cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30715473
title: The complete chloroplast genome of <i>Solanum lyratum</i> Thunberg (Solanaceae) and its phylogenetic analysis

description: The complete chloroplast genome of <i>Solanum lyratum</i> Thunberg was sequenced and analyzed, revealing a quadripartite structure with a total length of 155,870 base pairs. It comprises two regions with inverted repeat (IR) regions of 25,571 bp each, located between a large single-copy (LSC) region (86,319 bp) and a small single-copy (SSC) region (18,409 bp). Comprehensive genome annotation identified 128 functional genomic elements, consisting of 83 protein-coding genes, 37 tRNA sequences, and 8 rRNA sequences, with a guanine-cytosine content of 37.8%. Maximum likelihood (ML) analysis based on 86 conserved protein-coding loci from 38 taxa revealed a robust phylogenetic relationship between <i>S. dulcamara</i> and <i>S. lyratum</i>, with maximum bootstrap support (100%) at the branch node. The genomic data elucidated chloroplast architecture and speciation mechanisms in <i>Solanum</i>, particularly in <i>S. lyratum</i>. These findings provide critical insights into taxonomic classification, phylogenetic investigations, and the development of species-specific molecular markers.
DOI: 10.6084/m9.figshare.30715473.v1
title: The complete chloroplast genome of <i>Solanum lyratum</i> Thunberg (Solanaceae) and its phylogenetic analysis

description: The complete chloroplast genome of <i>Solanum lyratum</i> Thunberg was sequenced and analyzed, revealing a quadripartite structure with a total length of 155,870 base pairs. It comprises two regions with inverted repeat (IR) regions of 25,571 bp each, located between a large single-copy (LSC) region (86,319 bp) and a small single-copy (SSC) region (18,409 bp). Comprehensive genome annotation identified 128 functional genomic elements, consisting of 83 protein-coding genes, 37 tRNA sequences, and 8 rRNA sequences, with a guanine-cytosine content of 37.8%. Maximum likelihood (ML) analysis based on 86 conserved protein-coding loci from 38 taxa revealed a robust phylogenetic relationship between <i>S. dulcamara</i> and <i>S. lyratum</i>, with maximum bootstrap support (100%) at the branch node. The genomic data elucidated chloroplast architecture and speciation mechanisms in <i>Solanum</i>, particularly in <i>S. lyratum</i>. These findings provide critical insights into taxonomic classification, phylogenetic investigations, and the development of species-specific molecular markers.
DOI: 10.6084/m9.figshare.30610375
title: The complete mitochondrial genome of the symmetrical brain coral <i>Pseudodiploria strigosa</i> (Dana, 1846) (Scleractinia: Vacatina: Faviidae)

description: The complete mitochondrial genome (mitogenome) of the symmetrical brain coral <i>Pseudodiploria strigosa</i> (Dana, 1846) is sequenced for the first time in this study. The newly assembled mitogenome is 16,906 bp long and encodes 13 protein coding genes (PCGs), 2 tRNA genes (trnM[cat] and trnW[tca]), and 2 ribosomal genes (rrnL and rrnS). A group I intron bisected the PCG <i>nad5</i>. The studied mitogenome also includes two relatively long non-coding regions, one 910 bp long, located between <i>cox3</i> and <i>cox2</i> and a second 799 b long, located between <i>cox1</i> and trnM(cat). Mitochondrial synteny is identical to that previously reported in cofamilial corals. The mitogenome of <i>P. strigosa</i> is AT-rich with nucleotide use as follows: <i>A</i> = 24.84%, <i>C</i> = 13.21%, <i>G</i> = 20.41%, and <i>T</i> = 41.54%. A maximum-likelihood phylomitogenomic analysis that relied on the phylogenetic signal provided by translated PCGs supported the monophyly of the family Faviidae to which <i>P. strigosa</i> belongs. This newly assembled mitochondrial genome will be employed as a reference in studies biomonitoring this and other imperiled corals in the Caribbean basin using environmental DNA.
DOI: 10.6084/m9.figshare.30610375.v1
title: The complete mitochondrial genome of the symmetrical brain coral <i>Pseudodiploria strigosa</i> (Dana, 1846) (Scleractinia: Vacatina: Faviidae)

description: The complete mitochondrial genome (mitogenome) of the symmetrical brain coral <i>Pseudodiploria strigosa</i> (Dana, 1846) is sequenced for the first time in this study. The newly assembled mitogenome is 16,906 bp long and encodes 13 protein coding genes (PCGs), 2 tRNA genes (trnM[cat] and trnW[tca]), and 2 ribosomal genes (rrnL and rrnS). A group I intron bisected the PCG <i>nad5</i>. The studied mitogenome also includes two relatively long non-coding regions, one 910 bp long, located between <i>cox3</i> and <i>cox2</i> and a second 799 b long, located between <i>cox1</i> and trnM(cat). Mitochondrial synteny is identical to that previously reported in cofamilial corals. The mitogenome of <i>P. strigosa</i> is AT-rich with nucleotide use as follows: <i>A</i> = 24.84%, <i>C</i> = 13.21%, <i>G</i> = 20.41%, and <i>T</i> = 41.54%. A maximum-likelihood phylomitogenomic analysis that relied on the phylogenetic signal provided by translated PCGs supported the monophyly of the family Faviidae to which <i>P. strigosa</i> belongs. This newly assembled mitochondrial genome will be employed as a reference in studies biomonitoring this and other imperiled corals in the Caribbean basin using environmental DNA.
DOI: 10.6084/m9.figshare.30674700
title: Characterization of the complete chloroplast genome of <i>Cladopus doianus</i> Koriba

description: <i>Cladopus doianus</i> Koriba 1928, a species within the <i>Cladopus</i> genus, possesses remarkable aerial shoots and an extensive underground root system, making it an exceptional model for investigating the evolutionary aspects of angiosperm morphology. In this study, we employed Illumina sequencing to assemble and annotate the complete chloroplast (cp) genome of <i>C. doianus</i>. The cp genome is 133,017 base pairs in length, containing 107 unique genes: 73 protein-coding genes, 30 tRNA genes, and four rRNA genes. Notably, 17 of these genes are duplicated within the inverted repeat (IR) regions, comprising four rRNA genes, seven tRNA genes, and six protein-coding genes. Additionally, we constructed a phylogenetic tree of selected species within the Podostemaceae family, and the results were consistent with previous studies, indicating that <i>C. doianus</i> is closely related to <i>P. chiangmaiensis</i>. In conclusion, our study presents the first complete chloroplast genome of <i>C. doianus</i>, providing valuable insights for future research on the Podostemaceae family.
DOI: 10.6084/m9.figshare.30674700.v1
title: Characterization of the complete chloroplast genome of <i>Cladopus doianus</i> Koriba

description: <i>Cladopus doianus</i> Koriba 1928, a species within the <i>Cladopus</i> genus, possesses remarkable aerial shoots and an extensive underground root system, making it an exceptional model for investigating the evolutionary aspects of angiosperm morphology. In this study, we employed Illumina sequencing to assemble and annotate the complete chloroplast (cp) genome of <i>C. doianus</i>. The cp genome is 133,017 base pairs in length, containing 107 unique genes: 73 protein-coding genes, 30 tRNA genes, and four rRNA genes. Notably, 17 of these genes are duplicated within the inverted repeat (IR) regions, comprising four rRNA genes, seven tRNA genes, and six protein-coding genes. Additionally, we constructed a phylogenetic tree of selected species within the Podostemaceae family, and the results were consistent with previous studies, indicating that <i>C. doianus</i> is closely related to <i>P. chiangmaiensis</i>. In conclusion, our study presents the first complete chloroplast genome of <i>C. doianus</i>, providing valuable insights for future research on the Podostemaceae family.
DOI: 10.6084/m9.figshare.30500349
title: The complete mitochondrial genome of <i>Ischiodon scutellaris</i> (Diptera: Syrphidae: Syrphinae)

description: This study reports the first complete mitochondrial genome of <i>Ischiodon scutellaris</i>. The mitochondrial genome is 15,815 bp in length, with an A + T content of 80.7%. The genome contains 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region. All PCGs initiate with ATN (G/C/T), except <i>COX1</i>and <i>ND1</i>(TTG). Three PCGs (<i>COX1</i>, <i>ATP6</i>, <i>ND5</i>) terminate with an incomplete T stop codon. Phylogenetic analysis based on 13 PCG sequences using maximum likelihood revealed that <i>I. scutellaris</i> forms a sister clade with <i>Scaeva affinis</i> and clusters closely with multiple Eupeodes species. This study advances understanding of syrphid mitochondrial genomics and evolutionary relationships.
DOI: 10.6084/m9.figshare.30500349.v1
title: The complete mitochondrial genome of <i>Ischiodon scutellaris</i> (Diptera: Syrphidae: Syrphinae)

description: This study reports the first complete mitochondrial genome of <i>Ischiodon scutellaris</i>. The mitochondrial genome is 15,815 bp in length, with an A + T content of 80.7%. The genome contains 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region. All PCGs initiate with ATN (G/C/T), except <i>COX1</i>and <i>ND1</i>(TTG). Three PCGs (<i>COX1</i>, <i>ATP6</i>, <i>ND5</i>) terminate with an incomplete T stop codon. Phylogenetic analysis based on 13 PCG sequences using maximum likelihood revealed that <i>I. scutellaris</i> forms a sister clade with <i>Scaeva affinis</i> and clusters closely with multiple Eupeodes species. This study advances understanding of syrphid mitochondrial genomics and evolutionary relationships.
DOI: 10.6084/m9.figshare.30729133
title: Characteristics chloroplast genome of Yangxincai and correction of its Latin scientific name

description: Yangxincai, a “highcalcium vegetable,” is a hybrid of <i>Phedimus aizoon</i> L. and <i>Phedimus kamtschaticus </i>(Fisch., 1840), historically misidentified as <i>P. aizoon</i> L. owing to their morphological similarity. Uncertainty regarding its parentage has impeded official nomenclature and caused confusion in research. To clarify its maternal origin, we sequenced and assembled its complete chloroplast genome, 151,666 bp in length with a GC content of 37.73%, comprising LSC 83,128 bp, SSC 16,704 bp, and a pair of IRs (25,917 bp). A total of 128 genes were annotated,including 84 proteincoding, 36 tRNA, and 8 rRNA genes. Phylogenetic analysis of the maternally inherited chloroplast genome confirmed P. aizoon as the maternal parent, and we propose the corrected name <i>Phedimus aizoon </i>×<i> kamtschaticus</i> for this hybrid cultivar.
DOI: 10.6084/m9.figshare.30729133.v1
title: Characteristics chloroplast genome of Yangxincai and correction of its Latin scientific name

description: Yangxincai, a “highcalcium vegetable,” is a hybrid of <i>Phedimus aizoon</i> L. and <i>Phedimus kamtschaticus </i>(Fisch., 1840), historically misidentified as <i>P. aizoon</i> L. owing to their morphological similarity. Uncertainty regarding its parentage has impeded official nomenclature and caused confusion in research. To clarify its maternal origin, we sequenced and assembled its complete chloroplast genome, 151,666 bp in length with a GC content of 37.73%, comprising LSC 83,128 bp, SSC 16,704 bp, and a pair of IRs (25,917 bp). A total of 128 genes were annotated,including 84 proteincoding, 36 tRNA, and 8 rRNA genes. Phylogenetic analysis of the maternally inherited chloroplast genome confirmed P. aizoon as the maternal parent, and we propose the corrected name <i>Phedimus aizoon </i>×<i> kamtschaticus</i> for this hybrid cultivar.
DOI: 10.6084/m9.figshare.30570949.v1
title: Complete mitochondrial genome of the Korean Clawed Salamander <i>Onychodactylus koreanus</i> Min, Poyarkov & Vieites, 2012 (Caudata: Hynobiidae)

description: We report the complete mitochondrial genome of the Korean Clawed Salamander (<i>Onychodactylus koreanus</i>), endemic to the Korean Peninsula. The 16,445 bp mitogenome, assembled from Illumina HiSeq data, contains 37 genes (13 PCGs, 22 tRNAs and 2 rRNAs) plus the control region and has an A + T content of 68.6%. Phylogenetic analysis confirms it is a distinct lineage within <i>Onychodactylus</i>, closely related to <i>O. fischeri</i> and <i>O. zhaoermii</i>. These findings enhance our understanding of Hynobiidae diversity and evolution.
DOI: 10.6084/m9.figshare.30570949
title: Complete mitochondrial genome of the Korean Clawed Salamander <i>Onychodactylus koreanus</i> Min, Poyarkov & Vieites, 2012 (Caudata: Hynobiidae)

description: We report the complete mitochondrial genome of the Korean Clawed Salamander (<i>Onychodactylus koreanus</i>), endemic to the Korean Peninsula. The 16,445 bp mitogenome, assembled from Illumina HiSeq data, contains 37 genes (13 PCGs, 22 tRNAs and 2 rRNAs) plus the control region and has an A + T content of 68.6%. Phylogenetic analysis confirms it is a distinct lineage within <i>Onychodactylus</i>, closely related to <i>O. fischeri</i> and <i>O. zhaoermii</i>. These findings enhance our understanding of Hynobiidae diversity and evolution.
DOI: 10.6084/m9.figshare.30576049
title: Complete chloroplast genome and phylogenetic analysis of <i>Iris confusa</i> (Iridaceae)

description: <i>Iris confusa</i> Sealy is highly valued for its ornamental and medicinal applications. Here, we report the complete chloroplast genome sequence of <i>I. confusa</i> obtained using Illumina pair-end sequencing. The complete circular genome of <i>I. confusa</i> is 152,470 bp in length and contains a large single-copy region (83,251 bp), a small single-copy region (18,503 bp), and two short inverted repeat regions (25,358 bp). The genome sequence encodes 133 genes including 87 protein-coding genes, 8 ribosomal RNA genes, and 38 transfer RNA genes. This study will facilitate the understanding of chloroplast genome features of genus <i>Iris</i> and contribute to further studies on phylogenetic analyses.
DOI: 10.6084/m9.figshare.30576049.v1
title: Complete chloroplast genome and phylogenetic analysis of <i>Iris confusa</i> (Iridaceae)

description: <i>Iris confusa</i> Sealy is highly valued for its ornamental and medicinal applications. Here, we report the complete chloroplast genome sequence of <i>I. confusa</i> obtained using Illumina pair-end sequencing. The complete circular genome of <i>I. confusa</i> is 152,470 bp in length and contains a large single-copy region (83,251 bp), a small single-copy region (18,503 bp), and two short inverted repeat regions (25,358 bp). The genome sequence encodes 133 genes including 87 protein-coding genes, 8 ribosomal RNA genes, and 38 transfer RNA genes. This study will facilitate the understanding of chloroplast genome features of genus <i>Iris</i> and contribute to further studies on phylogenetic analyses.
DOI: 10.6084/m9.figshare.30576091
title: The complete chloroplast genome of the Korean endemic plant <i>Sorbaria sorbifolia</i> var. <i>glandulifolia</i> J.-H. Song & S.-P. Hong (Rosaceae) and phylogenetic analysis

description: <i>Sorbaria sorbifolia</i> var. <i>glandulifolia</i>, endemic to Korea, is distinguished by glandular trichomes on the abaxial leaflet surface. In this study, we present its first complete chloroplast genome (159,476 bp) with a typical quadripartite structure comprising 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. Phylogenetic analysis of 18 complete chloroplast genomes revealed that <i>S. sorbifolia</i> var. <i>glandulifolia</i> forms a monophyletic group with other <i>Sorbaria</i> species and clusters with <i>Adenostoma</i>. Furthermore, two well-supported clades within <i>Sorbaria</i> corresponded to the sections <i>Sorbaria</i> and <i>Kirilowiana</i>. This study provides the first chloroplast genome report for <i>S. sorbifolia</i> var. <i>glandulifolia</i>, offering valuable genomic insights for future phylogenetic and taxonomic research on the genus <i>Sorbaria</i>.
DOI: 10.6084/m9.figshare.30576091.v1
title: The complete chloroplast genome of the Korean endemic plant <i>Sorbaria sorbifolia</i> var. <i>glandulifolia</i> J.-H. Song & S.-P. Hong (Rosaceae) and phylogenetic analysis

description: <i>Sorbaria sorbifolia</i> var. <i>glandulifolia</i>, endemic to Korea, is distinguished by glandular trichomes on the abaxial leaflet surface. In this study, we present its first complete chloroplast genome (159,476 bp) with a typical quadripartite structure comprising 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. Phylogenetic analysis of 18 complete chloroplast genomes revealed that <i>S. sorbifolia</i> var. <i>glandulifolia</i> forms a monophyletic group with other <i>Sorbaria</i> species and clusters with <i>Adenostoma</i>. Furthermore, two well-supported clades within <i>Sorbaria</i> corresponded to the sections <i>Sorbaria</i> and <i>Kirilowiana</i>. This study provides the first chloroplast genome report for <i>S. sorbifolia</i> var. <i>glandulifolia</i>, offering valuable genomic insights for future phylogenetic and taxonomic research on the genus <i>Sorbaria</i>.
DOI: 10.6084/m9.figshare.30581998
title: Characterization of the complete mitochondrial genome and phylogenetic analysis of <i>Coelophora saucia</i> (Mulsant, 1850) (Coleoptera: Coccinellidae)

description: <i>Coelophora saucia</i> is an important natural enemy insect in agricultural production. We determined the complete mitochondrial genome of the <i>C. saucia</i> by high-throughput sequencing, and the mitogenome was 18,068 bp in length, with a GC content of 20.9%, encodes 2 ribosomal RNA genes, 22 transporter RNA genes, 13 protein-coding genes and with a non-coding control region. A phylogenetic tree was constructed using the maximum likelihood (ML) method, and the results indicated that the <i>C. saucia</i> was most closely related to <i>Propylea japonica</i> and <i>Propylea quattuordecimpunctata.</i>
DOI: 10.6084/m9.figshare.30581998.v1
title: Characterization of the complete mitochondrial genome and phylogenetic analysis of <i>Coelophora saucia</i> (Mulsant, 1850) (Coleoptera: Coccinellidae)

description: <i>Coelophora saucia</i> is an important natural enemy insect in agricultural production. We determined the complete mitochondrial genome of the <i>C. saucia</i> by high-throughput sequencing, and the mitogenome was 18,068 bp in length, with a GC content of 20.9%, encodes 2 ribosomal RNA genes, 22 transporter RNA genes, 13 protein-coding genes and with a non-coding control region. A phylogenetic tree was constructed using the maximum likelihood (ML) method, and the results indicated that the <i>C. saucia</i> was most closely related to <i>Propylea japonica</i> and <i>Propylea quattuordecimpunctata.</i>
DOI: 10.6084/m9.figshare.30518187
title: Characterization of the complete chloroplast genome sequence of <i>Asparagus densiflorus ‘</i>Sprengeri<i>’</i> Huttleston 1970 (Asparagaceae)

description: <i>Asparagus densiflorus ‘</i>Sprengeri<i>’</i> is an economically important ornamental and medicinal plant within the genus <i>Asparagus</i>. In this study, we sequenced and assembled its complete chloroplast (cp) genome using the Illumina NovaSeq platform. The circular cp genome is 157,116 bp in length with a GC content of 38%, comprising a large single-copy (LSC) region (85,327 bp), a small single-copy (SSC) region (18,677 bp), and two inverted repeat (IR) regions (26,556 bp each). The genome encodes 133 functional genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicates that <i>A. densiflorus ‘</i>Sprengeri<i>’</i> is most closely related to <i>A. densiflorus ‘</i>Myers’ and <i>A. falcatus</i>, suggesting a shared evolutionary lineage. This study will not only shed light on <i>A. densiflorus ‘</i>Sprengeri<i>’’</i>s evolutionary position but also provide valuable chloroplast genomic information for future studies into the origins and diversification of the genus <i>Asparagus</i> and the Asparagaceae family.
DOI: 10.6084/m9.figshare.30518187.v1
title: Characterization of the complete chloroplast genome sequence of <i>Asparagus densiflorus ‘</i>Sprengeri<i>’</i> Huttleston 1970 (Asparagaceae)

description: <i>Asparagus densiflorus ‘</i>Sprengeri<i>’</i> is an economically important ornamental and medicinal plant within the genus <i>Asparagus</i>. In this study, we sequenced and assembled its complete chloroplast (cp) genome using the Illumina NovaSeq platform. The circular cp genome is 157,116 bp in length with a GC content of 38%, comprising a large single-copy (LSC) region (85,327 bp), a small single-copy (SSC) region (18,677 bp), and two inverted repeat (IR) regions (26,556 bp each). The genome encodes 133 functional genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicates that <i>A. densiflorus ‘</i>Sprengeri<i>’</i> is most closely related to <i>A. densiflorus ‘</i>Myers’ and <i>A. falcatus</i>, suggesting a shared evolutionary lineage. This study will not only shed light on <i>A. densiflorus ‘</i>Sprengeri<i>’’</i>s evolutionary position but also provide valuable chloroplast genomic information for future studies into the origins and diversification of the genus <i>Asparagus</i> and the Asparagaceae family.
DOI: 10.6084/m9.figshare.30655716
title: Complete chloroplast genome sequence of <i>Protea cynaroides</i> ‘Red Rex’ (Proteaceae) and its phylogenetic analysis

description: <i>Protea cynaroides</i> ‘Red Rex’ (James Petiver 1698) is a perennial evergreen shrub of the Proteaceae family valued for ornamental and medicinal uses, yet its genomic data remain unexplored. Here, we report the complete chloroplast genome sequence (157,894 bp) of <i>P. cynaroides</i> ‘Red Rex’. The genome exhibits a quadripartite structure, including a large single-copy region (86,427 bp), a short single-copy region (18,553 bp), and two inverted repeats (26,457 bp each), with 38.06% GC content. A total of 130 genes were annotated. Phylogenetic analysis confirmed close relationships within Proteaceae, advancing insights into the genetics and evolution of <i>Protea</i>.
DOI: 10.6084/m9.figshare.30655716.v1
title: Complete chloroplast genome sequence of <i>Protea cynaroides</i> ‘Red Rex’ (Proteaceae) and its phylogenetic analysis

description: <i>Protea cynaroides</i> ‘Red Rex’ (James Petiver 1698) is a perennial evergreen shrub of the Proteaceae family valued for ornamental and medicinal uses, yet its genomic data remain unexplored. Here, we report the complete chloroplast genome sequence (157,894 bp) of <i>P. cynaroides</i> ‘Red Rex’. The genome exhibits a quadripartite structure, including a large single-copy region (86,427 bp), a short single-copy region (18,553 bp), and two inverted repeats (26,457 bp each), with 38.06% GC content. A total of 130 genes were annotated. Phylogenetic analysis confirmed close relationships within Proteaceae, advancing insights into the genetics and evolution of <i>Protea</i>.
DOI: 10.6084/m9.figshare.30579169
title: Complete chloroplast genomes analysis of <i>Lamium barbatum</i> and <i>Leucas ciliata</i> (Lamiaceae)

description: The two Lamioideae species, <i>Lamium barbatum</i> Siebold & Zucc. 1846, is distributed across Europe, North Africa, Asia, and North America, while <i>Leucas ciliata</i> Hochst. ex Benth. 1829 is found in southern China and Southeast Asia. We sequenced their complete chloroplast genomes using the Illumina platform, obtaining lengths of 150,887 bp and 151,259 bp, respectively. Phylogenetic analysis showed <i>Lamium barbatum</i> is closely related to four other <i>Lamium</i> species, including <i>Lamium takeshimense</i>, <i>Lamium album</i>, <i>Lamium amplexicaule</i>, and <i>Lamium galeobdolon</i>. The <i>Leucas ciliata</i> species clusters with <i>Leucas mollissima</i>. These findings provide valuable data for species identification, evolutionary research, and conservation genetics.