The Organization of the Plastid Chromosome
The first restriction maps of plastid DNAs showed the chloroplast chromosomes of maize［14，15］and of spinach［16］to be made up of two large inverted repeated segments separated by two regions of unique sequences.A number of plastid chloroplast chromosomes have been analyzed since then by electron microscopy［17］as well as by restriction endonuclease restriction site mapping.To date only those of pea and broad bean have been found to lack a pair of inverted repeated segments［18，19］and the chloroplast chromosome of Euglena gracilis is unique among those studied to date in containing three comparatively small repeated segments plus part of a repeaccd sequence that occurs still another time［20-22］.
The inverted repeated segments in maize were shown to contain copies of genes for 16S，23S，and 5S rRNAs［14，15］.These genes were mapped in detail by Southern［23］hybridization，heteroduplex mapping，and by R-Looping［24］.Besides establishing that the inverted repeats are 22 kbp（kilobase pairs）in length and showing the order of these genes on the chromosome to be 16，23，and 5S rRNA，it was determined that the genes for the two larger RNAs are separated by an intervening sequence of about 2，100 bp.This intervening region was subsequently shown to contain genes for alanine and isoleucine tRNAs［25］.The large inverted repeats of maize also contain a number of tRNAs that lie outside of the rRNA coding regions［26-28］as well as at least one UORF（unidentified open reading frame）.
The large repeated sequences in other plastid DNAs and the smaller tandemly repeated DNA sequences in Euglena have now been shown to also contain rRNA genes although these genes have generally not been mapped as precisely in the other higher plant chromosomes as they have been in maize，Chlamydomonas or Euglena（In maize，besides the mapping described above，the regions containing the 16 and 23S rDNAs plus the intervening sequence have been sequenced by Kossel and coworkers［25，29，30］.）(https://www.daowen.com)
Genes for plastid tRNAs have been assigned to restriction fragments of spinach［31］and maize［28］.Although fewer tRNA genes have been identified than are expected to be present（from consideration of codon usage and comparisons with other cases），it seems likely that plastid chromosomes contain genes for a complete set.It is interesting that the distribution of tRNA genes between the inverted repeated and the unique sequence regions is different in maize and spinach chloroplast chromosomes.The tRNAHisgene of maize is near a border inside each of the inverted repeats［26，28］；in the spinach chromosome there is one copy of this gene and it is in the large unique region，ie，outside of the inverted repeats，but near the edge of one of its inverted repeats［31］.A gene for leucine tRNA is in the unique region of maize but is in the inverted repeats of spinach.In a formal sense，rearrangements of this sort can be imagined to occur，at least in part，by movements of the tRNA genes into or out of the inverted repeats or by migration of the ends of the inverted repeats.It seems unlikely that the ends of both inverted repeats would migrate to precisely corresponding positions on the chromosome or that tRNA genes would simultaneously insert at exactly the same points in both of the inverted repeats；thus one must imagine that each event occurred one time（for each change）and was then copied into the second repeat or one of the repeats was lost.Any DNA sequence included between the borders of an inverted repeat is repeated.The genetic mechanism for repetition is not known but it seems that plastids can survive without it，as is seen in peas and broad beans.The rearrangement of large segments of plastid chromosome in relation to phylogeny has been addressed［19］.The relative locations of tRNA genes may provide useful information for phylogenetic analyses at different levels.
