Complete mitochondrial genome of Guigarracailaoensis Wang, Chen & Zheng, 2022 (Cypriniformes, Cyprinidae) and its phylogenetic implications.

Guigarracailaoensis is a member of family Cyprinidae, subfamily Labeoninae (Cypriniformes) which was recently discovered in southwestern China. Following its initial description, additional information on this species has remained notably scarce. In the current study, we assemble the complete mitochondrial genome (mitogenome) of G.cailaoensis using the Illumina sequencing platform. The mitogenome is identified as a circular, double-stranded DNA sequence of 16,593 base pairs, encompassing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Maximum-likelihood and Bayesian-inference approaches were used to construct phylogenetic trees for three datasets: (i) PCG sequences of the complete mitogenome (dataset 1); (ii) PCG sequences of the complete mitogenome combined with nuclear DNA (ncDNA) (Rag1) sequence (dataset 2); and (iii) ncDNA (Rag1) sequences (dataset 3). Phylogenetic analyses position G.cailaoensis as a sister taxon to the lineage consisting of Paraqianlabeolineatus Zhao, Sullivan, Zhang & Peng, 2014 and Pseudogyrinocheilusprochilus Fang, 1933 in dataset 1, and to Pseudogyrinocheilusprochilus in dataset 2, species lacking an oral disc on the lower lip. However, G.cailaoensis showed a close relationship to the lineage consisting of Discogobio and Discocheilus in dataset 3, species possessing an oral disc on the lower lip. Nonetheless, a variety of species with an oral disc on the lower lip are clustered into different lineages across the three datasets that may indicate that the development of the oral disc is homoplastic within the subfamily Labeoninae. The outcomes of this study have the potential to support conservation efforts for this species and to enrich our understanding of genetic resources in the area.

Characterization and Phylogenetic Analysis of the Chloroplast Genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor.

This study sequenced the complete chloroplast genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor using the Illumina NovaSeq and PacBio RSII platforms. Following sequencing, the genomes were assembled, annotated, comparatively analyzed, and used to construct a phylogenetic tree to explore their phylogenetic positions. Results indicated that the chloroplast genomes of S. japonica var. timoriensis and S. japonica var. discolor both displayed a typical double-stranded circular tetrameric structure, measuring 157,609 and 157,748 bp in length, respectively. Each genome contained 130 annotated genes, with similar total GC content and relative codon usage patterns, showing a distinct preference for A/U at the third codon position. Simple sequence repeat analysis identified 207 and 211 repeats in S. japonica var. timoriensis and S. japonica var. discolor, respectively, primarily the A/T type. Boundary condition analysis indicated no significant expansion or contraction in the inverted repeat regions with consistent gene types and locations across both varieties. Nucleotide polymorphism analysis highlighted greater variation in the intergenic regions than in the coding sequences of Stephania chloroplast genomes. Phylogenetic analyses demonstrated that the species Stephania clustered into a distinct, well-supported clade. Notably, Stephania japonica, along with S. japonica var. discolor and S. japonica var. timoriensis, established a monophyletic lineage. Within this lineage, S. japonica and S. japonica var. discolor were closely related, with S. japonica var. timoriensis serving as their sister taxon.

Development of polymorphic microsatellite markers for distylous-homostylous Primula secundiflora (Primulaceae) using HiSeq sequencing.

Primula secundiflora is an insect-pollinated, perennial herb belonging to the section Proliferae (Primulaceae) that exhibits considerable variation in its mating system, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers should provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in P. secundiflora.

Characterization of the complete chloroplast genome of Fibraurea recisa Pierre 1885 (Menispermaceae), an important medicinal herb from Yunnan, China.

Fibraurea recisa Pierre 1885, which belongs to the family Menispermaceae, is an important medicinal herb in Yunnan, China. Despite its importance, genetic studies on this species remain rare. Therefore, in the current study, we assembled the complete chloroplast genome of F. recisa. Results showed that the complete genome was 161,671 bp in length, including a large single-copy region (LSC, 91,071 bp), small single-copy region (SSC, 20,858 bp), and two inverted repeat regions (IRa and IRb, 24,871 bp). The genome consisted of 124 genes, including 87 protein-coding genes, 29 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that F. recisa was most closely related to species of Tinospora within Menispermaceae. Our complete chloroplast genome of F. recisa should contribute to the genetic resource assessment of this species as well as its future conservation and utilization.

Characterization of the complete chloroplast genome of Centranthera grandiflora Benth (Orobanchaceae), an important species of medicinal herb.

Centranthera grandiflora is an important medicinal herb within Orobanchaceae. To date, however, genetic studies on this species remain poor. Here, we assembled the complete chloroplast genome of C. grandiflora. Results showed that the genome was 147 655 bp in length, consisting of large and small single copy regions of length 83 550 and 14 891 bp, respectively, separated by two inverted repeat regions of 24 607 bp. Furthermore, the genome contained 132 genes, including 84 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that C. grandiflora is closely related to the species of Orobanchaceae. The complete chloroplast genome of C. grandiflora should help in the conservation of genetic resources and appropriate utilization of this medicinal herb in the future.

Genetic diversity and population demography of the endemic species Acrossocheilus longipinnis (Teleostei, Cyprinidae) based on mtDNA COI and cyt b gene sequences.

In this study, we investigated the population genetic structure and demographic history of Acrossocheilus longipinnis based on two mitochondrial genes (cytochrome b and cytochrome oxidase subunit I). A total of 14 haplotypes were identified for A. longipinnis. The total haplotype diversity and nucleotide diversity are 0.68586 and 0.00358, respectively, which suggest that A. longipinnis exhibits a low genetic diversity. The monophyly of A. longipinnis is not rejected by the analyses, and the species can be divided into two lineages. The analysis of molecular variance shows that more variation of genetic differentiation is present within populations than among populations. The negative values and mismatch analysis support that A. longipinnis underwent expansion and the times are estimated to be 0.07754 and 0.01977 MYA for the two lineages, respectively. These results reveal the genetic backgrounds of A. longipinnis and provide a rational basis for the implementation of more effective measures for its conservation.

Genetic diversity and population structure of Acrossocheilus yunnanensis (Teleostei, Cyprinidae) inferred from four mitochondrial gene sequences.

In this paper, we examine the genetic diversity, population structure and demographic history of Acrossocheilus yunnanensis inferred from four mitochondrial gene sequences. Twenty-two haplotypes were identified for A. yunnanensis. The total haplotype and nucleotide diversities of A. yunnanensis are 0.9206 and 0.024654, respectively. The monophyly of the haplotypes is supported by all phylogenetic analyses. All the haplotypes can be divided into four major lineages. The results of AMOVA and SAMOVA suggest that the best grouping pattern is to divide four groups, and that most of the variation of genetic divergence is present among these groups. The population expansion of A. yunnanensis is not supported by the analyses of population demography. Our results revealing the genetic background of A. yunnanensis will prove helpful in protecting its genetic diversity and utilizing this resource in a reasonable manner.

Altigena malihkaia, a new species of Labeonini (Teleostei: Cyprinidae) from the Irrawaddy River basin in Myanmar.

Altigena malihkaia, new species, is described from the Mali Hka River, a tributary of the Irrawaddy River in northern Myanmar. It is distinguished from all other species of the genus Altigena by having a combination of 45-49 lateral-line scales, 12-14 circumpeduncular scales, 17-20 pre-dorsal midline scales, wide head (96.8-138.5% HL), long postorbital length (64.6-81.0 % HL), and short dorsal-fin (length 21.9-26.2% SL).

A new genus and species of Labeonini (Teleostei: Cyprinidae) from the Pearl River in China.

Zuojiangia jingxiensis, both a new genus and species, is described from the Pearl River in China. It is distinguished from all other genera and species of Labeonini by the unique combination of modified oromandibular structures and head skeleton: a well-developed, pendulous, and conspicuously arched rostral fold, with an entirely crenulated margin; prominent papillae densely covering the margin of the rostral fold and anterior part of the lower lip; long postlabial grooves, partitioning the lower lip into three parts; transverse branch of dentary longer than half the length of the longitudinal branch; stubby lateral process present at the anterolateral margin of the longitudinal branch of the dentary, close to the corner; in the upper jaw, the premaxilla bears a triangular ascending process tapering to a point; maxilla exhibits a pair of articular heads at the anterodorsal margin, and a distinct fingerlike descending process posterior to the medial articular head embracing the ascending process of the premaxilla.

Complete mitochondrial genome of two endemic species to China: Discocheilus wui and Discocheilus wuluoheensis (Cypriniformes, cyprinidae).

The genus Discocheilus is endemic to China and only distributed in the Pearl River. The complete mitochondrial genome of Discocheilus wui and Discocheilus wuluoheensis were successfully sequenced in this study. The complete mitochondrial genomes of these two species are 16,589 bp and 16,587 bp in length, respectively. They both consist of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The gene compositions and genome organizations of the two species are similar to other fish. The complete mitochondrial genome sequence of these two species will contribute to reveal the genetic backgrounds for their conservation.

Molecular systematics of the Labeonini inhabiting the karst regions in southwest China (Teleostei, Cypriniformes).

The major phylogenetic pattern of the cyprinid tribe Labeonini has been revealed by previous molecular studies; however, the relationships within a clade that mainly inhabits the karst regions, which we refer to as the "karst group", in southwest China remain unresolved due to the low taxon sampling. This group includes more than 50% of the genera and species of Labeonini in China. Moreover, more than 90% of the genera of this group are endemic to China. In addition, some new genera and species of Labeonini have been discovered from these karst regions, but their taxonomic validity and phylogenetic position have not been examined. In this contribution, partial sequences of four nuclear (exon 3 of recombination activating protein 1, rhodopsin, early growth response protein 2B gene and interphotoreceptor retinoid binding protein gene) and three mitochondrial genes (cytochrome b, cytochrome oxidase subunit I and 16S ribosomal RNA) from 36 ingroup taxa and 25 outgroup taxa were analyzed to provide a hypothesis of the phylogenetic relationships within the labeonins of the karst regions in China. We propose that the monophyly of Parasinilabeo, Ptychidio, Rectoris and Semilabeo are supported. A new genus, Prolixicheilus, is erected for Pseudogyrinocheilus longisulcus. Cophecheilus bamen is the sister to Prolixicheilus longisulcus. Ptychidio, Pseudocrossocheilus, Semilabeo, Rectoris and Stenorynchoacrum are closely related with high support values. Sinocrossocheilus, Pseudogyrinocheilus, Paraqianlabeo, Hongshuia, Discogobio and Discocheilus form a clade together with high support. Considering molecular results and morphological differences, Parasinilabeo longicorpus and Ptychidio macrops might be the synonyms of Parasinilabeo assimilis and Ptychidio jordani respectively. Comprehensive taxonomic revisions of the two genera Parasinilabeo and Ptychidio may be necessary.

[Status and conservation of fishes in the middle and lower Langcangjiang River].

According to the extant records, there are a total of 165 species of fish along the middle and lower Langcangjiang River. However, in recent years, only 71 of these species have been be collected, indicating that fish resources of the middle and lower Langcangjiang River are declining, especially the medium-large and rare-endemic species. Accordingly, this study suggests several new initiatives, including controlling introduced species, restricting fishing intensity and implementing fish reproduction and release.