Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)

Abstract

A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and 34,224 fingerprints, onto the O. sativa genome sequence. The level of conservation of each chromosome between the two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene-rich regions. Further, this characteristic enabled localization of heterochromatic and euchromatic regions for each chromosome of both species. The alignment identified 16 locations containing expansions, contractions, inversions, and transpositions. By aligning 40% of the punctata BES on the map, 87% of the punctata FPC map covered 98% of the O. sativa genome sequence. The genome size of O. punctata was estimated to be 8% larger than that of O. sativa with individual chromosome differences of 1.5-16.5%. The sum of expansions and contractions observed in regions .500 kb were similar, suggesting that most of the contractions/ expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged $2 million years ago. C OMPARATIVE genome analysis is proving to be an excellent tool, not only to discover genes and understand their functions, but also to unravel the evolutionary relationships between species. Since related species are derived from recent common ancestors, it comes as no surprise that in both dicots and monocots extensive genetic collinearity was found when related species were mapped using common RFLP probe sets (Bonierbale et al. 1988;Hulbert et al. 1990;Ahn and Tanksley 1993;Jena et al. 1994). While extensive collinearity seems to be limited to the genus level among dicots (Tanksley et al.1988), sufficient collinearity exists to allow rough alignment of genetic maps across entire genomes throughout the entire cereal clade (Moore et al. 1995). The complete sequences of the model organisms Arabidopsis and rice (Arabi- Although rice is considered a model plant and placed at the center of the cereal crop syntenic circle (Moore et al. 1995; Gale and Devos 1998a,b;Devos 2005), only a few genomewide comparative analyses as yet have been performed using the rice genome sequence as a reference. The sorghum genome was compared to the rice genome sequence using two sorghum physical maps integrated with genetic markers and BAC hybridization data (Bowers et al. 2005). Various local rearrangements between other cereals and rice have been reported in sequence-level comparisons using the rice genome sequence as the reference (Chen et al. 1998;Goff et al. 2002;Bennetzen and Ma 2003;Sorrells Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. CW502583-CW509125, CW514009-539178, CW620733-CW624836, CW628185-633039, CW672722-CW676096, CW691361-692844, CW748472-CW754418, CW775494-CW77843...

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

“…As a first step toward a deeper evolutionary understanding of the genus, we developed a large array of publicly available genomic tools from BAC libraries 9,10 and BAC-end sequences to physical maps 11,12 and subgenome assemblies 13 . Comparisons of select orthologous regions have addressed the origin and evolutionary fate of genes [14][15][16] , as well as transposable element (TE) dynamics [17][18][19][20][21][22] and the effects of polyploidy 22,23 .…”

The Future of Rice Genomics: Sequencing the Collective Oryza Genome

“…The result of this Oryza Map Alignment Project (OMAP) was a set of bacterial artificial chromosome (BAC)-based physical maps (i.e., BAC libraries SNaPshot fingerprinted/BAC end sequenced (BES)/(Finger Printed Contigs (FPC) assembled) from 13 Oryza species (four AA genome types, and a single representative species of the nine other genome types [i.e., BB, CC, BBCC, CCDD, EE, FF, HHJJ, KKLL, and GG]) aligned to the rice reference genome (Rice Chromosome 3 Sequencing Consortium 2005; Ammiraju et al 2006;Kim et al 2007Kim et al , 2008Wing et al 2007;Goicoechea 2009). In addition, we generated five chromosome 3 short arm (Chr3S) RefSeqs with Sanger sequencing (i.e., genome types-AA, BB, CC, and BBCC), and three more using second generation sequencing methods (two AA and one FF).…”

Global Genomic Diversity of Oryza sativa Varieties Revealed by Comparative Physical Mapping

“…For insert sizing, 220 clones of each library were randomly selected, and the plasmids were restricted with NotI and analyzed on 1% agarose CHEF gels (Bio-Rad, Hercules, CA) with a 5-to 15-sec linear ramp time at 6 V/cm and 14°in 0.53 TBE buffer for 16 hr. BAC end sequencing and fingerprinting were performed following previous protocols Kim et al 2007;Lin et al 2012;. BESs with a quality score less than Phred 16 or total length ,100 bp were removed.…”

“…The physical maps of MH63 and ZS97 were aligned to reference sequences and displayed by SyMAP (Soderlund et al 2006). The contigs and alignments were manually edited and improved against the Nipponbare reference sequence as described by Kim et al (2007) and Lin et al (2012). …”

“…In other model systems, analyses of genome-wide structural variations have proved to be an effective strategy for uncovering the evolution process and relating the genetic diversity to the given phenotypes (Zhao et al 2004;Tuzun et al 2005;Kidd et al 2008;Nicholas et al 2009;Springer et al 2009;Zhang et al 2011). The BAC libraries, BESs, physical maps of MH63 and ZS97, and the integrated information provided here are invaluable resources for inter-and intra-subspecies genome-wide comparative analysis in O. sativa.The studies from OMAP shed light on the genome-wide structural variations between Nipponbare and wild rice species (Kim et al 2007(Kim et al , 2008Hurwitz et al 2010). Previously we constructed the physical maps of ZH11 and 93-11 and compared them with the Nipponbare and 93-11 reference sequences (Lin et al 2012;Pan et al 2013).…”