The complete chloroplast genome sequence of Hippeastrum rutilum (Amaryllidoideae).
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ABSTRACT:
SUBMITTER: Huang B
PROVIDER: S-EPMC7782897 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Hippeastrum vittatum (L'Hér.) Herb. is a perennial herb in the Amaryllidaceae, which has been used as a medicinal and ornamental plant. Here, we assembled and characterized the complete chloroplast (cp) genome of H. vittatum by high throughput sequencing. As a result, the length of the complete cp genome is 158,082 bp with a canonical quadripartite structure, consists of a large single-copy region (LSC) of 86,165 bp, a small single-copy region (SSC) of 18,283 bp, and two inverted repeat (IR) regions of 26,817 bp, each. A total of 137 genes were identified, including 87 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. The phylogenomic analysis was performed based on the complete cp genomes of 30 species, which revealed the closest relationship between H. vittatum and H. rutilum in the genus Hippeastrum.
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Project description:Hippeastrum is a genus of ornamental plants with large, brightly colored flowers. Due to the very high seed-setting rate of the hybridization of Hippeastrum, the large population of hybrid progeny and the existence of superparent inheritance, it is difficult to trace the origin of the varieties collected from the market during breeding. In this study, we analyzed the chloroplast genomes of Hippeastrum 'Milady', H. alberti, and H. reticulatum using the Illumina NovaSeq sequencing platform and generated full-length sequences of 158,067, 158,067, and 158,522 bp, respectively. All three genomes had the typical tetrad structure. The large single copy, small single copy, and inverted repeat regions of H. reticulatum were observed to be respectively 277, 138, and 20 bp longer than the corresponding regions of H. 'Milady' and H. alberti. The results of comparative analysis of simple sequence repeats (SSRs), Ka/Ks ratios, codon preferences, and complete sequences of chloroplasts of these three taxa and 14 other plant species were as follows. First, the chloroplast genomes of H. 'Milady', H. alberti, and H. reticulatum contain 209, 209, and 211 SSR sites, respectively, most of which (123, 123, and 122, respectively) are single nucleotide repeats. Second, leucine, arginine, and serine are the most frequently used amino acids in the three chloroplast genomes. Third, H. 'Milady', H. alberti, and H. reticulatum are more closely related to Lycoris and Narcissus than to Allium and Agapanthus. Our results will provide information on the study of origins or relatedness of native species, and the identification of cultivars.
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Project description:Hippeastrum rutilum (Ker-Gawl.) Herb. is a high-end ornamental flower in the family Amaryllidaceae. In this study, the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. was determined from Illumina pair-end sequencing data. The sequencing results indicated the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. 162,696 base pairs (bp) in length, including one large single-copy region (LSC, 86,933 bp), one small single-copy region (SSC, 5418 bp), and a pair of inverted repeat regions (IRs) of 34,932 bp. Besides, the complete chloroplast genome contained 128 genes, including 82 protein-coding genes, 38 tRNA, and 8 rRNA. The phylogenetic analysis suggested that H. rutilum (Ker-Gawl.) Herb. is closely related to H. rutilum. The complete chloroplast genome sequencing results will provide a reference for the further investigation and research of H. rutilum (Ker-Gawl.) Herb.
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Project description:The first complete chloroplast genome of Amomum villosum (Zingiberaceae) was reported in this study. The A. villosum genome was 163,608 bp in length, and comprised a pair of inverted repeat (IR) regions of 29,820 bp each, a large single-copy (LSC) region of 88,680 bp, and a small single-copy (SSC) region of 15,288 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and 8 rRNA genes (4 rRNA species). The overall AT content was 63.92%. Phylogenetic analysis showed that A. villosum was closely related to two species Amomum kravanh and Amomum compactum within the genus Amomum in family Zingiberaceae.
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Project description:The first complete chloroplast genome of Hedychium coronarium (Zingiberaceae) was reported in this study. The H. coronarium chloroplast genome was 163,949 bp in length and comprised a pair of inverted repeat (IR) regions of 29,780 bp each, a large single-copy (LSC) region of 88,581 bp and a small single-copy (SSC) region of 15,808 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and eight rRNA genes (four rRNA species). The nucleotide composition was asymmetric (31.68% A, 18.35% C, 17.74% G, 32.23% T) with an overall AT content of 63.92%. Phylogenetic analysis showed that H. coronarium was classified into a monophyletic group within the genus Hedychium in family Zingiberaceae.
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Project description:Kosteletzkya pentacarpos is a promising plant being developed as a salt-tolerant biofuel crop that also the ability to fix heavy metals. Here, high-throughput sequencing technology was used to sequence and assemble the chloroplast genome of K. pentacarpos. The full length of the chloroplast genome is 161,777 bp, comprising a large single-copy region of 90,019 bp, a small single-copy region of 18,978 bp, and a pair of inverted repeats of 26,390 bp. A total of 113 genes were annotated, including 79 protein-coding, 30 transfer RNA, and 4 ribosomal RNA genes. Phylogenetic analysis based on whole chloroplast genome sequences showed that K. pentacarpos has a close relationship with Abelmoschus in Malvaceae. This study increases the available genomic information on K. pentacarpos, and provides a basis for the rational exploitation and utilization of germplasm resources.
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Project description:Prunus mahaleb (L.) Mill. is a kind of ornamental species which originated from Europe and Western Asia. Here, we use Illumina paired-end sequencing to obtain the complete chloroplast genome of P. mahaleb. The complete cp genome of P. mahaleb with a size of 157,824 bp in length is a circular molecular genome, including a pair of inverted repeat (IR) region of 26,410 bp each, separated by a large single copy (LSC) region of 85,926 bp and a small single-copy (SSC) region of 19,078 bp. The genome consisted of 129 genes, including 84 protein-codon genes (PCGs), 37 tRNA genes, and eight rRNA genes. The GC content of the whole chloroplast genome is 36.7%. Phylogenetic analysis revealed that P. mahaleb was the closest related to P. cerasoides and P. maximowiczii.
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Project description:Artabotrys pilosus (Annonaceae) is endemic to China, this plant has high medicinal value and broad application prospect. In this study, we assembled and systematically analyzed the chloroplast genome of A. pilosus on the basis of DNA sequencing using high-throughput techniques. The chloroplast sequence of A. pilosus was 178,195 bp in length, including two inverted repeat regions of 42,150 bp, a large single-copy region of 90,797 bp and a small single-copy region of 3098 bp. It was predicted to contain 142 genes, of which 96 are coding, 38 are tRNA genes, and eight are rRNA genes. The overall GC content was 38.8%; this was higher in the IRs (40.4%) when compared to the LSC (37.6%) and the SSC (32%) regions. Phylogenetic analysis showed that A. pilosus is in subfamily Annonoideae.
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Project description:Erigeron breviscapus is a famous medicinal plant. However, the limited chloroplast genome information of E. breviscapus, especially for the chloroplast DNA sequence resources, has hindered the study of E. breviscapus chloroplast genome transformation. Here, the complete chloroplast (cp) genome of E. breviscapus was reported. This genome was 152,164bp in length, included 37.2% GC content and was structurally arranged into two 24,699bp inverted repeats (IRs) and two single-copy areas. The sizes of the large single-copy region and the small single-copy region were 84,657 and 18,109bp, respectively. The E. breviscapus cp genome consisted of 127 coding genes, including 83 protein coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For those genes, 95 genes were single copy genes and 16 genes were duplicated in two inverted regions with seven tRNAs, four rRNAs, and five protein coding genes. Then, genomic DNA of E. breviscapus was used as a template, and the endogenous 5' and 3' flanking sequences of the trnI gene and trnA gene were selected as homologous recombinant fragments in vector construction and cloned through PCR. The endogenous 5' flanking sequences of the psbA gene and rrn16S gene, the endogenous 3' flanking sequences of the psbA gene, rbcL gene, and rps16 gene and one sequence element from the psbN-psbH chloroplast operon were cloned, and certain chloroplast regulatory elements were identified. Two homologous recombination fragments and all of these elements were constructed into the cloning vector pBluescript SK (+) to yield a series of chloroplast expression vectors, which harbored the reporter gene EGFP and the selectable marker aadA gene. After identification, the chloroplast expression vectors were transformed into Escherichia coli and the function of predicted regulatory elements was confirmed by a spectinomycin resistance test and fluorescence intensity measurement. The results indicated that aadA gene and EGFP gene were efficiently expressed under the regulation of predicted regulatory elements and the chloroplast expression vector had been successfully constructed, thereby providing a solid foundation for establishing subsequent E. breviscapus chloroplast transformation system and genetic improvement of E. breviscapus.
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