Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Camellia sinensis sp. Baihaozao

Chen, Z.; College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology,; Zhu, Y.; Demonstration Base for Innovation and Entrepreneurship in the Efficient Utilization of Local Charact,; He, Z.; Tea Research Institute, Hunan Academy of Agricultural Sciences,; Li, H.; Taohuayuan Agricultural Development Co., Ltd.,; Huang, J.; Gong, Y.

doi:10.1101/2024.08.27.609997

bioRxiv · 10.1101/2024.08.27.609997

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Camellia sinensis sp. Baihaozao

Chen, Z.·College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology,·Zhu, Y.·Demonstration Base for Innovation and Entrepreneurship in the Efficient Utilization of Local Charact,·He, Z.·Tea Research Institute, Hunan Academy of Agricultural Sciences,·Li, H.·Taohuayuan Agricultural Development Co., Ltd.,·Huang, J.·Gong, Y.

View original source ↗Export metadata ↓

Abstract

Baihaozao (Camellia sinensis sp. Baihaozao) is esteemed in the domain of tea plant cultivation for its early harvest period, profusion of bud trichomes, and exceptional suitability for tea processing. Nevertheless, the intricate phylogenetic relationships among species within this genus remain ambiguous, primarily due to the limited availability of genomic data. This study endeavors to comprehensively investigate the genomic resources of Baihaozao by sequencing, assembling, and annotating its entire chloroplast (cp) genome. The sequencing results indicated that the total length of the Baihaozao cp genome is 157,052 base pairs (bp), with an overall guanine-cytosine (GC) content of 37.30%. The genome exhibits a typical quadripartite structure, consisting of a large single-copy region (LSC) of 86,586 bp, a small single-copy region (SSC) of 18,227 bp, and a pair of inverted repeats (IRs) totaling 52,162 bp. A total of 133 genes were identified within this genome, including 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, 87 protein-coding genes, and 1 pseudogene. Furthermore, the study identified 157 simple sequence repeats (SSRs) and 90 long repeat sequences. Analysis of codon usage bias indicated that codons encoding leucine (Leu) were the most frequently utilized, whereas those encoding cysteine (Cys) were the least utilized. Examination of nucleotide diversity within the Baihaozao cp genome revealed five highly variable regions with elevated Pi values (rps19, rpl32, ndhF, rpl22, matK), suggesting their potential utility as molecular markers. Phylogenetic analysis of 20 cp genomes of the Theaceae family indicated a close evolutionary relationship between Baihaozao and Camellia sinensis OL450428.1. This study not only provides valuable data support for elucidating the maternal origin of cultivated Camellia species but also holds significant scientific implications for further exploring the phylogenetic relationships and germplasm resource utilization of Camellia plants.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Chen, Z., College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology,, Zhu, Y., Demonstration Base for Innovation and Entrepreneurship in the Efficient Utilization of Local Charact,, He, Z., Tea Research Institute, Hunan Academy of Agricultural Sciences,, Li, H., Taohuayuan Agricultural Development Co., Ltd.,, Huang, J., Gong, Y.. 2024-08-28. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Camellia sinensis sp. Baihaozao. https://doi.org/10.1101/2024.08.27.609997

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗

bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗

bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗