A new record and a novel morph description of Boigastoliczkae (Squamata, Colubridae) from China.

Background: The Asian Cat Snake genus Boiga Fitzinger, 1826 includes 37 species, with high species diversity. Five species of Boiga have been recorded in China including B.multomaculata (Boie, 1827), B.kraepelini (Stejneger, 1902), B.cyanea (Duméril, Bibron & Duméril, 1854), B.guangxiensis (Wen, 1998) and B.siamensis (Nutaphand, 1971). Previously, the validity of the species Boigastoliczkae (Wall, 1909) was controversial. B.stoliczkae was considered in synonymy with B.ochracea. Currently, the taxonomy of B.multomaculata and B.ochracea (Theobald, 1868) was revised so that B.multomaculata and B.ochracea actually represent a single species and B.stoliczkae was recognised as a valid species. B.stoliczkae was previously known to be found in the west from central Nepal through Darjeeling, Sikkim and Bhutan to Arunachal Pradesh and Assam in north-eastern India. New information: One adult female specimen of the Asian Cat Snake was collected from Gyirong County, near the China-Nepal border, Tibet, China during fieldwork on August 2023. We compared morphology and mitochondrial DNA sequence data with all the species of the genus Boiga. Both datasets strongly supported referring the Chinese specimens to B.stoliczkae (Wall, 1909) due to the 21 mid-dorsal scale rows and the uncorrected p-distance (mitochondrial DNA gene cytochrome b) between this specimen and B.stoliczkae which is 1.7%. We further described morphological characters of the Chinese specimen in detail and compared these with the specimens that had been previously described. The dorsal ground colour of the Chinese specimen is dark brown, with a black stripe distributed almost evenly across the tail. This is a novel morph of the species B.stoliczkae. The newly-collected Chinese specimen expands the distribution of the species on the Himalaya range.

A new species of the genus Hebius (Squamata, Natricidae) from Yunnan, China.

A new species of the genus Hebius Thompson, 1913 is described from Yingjiang County, Dehong Dai and Jingpo Autonomous Prefecture, Yunnan Province, China, based on molecular and morphological evidence. It can be distinguished from its congeners by the following set of characters: (1) dorsal scale rows 19-17-17, feebly keeled; (2) ventrals 146-151; (3) nasal complete, nostril in the middle of the nasal; (4) supralabials 9, the fourth to sixth in contact with the eye; (5) infralabials 10-11, the first 5 touching the first pair of chin shields; (6) preoculars 2; (7) postoculars 3; (8) temporals 3, arranged in two rows (1+2); (9) maxillary teeth 31, the last 4 slightly enlarged, without diastema; (10) tail comparatively long, TAL/TL ratio 0.334 in the male; (11) dorsolateral series of irregular orange or ochre yellow blotches, extending from the neck to the posterior part of the tail; and (12) venter pale orange, tips of ventrals with subrectangular black blotches. All Hebius specimens were strongly recovered as monophyletic, in which Hebiustaronensis (Smith, 1940) and Hebiusvenningi (Wall, 1910) were monophyletic as sister to the Yingjiang County specimens. According to the p-distance of cytochrome b, the new species differs from its congeners by 9.7-15.4%.

Genome assembly and annotation of the king ratsnake, Elaphe carinata.

The king ratsnake (Elaphe carinata) of the genus Elaphe is a common large, non-venomous snake widely distributed in Southeast and East Asia. It is an economically important farmed species. As a non-venomous snake, the king ratsnake predates venomous snakes, such as cobras and pit vipers. However, the immune and digestive mechanisms of the king ratsnake remain unclear. Despite their economic and research importance, we lack genomic resources that would benefit toxicology, phylogeography, and immunogenetics studies. Here, we used single-tube long fragment read sequencing to generate the first contiguous genome of a king ratsnake from Huangshan City, Anhui province, China. The genome size is 1.56 GB with a scaffold N50 of 6.53M. The total length of the genome is approximately 621 Mb, while the repeat content is 42.26%. Additionally, we predicted 22,339 protein-coding genes, including 22,065 with functional annotations. Our genome is a potentially useful addition to those available for snakes.

A New Species of Pareas (Squamata, Pareidae) from Guangxi Province, China.

We described a new species of genus Pareas from Baise City, Guangxi Zhuang Autonomous Region, China, based on morphological and molecular evidence. Pareas baiseensis sp. nov. is distinguished from its congeners by the combination of (1) Yellowish-brown body colouration; (2) Frontal subhexagonal to diamond-shaped with its lateral sides converging posteriorly; (3) The anterior pair of chin shields is longer than it is broad; (4) Loreal not in contact with the eye, prefrontal in contact with the eye, two or three suboculars; (5) Rows of 15-15-15 dorsal scales, five rows of mid-dorsal scales keeled at the middle of the body, one vertebral scale row enlarged; (6) 187-191 ventrals, 89-97 subcaudals, all divided, cloacal plate single; (7) Two postocular stripes, the nuchal area forming a dark black four-pointed fork collar with the middle tines shorter than the outside tines. The genetic divergence (uncorrected p-distance) between the new species and other representatives of Pareas ranged from 13.9% to 24.4% for Cytochrome b (Cyt b) and 12.1% to 25.5% for NADH dehydrogenase subunit 4 (ND4). Phylogenetic analyses of mitochondrial DNA gene data recovered the new species from being the sister taxon to (P. boulengeri + P. chinensis) from China.

A new species of the genus Achalinus (Squamata: Xenodermidae) from Nanning, Guangxi, China.

We describe a new species of the genus Achalinus Peters, 1869 from Daming Mountain, Shanglin County, Nanning City, Guangxi Zhuang Autonomous Region, China, based on a single adult male specimen. It can be distinguished from all the other species in Achalinus by a combination of the following morphological characters: (1) a bright yellow collar around the neck, extending forward to the ventral of the head; (2) tail length comparatively long, TaL/Tol ratio 0.25; (3) DSR 23-23-23, moderately keeled; (4) VS 3+162; (5) SC 74, unpaired; (6) cloacal plate entire; (7) SPL 6, the fourth and fifth in contact with the eye; (8) IFL 6, the first three touching the first pair of chin shields; (9) a single loreal; (10) length of suture between internasal significantly longer than that between prefrontal, LSBI/LSBP ratio 1.34; (11) two pairs of chin shields; (12) longitudinal vertebral line absent. In addition, the uncorrected p-distances between the new species and other known congeners ranged from 6.3% to 25.4% for the cytochrome c oxidase subunit 1 (CO1). With the addition of the new species the total number of described Achalinus species is increased to 23 of which 17 are found in China.

A new species of the Genus Hebius Thompson, 1913 (Squamata: Colubridae) from Baise, Guangxi, China.

A new species of the genus Hebius Thompson, 1913 is described from Youjiang District, Baise City, Guangxi Zhuang Autonomous Region, China, based on a single adult female specimen. It can be distinguished from its congeners by the following combination of characters: (1) dorsal scale rows 19-17-17, feebly keeled except the outermost row; (2) tail length comparatively long, TAL/TL ratio 0.30 in females; (3) ventrals 160 (+ 3 preventrals); (4) subcaudals 112; (5) supralabials 9, the fourth to sixth in contact with the eye; (6) infralabials 10, the first 5 touching the first pair of chin shields; (7) preocular 1; (8) postoculars 2; (9) temporals 4, arranged in three rows (1+1+2); (10) maxillary teeth 30, the last 3 enlarged, without diastem; (11) postocular streak presence; (12) background color of dorsal brownish black, a conspicuous, uniform, continuous beige stripe extending from behind the eye to the end of the tail; (13) anterior venter creamish-yellow, gradually fades to the rear, with irregular black blotches in the middle and outer quarter of ventrals, the posterior part almost completely black. The discovery of the new species increases the number of species in the genus Hebius to 51.

The genome assembly and annotation of the many-banded krait, Bungarus multicinctus.

Snakes are a vital component of wildlife resources and are widely distributed across the globe. The many-banded krait Bungarus multicinctus is a highly venomous snake found across Southern Asia and central and southern China. Snakes are an ancient reptile group, and their genomes can provide important clues for understanding the evolutionary history of reptiles. Additionally, genomic resources play a crucial role in comprehending the evolution of all species. However, snake genomic resources are still scarce. Here, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides genomic information on the genes involved in venom gland functions.

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs.

DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.

A new species of the genus Achalinus (Squamata: Xenodermidae) from Ningshan County, Shaanxi Province, China.

A new species of odd-scaled snake in the genus Achalinus is described from Ningshan County, Shaanxi Province, China, based on seven female specimens. Morphologically, the new species can be distinguished from its congeners by the following combination of characters: (1) dorsum iridescent and uniformly dark brown in preservative, longitudinal vertebral line absent; (2) light brown beneath; (3) dotted black streak in the middle of the subcaudals absent; (4) tail length relatively short, TaL/ToL 12-16%, in females; (5) fewer subcaudals, 41-46 in females; (6) dorsal scales 23 rows throughout, strongly keeled; the outer-most rows on both sides are also keeled and slightly enlarged; (7) one loreal; (8) internasal not fused to prefrontal; (9) suture between internasals is similar in size when compared to the suture between prefrontals; (10) preocular and postocular absent; (11) 6 supralabials; (12) 5 infralabials, the first 3 (rarely 2) touching the first pair of chin shields; (13) 3 pairs of chin shields. A phylogenetic analysis using mitochondrial gene, cytochrome c oxidase subunit 1 (CO1), showed that this new species forms a monophyletic group with strong support. In addition, the uncorrected p-distances between the new species and other known congeners ranged from 3.4% to 13.0%. The recognition of the new species increases the number of described Achalinus species to 21.

A new species of the Genus Pelodiscus Fitzinger, 1835 (Testudines: Trionychidae) from Huangshan, Anhui, China.

A new species of the soft-shelled turtle genus Pelodiscus is described based on seven specimens from Huangshan, southern Anhui Province, China. The new species, Pelodiscus huangshanensis sp. nov., is distinguished from other species in the genus Pelodiscus by the following characteristics: (1) Small size (maximum carapace length of 101.16 mm and maximum body length of 190 mm); (2) keel high; (3) tiny yellowish-white spots on the throat; (4) no black pinstripes around the eyes; (5) white longitudinal bands on both sides of the neck in juveniles, absent in adults; (6) plastron yellowish-white, and only a dark patch on each side of the armpit; (7) many tubercles on the dorsal surface, but indistinct in the center; and (8) entoplastron ⌒ shaped. The phylogenetic relationships of the species in Pelodiscus were reconstructed using the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) genes. The new species formed a monophyletic clade with strong support. The uncorrected pairwise distances between the new species and other representatives of Pelodiscus ranged from 5.4% to 9.2% for cyt b and 4.1% to 7.6% for ND4. The new species brings the number of species of the genus Pelodiscus to six; five species are distributed in China, with three species endemic to China.

Mitochondrial genome of the Boulenger's Slug-eating snake Pareas boulengeri (Serpentes: Pareidae).

The Boulenger's Slug-eating snake Pareas boulengeri is a species of snake in the family Pareidae. The complete mitochondrial genome sequence (mitogenome) of this species was determined by shotgun sequencing. The total length of mitogenome is 16,778 bp and contains 13 protein-coding genes, 22 tRNA genes, two ribosome RNA genes, and two control regions (CR). Its base composition was 31.6% for A, 24.6% for T, 14.5% for G and 29.3% for C. All the protein-coding genes in P. boulengeri were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of P. boulengeri and 13 other related species was reconstructed using the maximum-likelihood (ML) method. The DNA data presented here will be useful to study the evolutionary relationships of P. boulengeri.

The complete mitochondrial genome of Sphenomorphus indicus (Reptilia: Scincidae).

The complete mitochondrial genome (mitogenome) sequence of Sphenomorphus indicus was sequenced and characterized by next-generation sequencing technology. The total length of mitogenome is 17,027 bp and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 non-coding regions (the control region and the putative L-strand replication origin). Most of the genes of S. indicus are encoded on the H-strand, except for the ND6 subunit gene and 8 tRNA genes which is distributed on the L-strand. Phylogenetic reconstruction suggested that S. indicus is the sister group of the S. incognitus within the genus Sphenomorphus. The complete mitochondrial genome sequence presented here will be useful to study the evolutionary relationships and genetic diversity of S. indicus.

Complete mitochondrial genome of the sharp-snouted pitviper Deinagkistrodon acutus (Reptilia, Viperidae).

The sharp-snouted pitviper, Deinagkistrodon acutus, belongs to the monotypic genus Deinagkistrodon of the family Viperidae. It is one of the important species of snakes for its commercial and medicinal value. Complete mitochondrial genome sequence of the D. acutus was sequenced by next-generation sequencing technology. The total mitochondrial genome is 17,538 bp in length, containing 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 control regions. Most of the genes of D. acutus are encoded on the H-strand, except for the ND6 subunit gene and eight tRNA genes which distribute on the L-strand. Phylogenetic reconstruction result indicated that our newly determined mitochondrial genome sequence could meet the demands. The complete mitochondrial genome sequence presented here will be useful to study the evolutionary relationships and genetic diversity of D. acutus.

Four complete mitochondrial genomes of living wild-type chinese giant salamander Andrias davidianus (Amphibia: Cryptobranchidae).

The Chinese giant salamander (CGS), Andrias davidianus (Amphibian, Caudata, Cryptobranchidae), is endemic to China. After overhunting in the 1990's, it is very difficult to find the CGS in the wild. Due to mating disorder, the captive breeding population is genetically confounded. The genetic backgrounds of all wild-release individuals in China are not explicit. Herein, we reported four living wild-type complete mitochondrial genomes of this species. The gene order and contents are identical to those found in typical vertebrates. Thirteen protein-coding genes (PCGs) of 7 A. davidianus (4 from this study, 3 retrieved from GenBank) and 11 other closely species retrieved from GenBank were used to reconstruct phylogenetic tree. The Maximum likelihood (ML) topology shown that the clade of CGS has two subclades with a high support (100%). This study provides partial fundamental information for further exploring the true genetic background of whole population of A. davidianus.

Mitochondrial genome of the Common burrowing snake Achalinus spinalis (Reptilia: Xenodermatidae).

Common burrowing snake Achalinus spinalis is the type species of Achalinus. The complete mitochondrial genome (mitogenome) sequence of A. spinalis was determined by using a PCR-based method. The total length of mitogenome is 17,165 bp and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions (CR). All the protein-coding genes in A. spinalis were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of A. spinalis and 12 other closely species was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of A. spinalis.

Complete mitochondrial genome of the Rufous burrowing snake, Achalinus rufescens (Reptilia: Xenodermatidae).

The complete mitochondrial genome (mitogenome) sequence of Achalinus rufescens was determined by using a PCR-based method. The total length of mitogenome is 17,339 bp and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions (D-loop). All the protein-coding genes of A. rufescens were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of A. rufescens and 11 other closely species was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of A. rufescens.

The complete mitochondrial genome of Zosterops japonicas (Aves, Zosteropidae).

The complete mitochondrial genome (mitogenome) sequence of Zosterops japonicus was determined by shotgun sequencing. The total length of mitogenome is 17 809 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions (CR). All the protein-coding genes in Z. japonicus were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of Z. japonicus and 13 other species belonging to order Passeriformes was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of Z. japonicus.

Complete mitochondrial genome sequence of Eurasian blackbird, Turdus merula (Aves: Turdidae).

The complete mitochondrial genome (mitogenome) sequence of Eurasian blackbird, Turdus merula was determined by shotgun sequencing. The total length of mitogenome is 16 730 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 1 control region (D-loop). All the protein-coding genes in T. merula were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The gene order and contents in the T. merula mitogenome is identical to that found in typical vertebrates. The phylogenetic tree of T. merula and 13 other species belonging to order Passeriformes was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of T. merula.

Complete mitochondrial genome of oriental magpie-robin Copsychus saularis (Aves: Muscicapidae).

The total length of mitogenome of Copsychus saularis is 16 827 bp and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one D-loop. The phylogenetic tree of C. saularis and 13 other species belonging to Passeriformes was built.