating, as well as in the extended pericentromere.