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      Organization of chloroplast psbA-trnH intergenic spacer in dicotyledonous angiosperms of the family Umbelliferae.

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          Abstract

          Chloroplast intergenic psbA-trnH spacer has recently become a popular tool in plant molecular phylogenetic studies at low taxonomic level and as suitable for DNA barcoding studies. In present work, we studied the organization of psbA-trnH in the large family Umbelliferae and its potential as a DNA barcode and phylogenetic marker in this family. Organization of the spacer in Umbelliferae is consistent with a general pattern evident for angiosperms. The 5'-region of the spacer situated directly after the psbA gene is more conserved in length compared to the 3'-region, which has greater sequence variation. This pattern can be attributed to the maintenance of the secondary structural elements in the 5'-region of the spacer needed for posttranscriptional regulation of psbA gene expression. In Umbelliferae only, the conserved region contains a duplication of the fragment corresponding to the loop of the stem-loop structure and an independent appearance of identical sequence complementarities (traits) necessary to stabilize the stem-loop structure in different lineages. The 3'-region of the spacer nearest to trnH ranges greatly in size, mainly due to deletions, and the decrease in spacer length is a general trend in the evolution psbA-trnH in Umbelliferae. The features revealed in spacer organization allow us to use it as phylogenetic marker, and indels seem to be more informative for analyses than nucleotide substitutions. However, high conservation among closely related taxa and occurrence of homoplastic inversions in the stem-loop structure limit its application as DNA barcode.

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          Author and article information

          Journal
          Biochemistry (Mosc)
          Biochemistry. Biokhimiia
          Pleiades Publishing Ltd
          1608-3040
          0006-2979
          Sep 2012
          : 77
          : 9
          Affiliations
          [1 ] Botanical Garden, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia.
          Article
          BCM77091273
          10.1134/S0006297912090131
          23157266
          d01a3d34-9994-4b75-866f-523a7bae1545
          History

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