ResearchPad - taxonomy https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Phylogeography of the widespread Caribbean spiny orb weaver <i>Gasteracantha cancriformis</i>]]> https://www.researchpad.co/article/elastic_article_12766 Modern molecular analyses are often inconsistent with pre-cladistic taxonomic hypotheses, frequently indicating higher richness than morphological taxonomy estimates. Among Caribbean spiders, widespread species are relatively few compared to the prevalence of single island endemics. The taxonomic hypothesis Gasteracantha cancriformis circumscribes a species with profuse variation in size, color and body form. Distributed throughout the Neotropics, G. cancriformis is the only morphological species of Gasteracantha in the New World in this globally distributed genus.MethodsWe inferred phylogenetic relationships across Neotropical populations of Gasteracantha using three target genes. Within the Caribbean, we estimated genetic diversity, population structure, and gene flow among island populations.ResultsOur findings revealed a single widespread species of Gasteracantha throughout the Caribbean, G. cancriformis, while suggesting two recently divergent mainland populations that may represent separate species, diverging linages, or geographically isolated demes. The concatenated and COI (Cytochrome c oxidase subunit 1) phylogeny supported a Caribbean clade nested within the New World. Genetic variability was high between island populations for our COI dataset; however, gene flow was also high, especially between large, adjacent islands. We found structured genetic and morphological variation within G. cancriformis island populations; however, this variation does not reflect genealogical relationships. Rather, isolation by distance and local morphological adaptation may explain the observed variation. ]]> <![CDATA[Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae]]> https://www.researchpad.co/article/elastic_article_11231 In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.

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<![CDATA[A new genus of sinogaleaspids (Galeaspida, stem-Gnathostomata) from the Silurian Period in Jiangxi, China]]> https://www.researchpad.co/article/elastic_article_8413 Galeaspids are an endemic clade of jawless stem-gnathostomes known as ostracoderms. Their existence illuminates how specific characteristics developed in jawed vertebrates. Sinogaleaspids are of particular interest among the galeaspids but their monophyly is controversial because little is known about Sinogaleaspis xikengensis. Newly discovered sinogaleaspids from the Lower Silurian of Jiangxi, China provide a wealth of data and diagnostic features used to establish the new genus, Rumporostralis gen. nov., for Sinogaleaspis xikengensis. A morphological study showed that the sensory canal system of sinogaleaspids had mosaic features similar to those of three known galeaspids. There are 3–8 pairs of transverse canals in the Sinogaleaspidae, which suggests that the sensory canal system of galeaspid probably had a grid distribution with transverse canals arranged throughout the cephalic division. Phylogenetic analysis of Galeaspida supports the monophyly of the Sinogaleaspidae, consisting of Sinogaleaspis, Rumporostralis, and Anjiaspis. However, Shuyu and Meishanaspis form another monophyletic group, Shuyuidae fam. nov., which is outside all other eugaleaspidiforms. We propose a cladistically-based classification of Galeaspida based on our analysis.

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<![CDATA[A new species of <i>Cenopalpus</i> Pritchard &amp; Baker (Acari: Tenuipalpidae) from Japan, with ontogeny of chaetotaxy and a key to the world species]]> https://www.researchpad.co/article/N8179289f-7933-4eb0-92ba-b50426ec4032 A new species of flat mite, Cenopalpus umbellatus sp. nov. (Acari: Trombidiformes: Tenuipalpidae) is described and illustrated based on females, males, deutonymphs, protonymphs and larvae. The morphological ontogeny in idiosomal and leg chaetotaxy is briefly described for all stages. Mite specimens were collected from the leaves of Rhaphiolepis indica var. umbellata Makino (Rosaceae), an evergreen shrub native to Japan. An identification key to the world species of Cenopalpus is also provided.

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<![CDATA[Taxonomic revision of the Mesoamerican genus Spathacanthus (Justicieae, Acanthoideae, Acanthaceae)]]> https://www.researchpad.co/article/N1c6a83a9-d085-4a75-9c16-cffb912d5bb3
Abstract

Spathacanthus is a Mesoamerican genus that occurs in tropical and temperate regions from southern Mexico to Costa Rica; its taxonomy has not been updated for two decades. In view of the fact that a new species has been discovered and that the interspecific affinities in this genus have not been addressed to date, the present study aims to revise the genus Spathacanthus. Specimens of plants of this genus collected from across the distribution range and deposited in herbaria and digital databases were reviewed. In parallel, a cladistic analysis was carried out, based on morphological characters in order to examine relationships between species. Four species of Spathacanthus were recognised: one endemic to Costa Rica, another micro-endemic to Veracruz in Mexico, one more restricted to the forests of Mexico and Guatemala and the last one more widely distributed. Reflecting the previously limited knowledge of the group, many of the specimens that we studied had been misidentified. A key to differentiate these species is provided, supplemented with photographs, drawings and other illustrations, morphological descriptions, synonymy and ecological data. Results, presented here, extend the distribution range of some taxa and a distribution map is presented. The cladistic analysis recovered the genus as monophyletic, showing that S. hoffmannii and S. hahnianus are sister taxa and S. magdalenae was found to be more closely related to S. parviflorus. These plants are vulnerable to degradation and habitat loss.

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<![CDATA[Specific clones of Trichomonas tenax are associated with periodontitis]]> https://www.researchpad.co/article/5c900d3bd5eed0c48407e3b6

Trichomonas tenax, an anaerobic protist difficult to cultivate with an unreliable molecular identification, has been suspected of involvement in periodontitis, a multifactorial inflammatory dental disease affecting the soft tissue and bone of periodontium. A cohort of 106 periodontitis patients classified by stages of severity and 85 healthy adult control patients was constituted. An efficient culture protocol, a new identification tool by real-time qPCR of T. tenax and a Multi-Locus Sequence Typing system (MLST) based on T. tenax NIH4 reference strain were created. Fifty-three strains of Trichomonas sp. were obtained from periodontal samples. 37/106 (34.90%) T. tenax from patients with periodontitis and 16/85 (18.80%°) T. tenax from control patients were detected by culture (p = 0.018). Sixty of the 191 samples were tested positive for T. tenax by qPCR, 24/85 (28%) controls and 36/106 (34%) periodontitis patients (p = 0.089). By combining both results, 45/106 (42.5%) patients were positive by culture and/or PCR, as compared to 24/85 (28.2%) controls (p = 0.042). A link was established between the carriage in patients of Trichomonas tenax and the severity of the disease. Genotyping demonstrates the presence of strain diversity with three major different clusters and a relation between disease strains and the periodontitis severity (p<0.05). More frequently detected in periodontal cases, T. tenax is likely to be related to the onset or/and evolution of periodontal diseases.

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<![CDATA[Twenty-six additional new combinations in the Magnolia (Magnoliaceae) of China and Vietnam]]> https://www.researchpad.co/article/N5202c181-3dfd-40bd-a433-1d24ad15de87

Abstract

In accordance with the previous reduction of the remaining genera of subfamily Magnolioideae (Magnoliaceae) into the genus Magnolia, twenty-six new nomenclatural combinations are formally made by transferring to Magnolia some additional Chinese and Vietnamese taxa from the segregate genera of Manglietia, Michelia and Yulania. The following nine new combinations are created from Manglietia, namely Magnolia admirabilis, M. albistaminea, M. guangnanica, M. jinggangshanensis, M. maguanica, M. pubipedunculata, M. pubipetala, M. rufisyncarpa and M. sinoconifera. Also, twelve new combinations are created from Michelia, namely Magnolia caloptila, M. caudata, M. fallax, M. gelida, M. hunanensis, M. maudiae var. rubicunda, M. multitepala, M. platypetala, M. rubriflora, M. septipetala, M. sonlaensis, M. xinningia. Finally, five new combinations are created from Yulania, namely Magnolia baotaina, M. pendula, M. pilocarpa var. ellipticifolia, M. puberula and M. urceolata.

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<![CDATA[Cicinnus chambersi: a new species of sack-bearer moth (Lepidoptera, Mimallonidae, Cicinninae) from southeastern Arizona, USA]]> https://www.researchpad.co/article/Nf3656480-0784-433f-84f8-cc546362da7c

Abstract

A new species of cicinnine Mimallonidae, Cicinnus chambersisp. nov., is described from the Sky Islands Region of southern Arizona, USA. The new species is closely related to C. mexicana (Druce), type locality Veracruz, Mexico, based on morphology and genetics. The other Cicinnus species known from the United States, the common C. melsheimeri (type locality Pennsylvania, USA) is morphologically and genetically distinct from both C. chambersi and C. mexicana. The new species is compared to C. mexicana and C. melsheimeri, as well as other Mexican Cicinnus. The life history of C. chambersi is unknown, but its description should facilitate future studies on this rarely reported North American mimallonid, a species which may have only recently become established in the United States. Cicinnus chambersi is the fifth known Mimallonidae species from the United States, and the first described from the country in nearly half a century.

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<![CDATA[Lithobius (Ezembius) varioporus, a new species from eastern China (Lithobiomorpha, Lithobiidae)]]> https://www.researchpad.co/article/N572199fd-7cd0-4e14-ac2f-61d95232cf44

Abstract

Lithobius (Ezembius) varioporussp. nov. (Lithobiomorpha, Lithobiidae), recently discovered from Longquanguan Town, Fuping County, Baoding City, Hebei Province, China, is described. Morphologically it resembles to Lithobius (Ezembius) laevidentata Pei, Ma, Hou, Zhu & Gai, 2015 from the Xinjiang Autonomous Region, but can be easily distinguished from the latter by the Tömösváry’s organ, slightly smaller than the adjoining ocelli, no secondary sexual modifications on male tibia 14 and 15, posterior accessory spine of legs 14 and 15 present and the number of coxal pores varying considerably from three to eight. The main morphological characters of the known Chinese species of the subgenusEzembius Chamberlin, 1919 based on adult specimens are presented.

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<![CDATA[A new species of Cosmocerca (Nematoda, Ascaridomorpha) from the marine toad Rhinella marina (Linnaeus) (Anura, Bufonidae) in Australia]]> https://www.researchpad.co/article/N7a14b3be-aba0-4af5-ad31-a88403016a0f

Abstract

The marine toad Rhinella marina (Linnaeus) (Anura, Bufonidae) is a notorious, exotic amphibian species in Australia. However, our present knowledge of the composition of the nematode fauna of R. marina is still not complete. In the present study, a new cosmocercid nematode, Cosmocerca multipapillatasp. nov., was described using both light and scanning electron microscopy, based on specimens collected from R. marina in Australia. Cosmocerca multipapillatasp. nov. can be easily distinguished from its congeners by the body size, the presence of lateral alae and well sclerotized gubernaculum, the number and arrangement of plectanes and rosettes and the length of spicules, oesophagus and tail.

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<![CDATA[Some new or poorly-known Zephroniidae (Diplopoda, Sphaerotheriida) from Vietnam]]> https://www.researchpad.co/article/N1c33df72-dbf1-4a33-8fe7-cbacb3918d00

Abstract

Three new species of the giant pill-millipede family Zephroniidae are described from southern Vietnam: Sphaerobelum pumatensesp. nov., Sphaeropoeus honbaensissp. nov. and Sphaeropoeus bidoupensissp. nov. Two species, Sphaerobelum bicorne Attems, 1938 and Sphaeropoeus maculatus (Verhoeff, 1924), are redescribed, the former from new material, the latter from type material with lectotype designation. A new transfer is proposed: Zephronia manca Attems, 1936, to the genus Sphaeropoeus Brandt, 1833, giving the new combination, Sphaeropoeus manca (Attems, 1936) comb. nov.

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<![CDATA[Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture]]> https://www.researchpad.co/article/N42b420df-f01d-4492-b8d8-193894490051

Abstract

During a survey of xylarialean fungi in Northern Iran, several specimens that showed affinities to the Hypoxylon rubiginosum complex were collected and cultured. A comparison of their morphological characters, combined with a chemotaxonomic study based on high performance liquid chromatography, coupled with diode array detection and mass spectrometry (HPLC-DAD/MS) and a multi-locus phylogeny based on ITS, LSU, rbp2 and tub2 DNA sequences, revealed a new species here described as Hypoxylon guilanense. In addition, Hypoxylon rubiginosumsensu stricto was also encountered. Concurrently, an endophytic isolate of the latter species showed strong antagonistic activities against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in a dual culture assay in our laboratory. Therefore, we decided to test the new Iranian fungi for antagonistic activities against the pathogen, along with several cultures of other Hypoxylon species that are related to H. rubiginosum. Our results suggest that the antagonistic effects of Hypoxylon spp. against Hym. fraxineus are widespread and that they are due to the production of antifungal phomopsidin derivatives in the presence of the pathogen.

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<![CDATA[Squamarina (lichenised fungi) species described from China belong to at least three unrelated genera]]> https://www.researchpad.co/article/Ncdda6351-f672-4023-99ae-f8ee246a86a8

Abstract

New collections of six Squamarina species from type localities in China were studied. The comparison of morphological characteristics and secondary metabolites with those of the type specimens and phylogenetic analyses suggest that S. callichroa and S. pachyphylla belong to Rhizoplaca, S. semisterilis belongs to Lobothallia and S. chondroderma should be retained in Lecanora temporarily. Only two species, S. kansuensis and S. oleosa, remain in Squamarina. The new combinations Lobothallia semisterilis (H. Magn.) Y. Y. Zhang, Rhizoplaca callichroa (Zahlbr.) Y. Y. Zhang and R. pachyphylla (H. Magn.) Y. Y. Zhang are proposed. Detailed descriptions to aid the identification of these species, distributions and phylogenetic trees, based on multiple collections, are presented. The generic concept of Squamarina is recircumscribed in this study.

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<![CDATA[A new species of the toothed toad Oreolalax (Anura, Megophryidae) from Sichuan Province, China]]> https://www.researchpad.co/article/Nfe9ecc3c-f3bd-4185-9355-fe8735eab0f6

Abstract

The toad genus Oreolalax is widely distributed in southwest China and northern Vietnam. A new species of the genus is described from Sichuan Province, China. Phylogenetic analyses based on the mitochondrial 12S rRNA and 16S rRNA gene sequences supported the new species as an independent clade clustered into the clade also containing O. nanjiangensis and O. chuanbeiensis. The new species can be distinguished from its congeners by a combination of the following characters: body size moderate (SVL 51.2–64.2 mm in males); head broad; tympanum hidden; interorbital region with dark triangular pattern; belly with marbling; male lacking spines on lip margin; spiny patches on chest small with thick sparse spines in male; nuptial spines thick and sparse; tibio-tarsal articulation reaching beyond nostril when leg stretched forward; toe webbing at base.

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<![CDATA[Two species of Thoracostomopsidae (Nematoda: Enoplida) from Jeju Island, South Korea]]> https://www.researchpad.co/article/Nd6f075e6-61c4-4ffd-9fc5-9d3a90d27b8d

During a survey of intertidal zones at beaches on Jeju Island, two species belonging to the family Thoracostomopsidae were discovered. One new species, Enoploides koreanus sp. nov. and one known species, Epacanthion hirsutum Shi & Xu, 2016 are reported. Along with morphological analysis, mitochondrial cytochrome oxidase c subunit 1 (mtCOI) sequences and 18S rRNA sequences of the species were also obtained and used to check relative p-distance and phylogenetic positions. While most species of Enoploides have long spicules, the new species belongs to a group of Enoploides with short spicules < 150 µm). Of the seven species with short spicules, the new species is most closely related to E. disparilis Sergeeva, 1974. They both have similar body length, fairly similar sized and shaped spicules with small gubernaculum running parallel to distal end of spicule, and an index value of b. The new species can be distinguished from E. disparilis by having pre-anal supplementary organ with short conical tail, while E. disparilis lacks pre-anal supplementary organ and has a long conico-cylindrical tail. Along with the description of the new species, the genus Enoploides Ssaweljev, 1912 is bibliographically reviewed and revised. Of 45 species described to date, 27 are now considered valid, 16 species inquirendae due to inadequate descriptions and ambiguity of the material examined, along with two cases of nomen nudum. With this review, we provide an updated diagnosis and list of valid species, a tabular key comparing diagnostic characters of all valid species, and a new complete key to species. One known species, Epacanthion hirsutum Shi & Xu, 2016, is reported in Korea for the first time. The morphology agrees well with the original description provided by Shi & Xu, 2016. As they had already reviewed the genus at the time of reporting four Epacanthion species, we provide only a description, depiction, and measurements for comparison purposes.

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<![CDATA[Integrative description of Diosaccus koreanus sp. nov. (Hexanauplia, Harpacticoida, Miraciidae) and integrative information on further Korean species]]> https://www.researchpad.co/article/N1778d794-f0e4-4483-a0ef-96454b2b0bda

Abstract

A new species of Diosaccus Boeck, 1873 (Arthropoda, Hexanauplia, Harpacticoida) was recently discovered in Korean waters. The species was previously recognized as D. ezoensis Itô, 1974 in Korea but, here, is described as a new species, D. koreanussp. nov., based on the following features: 1) second inner seta on exopod of fifth thoracopod apparently longest in female, 2) outer margin of distal endopodal segment of second thoracopod ornamented with long setules in male, 3) caudal seta VII located halfway from base of rami (vs. on anterior extremity in D. ezoensis), and 4) sixth thoracopod with three setae in female (vs. 2 setae in D. ezoensis). In addition, there is also a mitochondrial COI sequence difference of more than 19.93% with D. ezoensis registered in NCBI. A key to Diosaccus species of the world is also provided, and new morphological features and DNA sequences are presented for two other harpacticoid species, Parathalestris verrucosa Itô, 1970 and Peltidium quinquesetosum Song & Yun, 1999. In order to clearly identify harpacticoids at the species level, both morphological and DNA sequence characteristics should be considered.

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<![CDATA[Revision of the genus Hoplodrina Boursin, 1937 (Lepidoptera, Noctuidae, Xyleninae). I. Hoplodrina octogenaria (Goeze, 1781) and its sister species H. alsinides (Costantini, 1922) sp. rev. in Europe]]> https://www.researchpad.co/article/N0edc772b-3fac-452d-87a9-685bb59cfb30

Abstract

The taxonomic status of the European Hoplodrina octogenaria (Goeze, 1781) is discussed and its partly sympatric sister species, Hoplodrina alsinides (Costantini, 1922) sp. rev., is separated and re-described based on morphological and molecular taxonomic evidence. The adults and their genitalia are illustrated and DNA barcodes, as well as genome-wide single nucleotide polymorphism data collected by fractional genome sequencing (ddRAD), of the two species are provided.

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<![CDATA[Two new pseudoscorpion species (Pseudoscorpiones, Chthoniidae, Cheiridiidae) from the Tonga Islands, Polynesia, with a redescription of the genus Nesocheiridium]]> https://www.researchpad.co/article/N0afe97fc-4184-492a-85ac-3a712e683109

Abstract

The genera Tyrannochthonius Chamberlin, 1929 and Nesocheiridium Beier, 1957 are recorded from the Tonga Islands, Polynesia, for the first time. Tyrannochthonius euasp. nov. is described from the island of Eua. Nesocheiridium onevaisp. nov. is described from the island of Onevai. This is the first discovery of a representative of the genus Nesocheiridium in more than 60 years. The holotype of the type species, Nesocheiridium stellatum Beier, 1957, is redescribed, allowing a better understanding of this poorly known genus. The genus Nesocheiridium is diagnosed by the following combination of characters: integument coarsely granulate, dorsally granulo-reticulate; vestitural setae either relatively long, with a leaf-like outline, or arcuate with a small spine; cucullus short; only 10 abdominal tergites visible in dorsal view; cheliceral rallum of four blades; venom apparatus present in both chelal fingers; fixed chelal finger with granulate swelling mesally and seven trichobothria; trichobothria ib and ist located distad of granulate swelling; eb and esb situated close together at the base of the finger; moveable chelal finger with two trichobothria.

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<![CDATA[Study on the Pauropoda (Myriapoda) from Tibet, China – Part II: New species and new record of the genus Samarangopus]]> https://www.researchpad.co/article/Nd6677365-1f4f-4407-b808-59bd92d74001

Abstract

The pauropod family Eurypauropodidae Ryder, 1879 is recorded from Tibet, China for the first time. In this study, a new species Samarangopus zhongisp. nov. is described and illustrated from Motuo County, southeastern Tibet of China. It is distinguished from other species in this genus by having one pair of spiniform appendages on the sternum of the last trunk segment, 28–34 marginal protuberances on tergite I, the distal quarter of bothriotricha T3 golf-club-shaped, and the leaf-shaped seta st on tergum of pygidium. In addition, Samarangopus canalis Scheller, 2009 is newly recorded from China.

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<![CDATA[The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms]]> https://www.researchpad.co/article/N1f661d3e-d0c0-407e-92c0-bb72cd78029d

The mitochondrial genomes of flowering plants are well known for their large size, variable coding-gene set and fluid genome structure. The available mitochondrial genomes of the early angiosperms show extreme genetic diversity in genome size, structure, and sequences, such as rampant HGTs in Amborella mt genome, numerous repeated sequences in Nymphaea mt genome, and conserved gene evolution in Liriodendron mt genome. However, currently available early angiosperm mt genomes are still limited, hampering us from obtaining an overall picture of the mitogenomic evolution in angiosperms. Here we sequenced and assembled the draft mitochondrial genome of Magnolia biondii Pamp. from Magnoliaceae (magnoliids) using Oxford Nanopore sequencing technology. We recovered a single linear mitochondrial contig of 967,100 bp with an average read coverage of 122 × and a GC content of 46.6%. This draft mitochondrial genome contains a rich 64-gene set, similar to those of Liriodendron and Nymphaea, including 41 protein-coding genes, 20 tRNAs, and 3 rRNAs. Twenty cis-spliced and five trans-spliced introns break ten protein-coding genes in the Magnolia mt genome. Repeated sequences account for 27% of the draft genome, with 17 out of the 1,145 repeats showing recombination evidence. Although partially assembled, the approximately 1-Mb mt genome of Magnolia is still among the largest in angiosperms, which is possibly due to the expansion of repeated sequences, retention of ancestral mtDNAs, and the incorporation of nuclear genome sequences. Mitochondrial phylogenomic analysis of the concatenated datasets of 38 conserved protein-coding genes from 91 representatives of angiosperm species supports the sister relationship of magnoliids with monocots and eudicots, which is congruent with plastid evidence.

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