Guiqi Bi

Indian jujube (Ziziphus mauritiana) holds a prominent position in the global fruit and pharmaceutical markets. Here, we report the assemblies of haplotype-resolved, telomere-to-telomere genomes of autotetraploid wild and cultivated Indian jujube plants using a two-stage assembly strategy. The generation of these genomes permitted in-depth investiga...

The model plant Physcomitrium patens has played a pivotal role in enhancing our comprehension of plant evolution and development. However, the current genome harbours numerous regions that remain unfinished and erroneous. To address these issues, we generated an assembly using Oxford Nanopore reads and Hi-C mapping. The assembly incorporates telome...

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually, a process that can be time-consuming and prone to errors. The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations. The processing of a large number of sequences, howev...

The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 gigabases. Taxus shared an ancestra...

Changes in atmospheric CO2 concentration have played a central role in algal and plant adaptation and evolution. The commercially important red algal genus, Pyropia (Bangiales) appears to have responded to inorganic carbon (Ci) availability by evolving alternating heteromorphic generations that occupy distinct habitats. The leafy gametophyte inhabi...

Dracaena, a number of ornamental plant worldwide, is the only basal plant producing dragon’s blood and has significant economic values. Herein, the complete mitochondrial genomes (mitogenome) of Dracaena sp. C6 and Dracaena sp. CZ2 originating from Guangxi were first assembled. They exhibited a mitogenome structure with multi-partite recombination...

Saccharina japonica has been cultivated in China for almost a century. From Dalian to Fujian, the lowest and the highest seawater temperatures in the period of cultivation increased by 14℃ and 8℃, respectively. Its adaptation to elevated seawater temperature is an example of securing the natural habitats of a species. To decipher the mechanisms und...

Recent study evidence the traditional Chinese medicinal (TCM) plant-derived schaftoside shows promise as a potential drug candidate for COVID-19 treatment. However, the biosynthetic pathway of schaftoside in TCM plants remains unknown. In this study, the genome of the TCM herb Grona styracifolia (Osbeck) H.Ohashi & K.Ohashi (GSO), which is rich in...

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually, a process that can be time-consuming and prone to errors. The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations. The processing of a large number of sequences, howev...

The model plant Physcomitrium patens (P. patens) has played a pivotal role in enhancing our comprehension of plant evolution, growth, and development. However, the current genome harbors numerous intricate regions that remain unfinished and erroneous. To address these issues, we present an exemplary assembly of the P. patens nuclear genome, which i...

In the present study, the whole chloroplast (cp) genome of B. marginata was characterized for the first time and genomic features were comparatively analyzed with six relative species in Ulvales. The cp genome of B. marginata was 170, 562 bp in length, exhibiting similar general structure but different in GC content from Ulva and Pseudendoclonium....

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome‐phasing algorithm, SubPhaser, specifically designed...

Flowering plants (angiosperms) dominate our planet and sustain all life on Earth. However, evolutionary relationships among the angiosperm lineages that diverged early – Amborellales, Nymphaeales, Austrobaileyales and Mesangiospermae, which further comprises monocots and other four clades – have remained highly disputed likely because of their rapi...

Many fungi form persistent and dormant sclerotia with compact hardened mycelia during unfavorable circumstances. While most of these sclerotia are small in size, Wolfiporia cocos, a wood-decay fungus, grows into giant sclerotia, which are mainly composed of polysaccharides of linear (1→3)-β-D-glucans. To explore the underlying mechanism of converti...

The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 Gb. Taxus shared an ancestral whole...

Ulva compressa, known as the green tide forming species, was reported that can adapt to hypo‐salinity conditions such as estuaries and brackish lakes. To understand the underlying molecular mechanisms of hypo‐salinity stress tolerance, a transcriptome‐wide gene expression profiles in U. compressa was performed using digital gene expression profile....

Background: Ulva compressa, known as the green tide forming species, was reported that can adapt to hypo-salinity conditions such as estuaries and brackish lakes. To understand the underlying molecular mechanisms of hypo-salinity stress tolerance, a genome-wide gene expression profiles in U. compressa was performed using digital gene expression pro...

As an economically important alga growing in the intertidal zone, Pyropia yezoensis has the unique characteristics of adapting to high ultraviolet radiation in the open air and to desiccation conditions. In this experiment, light without UV-B radiation was used as a control, and low UV-B radiation of 0.5 W/m2 and high UV-B radiation of 2 W/m2 were...

Pyropia haitanensis (Bangiales, Rhodophyta), a major economically important marine crop, is also considered as an ideal research model of Rhodophyta to address several major biological questions such as sexual reproduction and adaptation to intertidal abiotic stresses. However, comparative genomic analysis to decipher the underlying molecular mecha...

Amentotaxus yunnanensis H. L. Li (Taxaceae) is a threatened plant species and a typical Plant Species with Extremely Small Population (PSESP). In this study, we sequenced the whole chloroplast (cp) genome of A. yunnanensis. The results showed that the plastid genome is 137,594 bp in size. In total, 118 unique genes were annotated, including 83 prot...

Pyropia yezoensis is an economically important marine macroalgae, naturally distributed in the upper intertidal zone. Owing to the nature of its habitat, the thallus will periodically be exposed to seawater or atmosphere, and can lose up to 95% of its cellular water content. This makes the alga an ideal research model to investigate the mechanisms...

The mitogen-activated protein kinase (MAPK) cascade is composed of three hierarchically organized protein kinases (MAP kinase kinase kinases, MAP kinase kinases, and MAPKs) and plays a vital role in regulating developmental processes and stress responses in plants. Pyropia yezoensis belongs to the old Rhodophyta and grows in intertidal zones. Altho...

Red algae are important primary photosynthetic organisms. The Bangiales comprise a morphologically diverse order of red algae. Until now, complete plastid genomes of the Bangiales were only mapped for foliose species. To date, no filamentous plastomes have been published. The aim of this study was to determine and analyze the complete plastid genom...

Background: Pyropia yezoensis, a marine red alga, is an ideal research model for studying the mechanisms of abiotic stress tolerance in intertidal seaweed. Real-time quantitative polymerase chain reaction (RT-qPCR) is the most commonly used method to analyze gene expression levels. To accurately quantify gene expression, selection and validation o...

Bangia fuscopurpurea is a traditional mariculture crop having high nutritional value, eicosapntemacnioc acid (EPA) production, and protein content. As an intertidal species, it can tolerate drastic changes in abiotic factors such as temperature, hydration, and light radiation; however, genomic information on the evolutionary aspect and mechanism of...

Phylogenetic relationships between the predicted desaturases of B. fuscopurpurea and that from other desaturase genes. (TIF)

List of organisms and desaturase protein sequences. (DOC)

RIN quality values for RNAs used for qPCR gene expression. (DOC)

Primers of the 12 B. fuscopurpurea genes used for quantitative real-time PCR analysis. (DOC)

Annotation results of B. fuscopurpurea genes/proteins based on different databases. (DOC)

The 273 unigenes related to fatty acid biosynthesis pathways. (DOC)

Various stress-treated B. fuscopurpurea samples used for transcriptome sequencing. (DOC)

The macroscopic and microscopic photos of Bangia fuscopurpurea gametophytes. (TIF)

The Arrau River turtle (Podocnemis expansa) is one of the largest side-neck turtles which listed as an endangered species in IUCN red list. In this study, the complete mitochondrial genome of P. expansa was determined by the sequencing of PCR fragments. The complete mitochondrial genome of P. expansa was 16,520 bp in length and encoded 13 protein-c...

Prunus serotina, with high wildlife value, is a tree with edible fruits that is native to North America. In this study, the complete chloroplast (cp) genome of Prunus serotina (Amygdaleae) was determined through Illumina sequencing method. The complete chloroplast genome of P. serotina was 158,788 bp in length and contained a pair of IR regions (26...

In this study, we presented the complete mitochondrial genome of Fusarium sp. It has a total length of 47, 74 bp, and the base composition of the mitogenome is as follows: A (34.1%), T (33.5%), C (14.7%), and G (17.7%). The mitogenome contains 23 protein-coding genes, 1 ribosomal RNA (rRNA), and 26 transfer RNA (tRNA) genes, all coded on the same s...

Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeli...

Nautilus pompilius has been listed as an endangered species by CITES due to low fecundity and overfishing. In this study, its whole circular mitochondrial genome (15,693 bp) was determined by polymerase chain reaction method. It contained the typical mitogenome gene set of 22 tRNAs, 13 protein coding genes (NAD1-6, NAD4L, COX1-3, Cob, ATP6 and ATP8...

Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes (ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic red alga Pyropia endiviifolia using the Illumina...

In this study, the complete plastid genome of Porphyridium purpureum strain CCMP1328 was recovered through Illumina sequencing data. This complete plastid genome of P. purpureum was 220,483 bp in length and contained a pair of IR regions (4604 bp). The pt genome of P. purpureum encoded 234 genes including 199 protein-coding genes, 29 tRNA genes, on...

In this study, we presented the complete mitochondrial genome of northern grasshopper mouse (Onychomys leucogaster). The circular genome is 16,370 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosome RNA genes, and 1 D-loop control regions. The overall nucleotide composition is: 31.2% A, 25.2% T, 29.9%...

In this study, we presented the complete mitochondrial genome of Tringa semipalmata. The circular genome is 16,603 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosome RNA genes and 1 D-loop control regions. The overall nucleotide composition is as follows: 31.2% A, 25.2% T, 29.9% C and 13.6% G, with a...

The threatened Okaloosa darter (Etheostoma okaloosae) is found almost exclusively in the Choctawhatchee Bay of Florida, and its habitat is threatened by natural disasters and water pollution. In this study, the complete mitochondrial genome of E. okaloosae has been determined by polymerase chain reaction method for the first time. The overall base...

The complete chloroplast genome of Gracilariopsis lemaneiformis was recovered from a Next Generation Sequencing dataset. Without quadripartite structure, this chloroplast genome (183,013 bp, 27.40% GC content) contains 202 protein-coding genes, 34 tRNA genes, three rRNA genes and one tmRNA gene. Synteny analysis showed plasmid incorporation regions...

In this study, the complete mitochondrial genome of the widespread invasive Argentine ant (Linepithema humile) was first determined. The mitochondrial genome is 16 098 bp in length, and encodes one D-loop region, two ribosomal RNA genes, 13 protein-coding genes, and 18 transfer RNA genes. Average GC content of this genome is 19.68%. nad6 and cob ge...

Batrachoseps nigriventris was classified in order Caudata, family Plethodontidae. In this study, we obtained the complete mitochondrial genome sequence of B. nigriventris, which was 17 403 bp in length. With a base composition of 33.5%A, 30.9%T, 21.4%C, and 14.2%G, this genome contained 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNA),...

Ficus racemosa, with immense medicinal value, and known as Cluster Fig Tree, Indian Fig Tree or Goolar (Gular) Figis, is a species of plant which belongs to family Moraceae. The complete chloroplast genome of Ficus racemosa was obtained by de novo assembly using next-generation sequencing data. The chloroplast genome of F. racemosa was 159 473 bp i...

In this study, we determined the mitochondrial genome of Rhynchophorus ferrugineus. The mitochondrial genome is 15 924 bp in length (GC content: 25.6%), encodes 2 ribosomal RNA genes, 13 protein-coding genes, 21 transfer RNA genes, and 1 D-loop region. nad6 and cob are overlapped by 30 bp and atp8 and atp6 are overlapped by 12 bp. The phylogenetic...

The complete mitochondrial genome sequence of Plodia Interpunctella (Lepidoptera: Pyralidae) was determined. The circular genome has a size of 15 733 base pairs, containing 36 gene protein-coding genes, two rRNA genes, and 21 tRNA genes. The overall base composition was 41.37% of A, 37.99% of T, 12.54% of G, and 8.10% of C. Furthermore, a phylogene...

The complete mitochondrial genome of Opsaridium microlepis was determined by using llumina sequencing method. The genome is 168 25 bp in length, comprising 13 protein-coding genes, 20 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region (D-loop region). Most genes are encoded on the heavy strand (H-strand), except for na...

In this study, complete mitochondrial genome of the large earth bumblebee, Bombus terrestris, was first determined. The mitochondrial genome is 174 000 bp in length, and encodes 1 D-loop region, 2 ribosomal RNA genes, 13 protein-coding genes and 20 transfer RNA genes. Average GC content of this genome is 15%. nad6 and cob are overlapped with 12 bp,...

The complete chloroplast sequence of Cryptophyceae algae Guillardia theta strain CCMP2712 was determined in this study. The genome consists of 138 455 bp containing a pair of rRNA-coding invert repeats of 4973 bp. The overall GC contents of the chloroplast genome were 32.9%. A total of 159 functional genes were annotated, which included 124 protein...

The complete mitochondrial DNA of pennate diatom Fistulifera solaris was determined. The circular mitochondrial genome is 39 648 bp in length with 28.1% GC content and contains 63 genes, including 33 protein-coding genes, three conserved open reading frame (ORF154, ORF192 and ORF251), 25 tRNA and 2 rRNA genes. All protein-coding genes have AUG as s...

Pseudo nitzschia multiseries are common members of phytoplankton communities, which can bring about blooms in coastal and ocean. Meanwhile, the neurotoxin was produced by this species can cause amnesic shellfish poisoning in both marine mammals and human beings. Whereas the lacking of plastid genome information on this species obstacles the study o...

Drosophila albomicans has been widely used as an important animal model for chromosome evolution. In this study, the mitochondrial genome sequence of this species is determined and described for the first time. The mitochondrial genome (15 849 bp) encompasses two rRNA, 22 tRNA, and 13 protein-coding genes. Genome content and structure are similar t...

454 GS FLX Titanium sequencing data were used to obtain the complete mitochondrial genome of Calliarthron tuberculosum (26,469 bp). The mitogenome contains 44 genes, including 2 ribosomal RNA, 19 transfer RNA, 5 ribosomal proteins, 1 ymf, 2 open reading frames (ORFs) and 16 genes involved in cellular respiration. The secY and rps12 are overlapped b...

Complete mitochondrial genome of Botryococcus braunii strain Showa was assembled and annotated. It contains 31 protein-coding genes, 23 tRNA genes and 3 rRNA (23S, 16S, 5S rRNA) genes. The 31 protein-coding genes include 5 atp genes, 3 cox genes, 9 nad genes, 12 ribosomal protein genes, cob and tatC genes. The presence of extra non-coding regions m...

Pyropia yezoensis is a model organism often used to investigate the mechanisms underlying stress tolerance in intertidal zones. The digital gene expression (DGE) approach was used to characterize a genome-wide comparative analysis of differentially expressed genes (DEGs) that influence the physiological, developmental or biochemical processes in sa...

An assessment with assistance of DNA barcoding was conducted on green macroalgae in coastal zone around Qingdao, China, during the period of April-December, 2011. Three markers were applied in molecular discrimination, including the plastid elongation factor tufA gene, the internal transcribed spacer (ITS) region of the ribosomal cistron and rubisc...

Pyropia haitanensis and P. yezoensis are two economically important marine crops that are also considered to be research models to study the physiological ecology of intertidal seaweed communities, evolutionary biology of plastids, and the origins of sexual reproduction. This plastid genome information will facilitate study of breeding, population...

Primers used for gap filling and assembly validation. (DOC)

Gene content comparisons between plastid genomes. (DOC)

Plastid and cyanobacterial genomes used in the gene content comparisons and the phylogenetic studies. (DOC)