"... In PAGE 13: ... Comparisons with other Nonphotosynthetic Lineages Despite some differences in patterns of evolution, many parallels exist between plastid genome evolution in Cus- cuta and that of the related but independently derived par- asitic lineage Orobanchaceae, including Epifagus. Both lineages show overall increased rates of nucleotide substi- tution, relaxed selective constraint, and lack any apprecia- ble shift in synonymous codon usage in spite of loss of multiple tRNAs [46]( Table5 ). Substantial gene loss is observed in both lineages; in addition to sharing loss of all ndh and rpo genes with C.... In PAGE 19: ... Due to difference in genome content, the total number of codons was different for all taxa. Table5... ..."

"... In PAGE 2: ... In total, using ADHoRe, we detected 105 cases of micro- colinearity between Arabidopsis and rice before removing nonsignificant colinear regions, from which 75 are between individual rice BACs and a segment of the Arabidopsis genome and 30 are between overlapping rice clones and an Arabidopsis genomic segment. Applying the default 99% cut-off level, which retains all colinear regions that have a probability to be generated by chance of lt;1%, 24 segments showing conserved gene content and order between Arabidopsis and rice remain (listed in Table1 ). Of these statistically significant regions, 18 (69%) show colinearity between an individual rice BAC and an Arabidopsis genomic segment, whereas 8 (31%) show co- linearity between Arabidopsis and overlapping rice BACs.... ..."

"... In PAGE 5: ... Although it is well known that transcript sequence data are the most important re- source in the gene identification, we were interested in ascertain- ing the contribution of the Poaceae (excluding rice) TAs and maize/sorghum genomic sequences relative to the rice TAs in providing support for genome annotation. Not surprisingly, the rice TA data set yielded the best contribution among the three major Poaceae data resources (Table3 ). Interestingly, the non- rice Poaceae TAs had a comparable number of rice homologs as the maize and sorghum genome assemblies, suggesting broad representation of the Poaceae transcriptome in the collective Poaceae TA data set.... ..."

"... In PAGE 10: ... In genes with cis-element more than one element in total number of each type of element, we showed cis- element profile of 116 (rice) and 94 (Arabidopsis) clones in Supplemental Tables S6 and S7, respectively. The results of comparison between 116 clones responsive to ABA in rice and 94 clones of corresponding Arabidopsis genes are summarized in Table5 . From all detected cis-elements, we selected cis- elements for determination of specific elements that were present in at least two genes in either species and specific element were more than H110062-fold in the ratio of (rice/Arabi- dopsis).... In PAGE 12: ...species. Six kinds of cis-elements for dehydration-stress re- sponse (ACGTATERD1, MYB1AT, ABRELATERD1, MYB2CONSENSUSAT, MYCATERD1, MYCCONSEN- SUSAT) were specified as elements in Arabidopsis (italic characters in cis-element column in Table5 ). The speci- ficities of Arabidopsis cis-elements for dehydration stress might be derived from differences in the growth environ- ments of each species.... In PAGE 12: ... These six kinds of elements do not exist in rice. However, the number of cis-elements for protein storage was remarkably rich in both species ( com- mon in specificorcommon column in Table5 ), and the number of other elements for protein storage (H11002300ELE- MENT, RYREPEATGMGY2, RYREPEATLEGUMIN- BOX, RYREPEATBNNAPA) were richer in the upstream regions of genes of rice than in those of Arabidopsis.We suggest that Arabidopsis might use these conserved ele- ments for protein storage.... In PAGE 13: ...for expression of the amylase gene (CGACGOSAMY3) was specified as an element in rice may suggest the view that the difference in these elements is derived from differences in organization between rice and Arabidopsis. Although the cis-element MYBCORE for water-stress response appears in both species as a common cis-element in Table5 , the number of elements in rice was 1.34 times that in Arabi- dopsis.... In PAGE 13: ... These results suggest that rice might use a slightly different mechanism for response to water stress. Two kinds of ABA-responsive element (RAV1AAT, DPBFCORED- CDC3) and one GA-responsive element (DOFCOREZM) were rich in cis-elements conserved between rice and Ara- bidopsis ( common in specificorcommon column in Table5 ). We suggest that each species might have a com- mon pathway for ABA or GA metabolism.... ..."

"... In PAGE 5: ...Table4 . Those ESTs that exhibit an abundance of 10 or more are considered here.... ..."

"... In PAGE 6: ... For many microbial genomes, the algorithm that has hitherto been employed is GeneMark. Comparison with existing annotation, for example, shows that in the plastid-like genome GeneScan pre- dicted about 90% of the genes and 50% of hypotheti- cal ORFs correctly with the overall accuracy of 80% (see Table4 ). In M.... ..."