Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
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An endemic endangered species, Aster altaicus var. uchiyamae (Danyang aster) B2015-0044, is cultivated at the Shingu Botanical Garden, which serves as the ex situ conservation institution for this species. In this work, we sequenced the chloroplast genome of A. altaicus var. uchiyamae B2015-0044. We found that the chloroplast (cp) genome of B2015-0044 was 152,457 base pairs (bps) in size: 84,247 bps of large single copy regions (LSC), 25,007 bps of inverted repeats (IRs), and 18,196 bps of small single copy regions. The B2015-0044 cp genome contains 79 protein-coding genes (PCGs), 4 RNA genes, 29 tRNA genes, and 3 pseudogenes. These results were identical to a previously reported cp genome (Park et al., 2017), except for two sites in introns and three in intergenic spacer (IGS) regions. For the intronic differences, we found that clpP.i1 had a 1-bp small simple repeat (SSR) (T) and petD.i had a 3-bp SSR (ATT). We found 1-bp SSRs in the IGSs of trnT_ggu~psbD and psbZ~trnG_gcc, C and A, respectively. The IGS of (ndhF)~rpl32 had a SNP. Based on our results, the cp genome of the A. altaicus var. uchiyamae can be classified into two genotypes, [C]1-[A]12-[T]12-[ATT]4-C and [C]2-[A]11-[T]11-[ATT]2-A.
Abstract
An endemic endangered species, Aster altaicus var. uchiyamae (Danyang aster) B2015-0044, is cultivated at the Shingu Botanical Garden, which serves as the ex situ conservation institution for this species. In this work, we sequenced the chloroplast genome of A. altaicus var. uchiyamae B2015-0044. We found that the chloroplast (cp) genome of B2015-0044 was 152,457 base pairs (bps) in size: 84,247 bps of large single copy regions (LSC), 25,007 bps of inverted repeats (IRs), and 18,196 bps of small single copy regions. The B2015-0044 cp genome contains 79 protein-coding genes (PCGs), 4 RNA genes, 29 tRNA genes, and 3 pseudogenes. These results were identical to a previously reported cp genome (Park et al., 2017), except for two sites in introns and three in intergenic spacer (IGS) regions. For the intronic differences, we found that clpP.i1 had a 1-bp small simple repeat (SSR) (T) and petD.i had a 3-bp SSR (ATT). We found 1-bp SSRs in the IGSs of trnT_ggu~psbD and psbZ~trnG_gcc, C and A, respectively. The IGS of (ndhF)~rpl32 had a SNP. Based on our results, the cp genome of the A. altaicus var. uchiyamae can be classified into two genotypes, [C]1-[A]12-[T]12-[ATT]4-C and [C]2-[A]11-[T]11-[ATT]2-A.
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