Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Abstract

Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.

Polyploidization increases meiotic recombination frequency in Arabidopsis

“…Although the assay used here is restricted to quantifying recombination rates between a specific marker pair, it is unlikely that the segment defined by this pair represents an exceptional region of the genome. The markers encompass 5 Mb, approximately 20% of chromosome 3, outside of the centromere [17] and can be considered as typical of the euchromatin fraction of the Arabidopsis genome. Moreover, a region of this size is expected to include several recombinational hot and cold spots and thereby balance most of the local fluctuations in MRFs that have been reported across the Arabidopsis chromosomes [18].…”

Comparative transcriptome analysis of wheat embryo and endosperm responses to ABA and H2O2 stresses during seed germination

“…According to our results, only CA602902 was expressed in embryo and endosperm (Tables 1 and 2 ). The CA602902 gene was involved in biotic stress responses, and similar genes (prp4, At3g19690, Os07g0129200) have been found in maize [ 45 ], Arabidopsis [ 46 ], and rice [ 47 ].…”

Expression of four phosphate transporter genes from Finger millet (Eleusine coracana L.) in response to mycorrhizal colonization and Pi stress

“…The branch lengths are proportional to the phylogenetic distances. The sequences of Oryza sativa (Paszkowski et al 2002) , Zea mays (Alexandrov et al 2009; Schnable et al 2009) and Arabidopsis thaliana (Erfle et al 2000; Mayer et al 1999) phosphate transporter genes have accession number as OsPT1 (Q8H6H4), OsPT2 (Q8GSD9), OsPT3 (AAN39044), OsPT4 (Q01MW8), OsPT5 (AAN39046), OsPT6 (NP_001062527), OsPT7 (AAN39048), OsPT8 (AAN39049) OsPT9 (AAN39050), OsPT10 (AAN39051), OsPT11 (AAN39052), OsPT12 (AAN39053), OsPT13 (AAN39054), GRMZM2G070087 (NM_001196972), GRMZM2G326707 (NM_001279426), GRMZM2G154090 (NP_001105816), GRMZM2G112377 (NP_001105817), GRMZM2G045473 (NP_001132684), GRMZM2G075870 (NP_001151202), GRMZM2G139639 (NP_001149892), GRMZM5G881088 (NP_001105776), GRMZM2G170208 (NP_001266911), GRMZM2G159075 (AFW57855), GRMZM2G041595 (DAA64043), GRMZM2G009779 (XP_008669651), GRMZM2G009800 (DAA38524), AtPT1 (NP_199149), AtPT2 (NP_181428), AtPT3(NP_199150), AtPT5(NP_180842), AtPT6 (NP_199148), AtPT7 (NP_191030), AtPT8 (NP_173510), AtPT9 (NP_177769). The accession number for AtCaM1 is NP_001154755.…”