cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26578179
title: Sequencing of the complete plastome of the thermal adder’s-tongue fern, <i>Ophioglossum thermale</i> Kom. (Ophioglossaceae)

description: The Ophioglossaceae family, one of the oldest orders of extant ferns, exhibits diverse morphological and chromosomal characteristics. This study presents the first complete plastome sequence of thermal adder’s-tongue fern (<i>Ophioglossum thermale</i>), a species renowned for its antioxidant properties in traditional Chinese medicine. Our analyses revealed 27 simple sequence repeats (SSRs) in the plastome, with variations in SSR frequencies compared to related genera. Our phylogenetic analyses placed <i>O. thermale</i> within the <i>Ophioglossum</i> s.s. clade, supporting previous studies and suggesting polyphyly within the genus <i>Ophioglossum</i> based on the sensu PPG I system. The enlarged noncoding regions in fern organelles (ENRFOs) resulting from foreign DNA insertions in <i>O. thermale</i> were identified in the <i>ycf2-trnH</i> and <i>trnT-trnfM</i> regions, similar to other <i>Ophioglossum</i> species. ENRFOs were found at the LSC and SSC, but not in IRs in Ophioglossaceae. Consequently, foreign DNA insertions and lineage-specific SSRs shed light on plastome evolution in the Ophioglossaceae family.
DOI: 10.6084/m9.figshare.26578179.v1
title: Sequencing of the complete plastome of the thermal adder’s-tongue fern, <i>Ophioglossum thermale</i> Kom. (Ophioglossaceae)

description: The Ophioglossaceae family, one of the oldest orders of extant ferns, exhibits diverse morphological and chromosomal characteristics. This study presents the first complete plastome sequence of thermal adder’s-tongue fern (<i>Ophioglossum thermale</i>), a species renowned for its antioxidant properties in traditional Chinese medicine. Our analyses revealed 27 simple sequence repeats (SSRs) in the plastome, with variations in SSR frequencies compared to related genera. Our phylogenetic analyses placed <i>O. thermale</i> within the <i>Ophioglossum</i> s.s. clade, supporting previous studies and suggesting polyphyly within the genus <i>Ophioglossum</i> based on the sensu PPG I system. The enlarged noncoding regions in fern organelles (ENRFOs) resulting from foreign DNA insertions in <i>O. thermale</i> were identified in the <i>ycf2-trnH</i> and <i>trnT-trnfM</i> regions, similar to other <i>Ophioglossum</i> species. ENRFOs were found at the LSC and SSC, but not in IRs in Ophioglossaceae. Consequently, foreign DNA insertions and lineage-specific SSRs shed light on plastome evolution in the Ophioglossaceae family.
DOI: 10.6084/m9.figshare.26780693
title: Two complete mitochondrial genomes of <i>Boulenophrys</i> (Anura: Megophryidae: Megophryinae): characteristics and phylogenetic implications

description: The Chinese horned toads, <i>Boulenophrys boettgeri</i> (Boulenger, 1899) and <i>Boulenophrys kuatunensis</i> (Pope, 1929), are two captivating species within the family Megophryidae, which inhabit the mountainous streams in the Eastern of China. In this study, two new complete mitochondrial genomes of <i>B. boettgeri</i> and <i>B. kuatunensis</i> were sequenced, assembled, and annotated using next-generation sequencing. The length of mitochondrial genomes of <i>B. boettgeri</i> and <i>B. kuatunensis</i> was 16,597 and 17,921 bp, respectively, with both containing 13 protein coding genes, 22 tRNA genes, two rRNA genes, and one putative control region. Phylogenetic relationships based on protein-coding mitochondrial genes showed that the two <i>Boulenophrys</i> species formed a cluster with other <i>Boulenophrys</i> species. The two new sequences provide valuable insights into the mitochondrial genomes of these two species, offering important data for understanding the phylogenetic relationships of the genus <i>Boulenophrys</i>.
DOI: 10.6084/m9.figshare.26534163
title: The complete mitochondrial genome of the shield-faced leaf-nosed bat from Yunnan Province in China

description: In this study, we sequenced the complete mitochondrial genome of the shield-faced leaf-nosed bat (<i>Hipposideros lylei</i> Thomas, 1914) using the Illumina platform. The mitochondrial genome of <i>H. lylei</i> is 16,856 bp in length, encoding 37 genes, which include 13 protein-coding genes, 22 tRNA genes, two rRNA genes, one replication start, and one non-coding control region (D-loop) of 417 bp in length. It has a G + C content of 42.0%, lower than the A + T content, indicating an obvious AT base preference. Phylogenetic analyses revealed that <i>H. lylei</i> clusters with three species of the genus <i>Hipposideros</i> in one branch and is relatively closely related to <i>H. armiger</i> and <i>H. larvatus</i>.
DOI: 10.6084/m9.figshare.26534163.v1
title: The complete mitochondrial genome of the shield-faced leaf-nosed bat from Yunnan Province in China

description: In this study, we sequenced the complete mitochondrial genome of the shield-faced leaf-nosed bat (<i>Hipposideros lylei</i> Thomas, 1914) using the Illumina platform. The mitochondrial genome of <i>H. lylei</i> is 16,856 bp in length, encoding 37 genes, which include 13 protein-coding genes, 22 tRNA genes, two rRNA genes, one replication start, and one non-coding control region (D-loop) of 417 bp in length. It has a G + C content of 42.0%, lower than the A + T content, indicating an obvious AT base preference. Phylogenetic analyses revealed that <i>H. lylei</i> clusters with three species of the genus <i>Hipposideros</i> in one branch and is relatively closely related to <i>H. armiger</i> and <i>H. larvatus</i>.
DOI: 10.6084/m9.figshare.26538008
title: The complete chloroplast genome of <i>Gardenia stenophylla</i> Merr (Rubiaceae) and its phylogenetic analysis

description: <i>Gardenia stenophylla</i> Merr, a member of the genus <i>Gardenia</i> in the family Rubiaceae, possesses significant medicinal and ornamental value and is widely distributed in China. This study reports the newly sequenced chloroplast genome of <i>Gardenia stenophylla</i> Merr. The complete chloroplast genome of <i>Gardenia stenophylla</i> Merr (155,109 bp, GC content of 37.5%) was shown to have a typical quadripartite structure, containing a pair of inverted repeat regions (IRs) of 28,802 bp separated by a large single-copy (LSC) region of 85,396 bp and a small single-copy (SSC) region of 18,109 bp. The chloroplast genome contained 151 genes encoding 106 proteins, 37 tRNAs, and eight rRNAs. The <i>Gardenia stenophylla</i> Merr chloroplast genome displayed the closest phylogenetic relationship to <i>Gardenia jasminoides</i> and <i>Gardenia jasminoides</i> var. grandiflora. These data will assist in future molecular phylogenetics of the Rubiaceae.
DOI: 10.6084/m9.figshare.26538008.v1
title: The complete chloroplast genome of <i>Gardenia stenophylla</i> Merr (Rubiaceae) and its phylogenetic analysis

description: <i>Gardenia stenophylla</i> Merr, a member of the genus <i>Gardenia</i> in the family Rubiaceae, possesses significant medicinal and ornamental value and is widely distributed in China. This study reports the newly sequenced chloroplast genome of <i>Gardenia stenophylla</i> Merr. The complete chloroplast genome of <i>Gardenia stenophylla</i> Merr (155,109 bp, GC content of 37.5%) was shown to have a typical quadripartite structure, containing a pair of inverted repeat regions (IRs) of 28,802 bp separated by a large single-copy (LSC) region of 85,396 bp and a small single-copy (SSC) region of 18,109 bp. The chloroplast genome contained 151 genes encoding 106 proteins, 37 tRNAs, and eight rRNAs. The <i>Gardenia stenophylla</i> Merr chloroplast genome displayed the closest phylogenetic relationship to <i>Gardenia jasminoides</i> and <i>Gardenia jasminoides</i> var. grandiflora. These data will assist in future molecular phylogenetics of the Rubiaceae.
DOI: 10.6084/m9.figshare.26779518
title: The complete mitochondrial genome of the blackskin catfish (<i>Clarias meladerma</i>: Clariidae) from Rokan River, Riau, Indonesia

description: <i>Clarias meladerma</i> Bleeker, 1846, a native catfish species in Indonesia belonging to the family Clariidae. The present study the complete mitochondrial genome sequence of <i>C. meladerma</i> from the Rokan River was sequenced by using next-generation sequencing, and its phylogenetic relationship was analyzed. The mitochondrial genome comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a total length of 16,808 bp. The mitogenome of <i>C. meladerma</i> exhibits a base composition of 32.49% adenine, 25.75% thymine, 14.51% guanine, and 27.25% cytosine. Phylogenetic analysis indicated that <i>C. meladerma</i> has the same clade with <i>C. macrocephalus, C. batrachus</i>, and <i>C. fucus</i>. In essence, the findings of this study lay down a genetic foundation for future investigations into <i>C. meladerma</i>.
DOI: 10.6084/m9.figshare.26779518.v1
title: The complete mitochondrial genome of the blackskin catfish (<i>Clarias meladerma</i>: Clariidae) from Rokan River, Riau, Indonesia

description: <i>Clarias meladerma</i> Bleeker, 1846, a native catfish species in Indonesia belonging to the family Clariidae. The present study the complete mitochondrial genome sequence of <i>C. meladerma</i> from the Rokan River was sequenced by using next-generation sequencing, and its phylogenetic relationship was analyzed. The mitochondrial genome comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a total length of 16,808 bp. The mitogenome of <i>C. meladerma</i> exhibits a base composition of 32.49% adenine, 25.75% thymine, 14.51% guanine, and 27.25% cytosine. Phylogenetic analysis indicated that <i>C. meladerma</i> has the same clade with <i>C. macrocephalus, C. batrachus</i>, and <i>C. fucus</i>. In essence, the findings of this study lay down a genetic foundation for future investigations into <i>C. meladerma</i>.
DOI: 10.6084/m9.figshare.26779722
title: Complete mitochondrial genome of <i>Colias sifanica</i> Grum-Grshimailo, 1891 (Lepidoptera: Pieridae) from montane region in northwestern China

description: <i>Colias sifanica</i> Grum-Grshimailo, 1891, is a typical montane butterfly species which occurs on the Qinghai-Tibet Plateau (QTP) and adjacent regions in China. In this study, the complete mitochondrial genome of this species was assembled from data generated by next-generation sequencing. The mitogenome was 15,151 bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The base composition of the <i>C. sifanica</i> mitogenome was 39.7% A, 41.3% T, 11.3% C and 7.7% G, significantly AT biased as commonly found in other Pieridae mitogenomes. Phylogenetic analyses based on all PCGs using both the maximum likelihood and Bayesian inference methods indicated that <i>C. sifanica</i> is closely related to <i>C. fieldii</i> with high support values, and the phylogenetic relationship of (<i>Dercas</i> + ((<i>Gandaca</i> + <i>Gonepteryx</i>) + (<i>Phoebis</i> + (<i>Anteos</i> + (<i>Catopsilia</i> + (<i>Zerene</i> + <i>Colias</i>))))))) was shown for the tribe Coliadini. Though both the mitogenomic gene order and overall base composition were found to be conserved, different Ka/Ks ratios for several mitogenomic PCGs were detected between <i>Colias</i> and other species in the tribe Coliadini.
DOI: 10.6084/m9.figshare.26779722.v1
title: Complete mitochondrial genome of <i>Colias sifanica</i> Grum-Grshimailo, 1891 (Lepidoptera: Pieridae) from montane region in northwestern China

description: <i>Colias sifanica</i> Grum-Grshimailo, 1891, is a typical montane butterfly species which occurs on the Qinghai-Tibet Plateau (QTP) and adjacent regions in China. In this study, the complete mitochondrial genome of this species was assembled from data generated by next-generation sequencing. The mitogenome was 15,151 bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The base composition of the <i>C. sifanica</i> mitogenome was 39.7% A, 41.3% T, 11.3% C and 7.7% G, significantly AT biased as commonly found in other Pieridae mitogenomes. Phylogenetic analyses based on all PCGs using both the maximum likelihood and Bayesian inference methods indicated that <i>C. sifanica</i> is closely related to <i>C. fieldii</i> with high support values, and the phylogenetic relationship of (<i>Dercas</i> + ((<i>Gandaca</i> + <i>Gonepteryx</i>) + (<i>Phoebis</i> + (<i>Anteos</i> + (<i>Catopsilia</i> + (<i>Zerene</i> + <i>Colias</i>))))))) was shown for the tribe Coliadini. Though both the mitogenomic gene order and overall base composition were found to be conserved, different Ka/Ks ratios for several mitogenomic PCGs were detected between <i>Colias</i> and other species in the tribe Coliadini.
DOI: 10.6084/m9.figshare.26762611.v1
title: The complete chloroplast genome sequence and phylogenetic analysis of <i>Tragopogon pratensis</i> L. (Asteraceae)

description: Currently, the phylogenetic relationships of <i>Tragopogon pratensis</i> Linnaeus (1753) remain unclear. This study presents the first report on the complete chloroplast genome of <i>T. pratensis</i>, which is a quadripartite structure with a length of 153,002 bp and containing a large single copy (LSC, 84,225 bp) region, a small single copy (SSC, 18,407 bp) region, a pair of inverted repeats (IR, 25,185 bp) regions. A total of 134 genes are identified, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes, and 2 pseudogenes. Phylogenetic analysis revealed that <i>T. pratensis</i> is most closely related to <i>T. dubius</i> and <i>that Tragopogon</i> is a monophyletic genus.
DOI: 10.6084/m9.figshare.26762611
title: The complete chloroplast genome sequence and phylogenetic analysis of <i>Tragopogon pratensis</i> L. (Asteraceae)

description: Currently, the phylogenetic relationships of <i>Tragopogon pratensis</i> Linnaeus (1753) remain unclear. This study presents the first report on the complete chloroplast genome of <i>T. pratensis</i>, which is a quadripartite structure with a length of 153,002 bp and containing a large single copy (LSC, 84,225 bp) region, a small single copy (SSC, 18,407 bp) region, a pair of inverted repeats (IR, 25,185 bp) regions. A total of 134 genes are identified, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes, and 2 pseudogenes. Phylogenetic analysis revealed that <i>T. pratensis</i> is most closely related to <i>T. dubius</i> and <i>that Tragopogon</i> is a monophyletic genus.
DOI: 10.6084/m9.figshare.26763853
title: Structures and genetic information of control region in mitogenomes of Odonata

description: Mitogenome data of Odonata is accumulating and widely used in phylogenetic analysis. However, noncoding regions, especially control region, were usually omitted from the phylogenetic reconstruction. In an effort to uncover the phylogenetic insights offered by the control region, we have amassed 65 Odonata mitogenomes and conducted an examination of their control regions. Our analysis discovered that species belonging to Anisoptera and Anisozygoptera exhibited a stem-loop structure, which was formed by a conserved polyC-polyG stretch located near the <i>rrns</i> gene (encoding 12S rRNA). Conversely, the polyC-polyG region was not a conserved fragment in Zygoptera. The length and number of repetitions within the control region were identified as the primary determinants of its overall length. Further, sibling species within Odonata, particularly those in the genus <i>Euphaea</i>, displayed similar patterns of repetition in their control region. Collectively, our research delineates the structural variations within the control region of Odonata and suggests the potential utility of this region in elucidating phylogenetic relationships among closely related species.
DOI: 10.6084/m9.figshare.26763853.v1
title: Structures and genetic information of control region in mitogenomes of Odonata

description: Mitogenome data of Odonata is accumulating and widely used in phylogenetic analysis. However, noncoding regions, especially control region, were usually omitted from the phylogenetic reconstruction. In an effort to uncover the phylogenetic insights offered by the control region, we have amassed 65 Odonata mitogenomes and conducted an examination of their control regions. Our analysis discovered that species belonging to Anisoptera and Anisozygoptera exhibited a stem-loop structure, which was formed by a conserved polyC-polyG stretch located near the <i>rrns</i> gene (encoding 12S rRNA). Conversely, the polyC-polyG region was not a conserved fragment in Zygoptera. The length and number of repetitions within the control region were identified as the primary determinants of its overall length. Further, sibling species within Odonata, particularly those in the genus <i>Euphaea</i>, displayed similar patterns of repetition in their control region. Collectively, our research delineates the structural variations within the control region of Odonata and suggests the potential utility of this region in elucidating phylogenetic relationships among closely related species.
DOI: 10.6084/m9.figshare.26468427
title: The plastome and phylogenetic status of <i>Cotoneaster rosiflorus</i> (Rosaceae)

description: Endemic to Taiwan Province, China, <i>Cotoneaster rosiflorus</i> Kun-Cheng Chang & Fu-Yuan Lu 2011 (Rosaceae) holds significant ecological and ornamental importance. Despite its value, research on its molecular data and phylogenetic position has remained limited. In this study, we addressed this gap by sequencing the genome-skimming data, assembling its plastome, and investigating its phylogenetic position. The plastome, spanning 159,449 bp in length, consisted of a large single-copy (87,433 bp), a small single-copy (19,262 bp), and two inverted repeat regions (26,377 bp). We annotated a total of 128 functional genes, including 84 protein-coding genes, 36 transfer genes, and eight ribosomal RNA genes. The phylogenetic results indicated that <i>C. rosiflorus</i> is closely related to <i>C. dammerii</i>, suggesting that <i>C. rosiflorus</i> might have captured its chloroplast from <i>C. dammerii</i> through hybridization and introgression events. This study offered valuable insights for forthcoming phylogenetic and population genetic investigations of <i>Cotoneaster</i>.
DOI: 10.6084/m9.figshare.26468427.v1
title: The plastome and phylogenetic status of <i>Cotoneaster rosiflorus</i> (Rosaceae)

description: Endemic to Taiwan Province, China, <i>Cotoneaster rosiflorus</i> Kun-Cheng Chang & Fu-Yuan Lu 2011 (Rosaceae) holds significant ecological and ornamental importance. Despite its value, research on its molecular data and phylogenetic position has remained limited. In this study, we addressed this gap by sequencing the genome-skimming data, assembling its plastome, and investigating its phylogenetic position. The plastome, spanning 159,449 bp in length, consisted of a large single-copy (87,433 bp), a small single-copy (19,262 bp), and two inverted repeat regions (26,377 bp). We annotated a total of 128 functional genes, including 84 protein-coding genes, 36 transfer genes, and eight ribosomal RNA genes. The phylogenetic results indicated that <i>C. rosiflorus</i> is closely related to <i>C. dammerii</i>, suggesting that <i>C. rosiflorus</i> might have captured its chloroplast from <i>C. dammerii</i> through hybridization and introgression events. This study offered valuable insights for forthcoming phylogenetic and population genetic investigations of <i>Cotoneaster</i>.
DOI: 10.6084/m9.figshare.26509204.v1
title: The complete chloroplast genome of <i>Taraxacum albidum</i> (Asteraceae), a Japanese endemic dandelion

description: <i>Taraxacum albidum</i>, a perennial herb of the Asteraceae family, exhibits both tetraploid and pentaploid in Japan. This study sequenced and characterized the complete chloroplast genome of <i>T. albidum</i>, revealing a 151,451 bp sequence with a typical quadripartite structure, comprising one large single-copy (LSC) region of 84,052 bp, one small single-copy (SSC) region of 18,541 bp, and two inverted repeat (IR) regions, IRa and IRb, each 24,429 bp in length. The chloroplast genome, excluding duplicates, contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The GC content of this genome was 37.7%. Phylogenetic analysis revealed that <i>T. albidum</i> is most closely related to <i>T. mongolicum</i>, with the chloroplast genome sequences being nearly identical, differing by only one nucleotide. These findings suggest that the maternal lineage of <i>T. albidum</i> likely originates from <i>T. mongolicum</i> or its closely related species.
DOI: 10.6084/m9.figshare.26509204
title: The complete chloroplast genome of <i>Taraxacum albidum</i> (Asteraceae), a Japanese endemic dandelion

description: <i>Taraxacum albidum</i>, a perennial herb of the Asteraceae family, exhibits both tetraploid and pentaploid in Japan. This study sequenced and characterized the complete chloroplast genome of <i>T. albidum</i>, revealing a 151,451 bp sequence with a typical quadripartite structure, comprising one large single-copy (LSC) region of 84,052 bp, one small single-copy (SSC) region of 18,541 bp, and two inverted repeat (IR) regions, IRa and IRb, each 24,429 bp in length. The chloroplast genome, excluding duplicates, contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The GC content of this genome was 37.7%. Phylogenetic analysis revealed that <i>T. albidum</i> is most closely related to <i>T. mongolicum</i>, with the chloroplast genome sequences being nearly identical, differing by only one nucleotide. These findings suggest that the maternal lineage of <i>T. albidum</i> likely originates from <i>T. mongolicum</i> or its closely related species.
DOI: 10.15468/dl.e84hbr
title: Occurrence Download

description: A dataset containing 803 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Heliotropium anomalum Hook. & Arn.)"
 ]
}

 The dataset includes 803 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0108900-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yky9z9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Duttaphrynus melanostictus (Schneider, 1799))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Specimen)",
 "Country is one of (Madagascar)",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 20000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0108902-240626123714530/datasets/export for details.
DOI: 10.15468/dl.a8aq9x
title: Occurrence Download

description: A dataset containing 512 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Hibiscus arnottianus A.Gray)"
 ]
}

 The dataset includes 512 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0108903-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y77whw
title: Occurrence Download

description: A dataset containing 27563 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Heliotropium curassavicum L.)"
 ]
}

 The dataset includes 27563 records from 499 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0108901-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.