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Characterization of the complete chloroplast genome of Davidia involucrata Baill. (Nysssaceae), an endangered species endemic to China.

ABSTRACT: Davidia involucrata Baill. is a kind of tertiary paleotropical plant floristic relic species unique to China. This rare plant is disappearing due to poor adaptability and serious poaching. We first assembled the complete chloroplast (cp) genome of Davidia involucrata Baill. by Illumina paired-end reads data. The whole genome was 169,085 bp, consisting of a pair of inverted repeats of 169,379 bp, large single copy region and a small single copy region (96,712 and 67,667 bp in length, respectively). The cp genome contained 90 genes, including 64 protein-coding genes, 22 trRNA genes and 4 rRNA genes. The overall GC content of the whole genome was 38.04%. A neighbor-joining phylogenetic analysis demonstrated a close relationship between Davidia involucrata Baill. and Nyssa yunnanensis.

SUBMITTER: Qi Z

PROVIDER: S-EPMC7748617 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of Davidia involucrata.

Project description:Davidia involucrata Baill. is a kind of tertiary paleotropical plant floristic relic species unique to China. This rare plant is disappearing due to poor adaptability and serious poaching. Davidia involucrata has been listed as a national first-level protected wild plant, a unique genus plant unique to China, a relic plant, and a well-known ornamental plant in the world. It is a national-level protected plant. In this study, the complete chloroplast genome sequence of D. involucrata was characterized from Illumina pair-end sequencing. The chloroplast genome of D. involucrata was 158,118 bp in length, containing a large single-copy (LSC) region of 87,329 bp, a small single-copy (SSC) region of 18,869 bp, and two inverted repeat (IR) regions of 25,960 bp. The overall GC content is 37.80%, while the corresponding values of the LSC, SSC, and IR regions are 36.0%, 31.6%, and 43.1%, respectively. The genome contains 132 complete genes, including 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete chloroplast genomes showed that D. involucrata and Camptotheca acuminate clustered together as sisters to other related species.

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Characterization of the complete chloroplast genome of Alsophila spinulosa, an endangered species endemic to China.

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Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill.

Project description:Davidia involucrata Baill. is a rare plant endemic to China. Its exclusive evolutionary position and specific floral organs endow it with a high research value. However, a lack of genomic resources has constrained the study of D. involucrata functional genomics. Here, we report D. involucrata transcriptome reads from different floral tissues pooled from six individuals at two developmental stages using Illumina HiSeq technology and the construction of a high-quality reference gene set containing a total of 104,463 unigenes with an N50 of 1,693 bp and 48,529 high-quality coding sequences. The transcriptome data exhibited 89.24% full-length completeness with respect to the benchmarking universal single-copy (BUSCO) dataset and a PLAZA CoreGF weighted score of 98.85%. In total, 65,534 (62.73%) unigenes were functionally annotated, including 58 transcription factor families and 44,327 simple sequence repeats (SSRs). In addition, 96 known and 112 novel miRNAs were identified in the parallel small RNA sequencing of each sample. All these high-quality data could provide a valuable annotated gene set for subsequent studies of D. involucrata.

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Characterization of the complete chloroplast genome of Saussurea involuerata (Compositae), an endangered species endemic to China.

Project description:Saussurea involuerata (S. involuerata), a kind of composite and perennial herbage plant, is a rare and precious alpine medicinal plants with high medicinal value, it can regulate human's body and has health care function, therefore attracts attention of many scholars. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of S. involucrata by Illumina paired-end reads data. The whole genome was 152,490 bp, consisting of a pair of inverted repeats of 69,041 bp, large and small single-copy regions of 69,045bp and 18,638 bp in length, respectively. The cp genome contained 134 genes, including 90 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome was 37.7%. A neighbor-joining phylogenetic analysis demonstrated a close relationship between S. involuerata and Arctium lappa.

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Characterization of the complete chloroplast genome of Pinus wangii (Pinaceae), an endangered and endemic species in China.

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Characterization of the complete chloroplast genome of Ginkgo biloba L. (Ginkgoaceae), an endangered species endemic to China.

Project description:Ginkgo biloba L. is the oldest relict plant among the gymnosperms, left after the quaternary glacial movement. There are few living G. biloba and few old trees over a hundred years old. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of G. biloba L. by Illumina paired-end reads data. The whole genome was 156,988 bp, consisting of a pair of inverted repeats of 34,056 bp, large and small single copy regions of 56,819 and 22,763 bp in length, respectively. The cp genome contained 131 genes, including 84 protein-coding genes, 31 trRNA genes and 5 rRNA genes. The overall GC content of the whole genome was 39.6%. A neighbour-joining phylogenetic analysis demonstrated a close relationship between G. biloba L. and Cycas revoluta.

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The complete chloroplast genome of Sauvagesia rhodoleuca, an endangered species endemic to China.

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The complete chloroplast genome of Zelkova schneideriana (Rosales: Ulmaceae), an Endangered species endemic to China.

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