The complete mitochondrial genome of the lipid-producing yeast Rhodotorula toruloides

ABSTRACT Mitochondria are semi-autonomous organelles with their own genome and crucial to cellular material and energy metabolism. Here, we report the complete mitochondrial genome of a lipid-producing basidiomycetous yeast Rhodotorula toruloides NP11. The mitochondrial genome of R. toruloides NP11 was assembled into a circular DNA molecule of 125937bp, encoding 15 proteins, 28 transfer RNAs, 2 ribosomal RNA subunits and 10 open reading frames with unknown function. The G + C content (41%) of the mitochondrial genome is substantially lower than that of the nuclear genome (62%) of R. toruloides NP11. Further reanalysis of the transcriptome data confirmed the transcription of four mitochondrial genes. The comparison of the mitochondrial genomes of R. toruloides NP11 and NBRC0880 revealed a significant genetic divergence. These data can complement our understanding of the genetic background of R. toruloides and provide fundamental information for further genetic engineering of this strain.

A new species of the genus Lycodon (Serpentes, Colubridae) from Guangxi, China

A new species of colubrid snake, Lycodon cathayasp. nov., is described based on two adult male specimens collected from Huaping Nature Reserve, Guangxi, southern China. In a phylogenetic analyses, the new species is shown to be a sister taxon to the clade composed of L. futsingensis and L. namdongensis with low statistical support, and can be distinguished from all known congeners by the significant genetic divergence in the mitochondrial cytochrome b gene fragment (p-distance ≥ 7.9%), and morphologically by the following combination of characters: (1) dorsal scales in 17–17–15 rows, smooth throughout; (2) supralabials eight, third to fifth in contact with eye, infralabials nine; (3) ventral scales 199–200 (plus two preventral scales), subcaudals 78; (4) loreal single, elongated, in contact with eye or not, not in contact with internasals; (5) a single preocular not in contact with frontal, supraocular in contact with prefrontal, two postoculars; (6) maxillary teeth 10 (4+2+2+2); (7) two anterior temporals, three posterior temporals; (8) precloacal plate entire; (9) ground color from head to tail brownish black, with 31–35 dusty rose bands on body trunk, 13–16 on tail; (10) bands in 1–2 vertebral scales broad in minimum width; (11) bands separate ground color into brownish black ellipse patches arranged in a row along the top of body and tail; (12) elliptical patches in 3–6 scales of the vertebral row in maximum width; (13) ventral surface of body with wide brownish black strip, margined with a pair of continuous narrow greyish white ventrolateral lines. With the description of the new species, 64 congeners are currently known in the genus Lycodon, with 16 species occurring in China.

A new pit viper of the genus Trimeresurus (Lacépède, 1804) (Squamata: Viperidae) from Southwest China

The white-lipped tree viper, Trimeresurus albolabris Gray, is one of the most common species of the genus Trimeresurus with a wide distribution from India eastwards to China and southwards to Indonesia. However, this species was previously split into five geographical clades with significant genetic divergence. Recent surveys in Yingjiang County, Yunnan Province, China resulted in the discovery of one cryptic species of the subgenus Trimeresurus. Combining molecular, morphological and ecological data, we describe it as a new species Trimeresurus caudornatus sp. nov. The new species differs from other Trimeresurus species by a combination of the following characteristics: (1) Head and body generally dark green, postocular stripes absent in both genders, upper labials light green; (2) ventrolateral stripe faint green yellow, present on the first row of DSR in both genders; (3) iris golden yellow in both genders; (4) dorsal tail mostly dark red, lateral and ventral green; an orange red stripe along the ventral part of the tail; (5) DSR 21/22 –21–15, VEN 161–163, SC 52–72; (6) first upper labial partially fused to the nasal. The new species was shown to be a strongly supported monophyletic group (BPP 100%) and sister to T. septentrionalis. The uncorrected pairwise distances of mitochondrial gene Cytb between the new species and other species of the subgenus Trimeresurus, ranging from 0.059 (T. septentrionalis) to 0.134 (T. kanburiensis).

A new species of the genus Achalinus from southwestern Guangdong Province, China (Squamata: Xenodermatidae)

A new species of xenodermatid snake, Achalinus yunkaiensis J. Wang, Y. Li & Y.Y. Wang, sp. nov. was described based on a series of specimens collected from Dawuling Forestry Station located in the Yunkai Mountains of western Guangdong Province. It can be distinguished from known congeners by a significant genetic divergence at the mitochondrial CO1 gene fragment examined (p-distance ≥ 12.0%) and the following combination of characters: (1) dorsal scales strongly keeled, in 23 rows throughout the body, the most outer row on each side smooth and significantly enlarged; (2) tail relatively shorter, TaL/TL ratio 18.5–20.0%; (3) maxillary teeth 20–22; (4) length of suture between internasals subequal to that between the prefrontals; (5) nasal divided into two sections by nasal cleft, posterior one half as long as anterior; (6) loreal elongated, nearly twice as wide as high; (7) supralabials six; (8) infralabials six; (9) temporals 2+2+3 (rarely 2+2+4), the two anterior temporals in contact with eye; (10) ventrals 151–162, subcaudals 49–56 arranged in single row, not paired; (11) cloacal entire; (12) uniform brown (in adults) or black (in juveniles) above, tinged weakly iridescent, with a longitudinal dark-colored vertebral line; (13) light brown (in adults) or greyish white (in juveniles) beneath; and (14) dorsum with a longitudinal dark brown vertebral stripe from posterior margin of parietals to tail tip. Currently, 13 species are known in the genus Achalinus, with seven from mainland China.

A new species of the genus Hebius (Squamata: Colubridae: Natricinae) from Hunan Province, China

A new snake species of the genus Hebius is described on the basis of three specimens from Hunan Province, China. The new species can be distinguished from its congeners by a significant genetic divergence of 6.1%–12.9% of the mitochondrial cytb gene and a combination of the following morphological characters: (1) tail long, approximately 25% of the total length; (2) dorsal scale rows 19-19-17, vertebral scales enlarged, smooth, 2nd–10th rows distinctly keeled; (3) anterior temporals 2, preocular 1, postoculars 3; (4) ventrals 160–164; (5) internasals narrowed anteriorly; (6) a pair of occipital spots and a pale postparietal streak; (7) a pale brown or beige dorsolateral stripe on the 4th–6th scale rows; (8) ventral scales brick-red at their outer border, with a row of well-defined dark blotches; (9) maxillary teeth 21, gradually enlarged, followed by 2 moderately enlarged posterior teeth, without diastema; (10) nostrils lateral.

Redescription of Hargeria rapax (Harger, 1879) and description of H. chetumalensis a new species from the Mexican Caribbean (Crustacea, Peracarida, Tanaidacea, Leptocheliidae) based upon morphological and molecular evidence

Until now, Hargeria was considered a monospecific leptocheliid genus, with the species Hargeria rapax considered a taxon with a wide distribution, from the Northwestern Atlantic to the Mexican Caribbean. Herein, after a detailed revision of type and topotype materials and specimens collected from the Mexican Caribbean, a new species H. chetumalensis sp. nov. is described, and the redescription of H. rapax is provided. Also, we found a significant genetic divergence between the two species based on the nucleotide sequences of cytochrome oxidase subunit I, which support the morphological data. The morphological features used to recognize both species are also adequate to link males, females, and juvenile stages, although these species have a high intraspecific polymorphism.

Cladocopium community divergence in two Acropora coral hosts across multiple spatial scales

Many broadly-dispersing corals acquire their algal symbionts (Symbiodiniaceae) ‘horizontally’ from their environment upon recruitment. Horizontal transmission could promote coral fitness across diverse environments provided that corals can associate with divergent algae across their range and that these symbionts exhibit reduced dispersal potential. Here we quantified community divergence of Cladocopium algal symbionts in two coral host species (Acropora hyacinthus, Acropora digitifera) across two spatial scales (reefs on the same island, and between islands) across the Micronesian archipelago using microsatellites. We find that both hosts associated with two genetically distinct Cladocopium lineages (C40, C21), confirming that Acropora coral hosts associate with a range of Cladocopium symbionts across this region. Both C40 and C21 exhibited extensive clonality. Clones not only existed across host conspecifics living on the same reef, but also spanned host species, reef sites within islands, and even different islands. Both Cladocopium lineages exhibited moderate host specialization and divergence across islands. In addition, within every island, algal symbiont communities were significantly clustered by both host species and reef site, highlighting that coral-associated Cladocopium communities are structured across small spatial scales and within hosts on the same reef. This is in stark contrast to their coral hosts, which never exhibited significant genetic divergence between reefs on the same island. These results support the view that horizontal transmission could improve local fitness for broadly dispersing Acropora coral species.

DNA testing of edible crabs from seafood shops on the Odisha coast, India

Seafood consumption is highly demanding due to the important source of protein it contains, as well as being rich in omega-3 fatty acids. However, the adulteration of seafood is an alarming issue worldwide, including India. This study deals with edible crabs from seafood shops on the Odisha state coast in eastern India. The generated DNA barcode sequences successfully identified most of the studied brachyuran crab species by similarity search results in global databases. The species were also delimited by significant genetic divergence and Neighbour-Joining phylogeny. Additionally, the study detected the contamination of unknown organisms in the commercialized crab recipes from seafood shops. The DNA based species detection of brachyuran crab may be useful to resolve many ambiguities in species identification and monitoring of commercialized seafood concerning food safety.

COXI based phylogenetic analysis of Caucasian clade of European Troglocaris (Crustacea: Decapoda: Atyidae) with the suggestion of a new taxonomic group structure

New genetic data on Caucasian troglobiotic shrimps collected from the territory of Russia, Abkhazia and Western Georgia are presented. Based on new genetic data on the marker region of subunit I of cytochrome oxidase of mitochondrial DNA (COXI mtDNA) of Caucasian species and other taxa of European cave shrimps (Troglocaris s.l.) from GenBank (NCBI) database, a new generic structure is presented. Based on a significant genetic divergence of COXI mtDNA subgenera of Troglocaris s.l., namely Troglocaris s.s., Xiphocaridinella and Spelaeocaris, should be considered as separate genera while Troglocaris (Troglocaridella) hercegovinensis (Babić, 1922) is suggested to be transferred within Dinaric genus Spelaeocaris as Spealeocaris hercegovinensis (Babić, 1922) comb. nov. Besides, Troglocaris bosnica shows a significant a genetic difference (at the level of the separate genus) from the remaining representatives of the genus Troglocaris s.s. Moreover, p-distances (COXI) of about 17% are supposed for generic separation within European Troglocaris-related atyid shrimps and 5% for separation of cryptic species within Caucasian Xiphocaridinella. A list of all known taxa of Troglocaris-related atyid shrimps of the European part and a discussion of the general distribution of troglocaridid atyid shrimps in the Balkans and the Caucasus are presented. A new version of divergence events between Dinaric–Caucasian Troglocaris lineages (genera) based on new genetic data is suggested.

Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom

Diatoms contribute roughly 20% of global primary production, but the factors determining their ability to adapt to global warming are unknown. Here we quantify the capacity for adaptation to warming in the marine diatom Thalassiosira pseudonana. We found that evolutionary rescue under severe warming was slow but adaptation to more realistic scenarios, where temperature increases were moderate or where they fluctuated between benign and severe conditions, was rapid. Adaption to warming was linked to major phenotypic changes in metabolism and elemental composition. Whole genome re-sequencing identified significant genetic divergence both among populations adapted to the different warming regimes and between the evolved and ancestral lineages. Consistent with the phenotypic changes, the most rapidly evolving genes were associated with transcriptional regulation, cellular response to oxidative stress and redox homeostasis. These results demonstrate that evolution of thermal tolerance in marine diatoms can be rapid, particularly in fluctuating environments, and is underpinned by major genomic and phenotypic divergence.