Genome Assembly for a Yunnan-Guizhou Plateau “3E” Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications

Abstract

A Yunnan-Guizhou Plateau fish, the Kanglang white minnow (Anabarilius grahami), is a typical “3E” (Endangered, Endemic, and Economic) species in China. Its distribution is limited to Fuxian Lake, the nation’s second deepest lake, with a significant local economic value but a drastically declining wild population. This species has been evaluated as VU (Vulnerable) in the China Species Red List. As one of the “Four Famous Fish” in Yunnan province, the artificial breeding has been achieved since 2003. It has not only re-established its wild natural populations by reintroduction of the artificial breeding stocks, but also brought a wide and popular utilization of this species to the local fish farms. A. grahami has become one of the main native aquaculture species in Yunnan province, and the artificial production has been emerging in steady growth each year. To promote the conservation and sustainable utilization of this fish, we initiated its whole genome sequencing project using an Illumina Hiseq2500 platform. The assembled genome size of A. grahami is 1.006 Gb, accounting for 98.63% of the estimated genome size (1.020 Gb), with contig N50 and scaffold N50 values of 26.4 kb and 4.41 Mb, respectively. Approximately about 50.38% of the genome was repetitive. A total of 25,520 protein-coding genes were subsequently predicted. A phylogenetic tree based on 4,580 single-copy genes from A. grahami and 18 other cyprinids revealed three well-supported subclades within the Cyprinidae. This is the first inter-subfamily relationship of cyprinids at genome level, providing a simple yet useful framework for understanding the traditional but popular subfamily classification systems. Interestingly, a further population demography of A. grahami uncovered a historical relationship between this fish and Fuxian Lake, suggesting that range expansion or shrinkage of the habitat has had a remarkable impact on the population size of endemic plateau fishes. Additionally, a total of 33,836 simple sequence repeats (SSR) markers were identified, and 11 loci were evaluated for a preliminary genetic diversity analysis in this study, thus providing another useful genetic resource for studying this “3E” species.

Evolution of the intermuscular bones in the Cyprinidae (Pisces) from a phylogenetic perspective

“…The ancestral state reconstruction uncovered some groups, especially those in some monophyletic putative subfamilies, and had similar values to the ancestral number of IBs, such as Hypophthalmichthyinae (109–118), Xenocyprinae (109–134), Leuciscinae (114–141), Cultrinae (119–139), and Gobiobotinae (105–113). For a controversial phylogenetic position of Tinca (see more details in Jiang et al, ), the number of IBs showed closer relationship to Acheilognathinae than to other Leuciscinae, which was consistent with the current phylogenetic relationship in Figure . Another interesting pattern was detected in Sinocyclocheilus , the total number of IBs, epineurals, and epipleurals was distinctly varied, and these typical cave fishes (troglobites) had fewer IBs than atypical cave species (troglophiles; terms according to Zhao, Gozlan, & Zhang, ).…”

“…The tree topology (Figure ) was largely consistent with most of the previous genetic studies derived from different DNA fragments (Wang et al, ; Yang, Sado, et al, ). The three major subclades (Clades I, II, and III) were also identical with those found by Jiang et al (), who provided a well‐resolved inter‐subfamily relationship of cyprinids at genome level (although the monophyly of each subfamily was beyond their aims for that paper). In this study, discussion of the deep phylogenetic relationship of the Cyprinidae is not our main focus; however, the tree we present here indicates that most of the morphological‐based subfamilies proposed by Chen () are not monophyletic groups (Figure ), thus implying this popular 12‐subfamily classification (Chen, ) needs to be revised.…”

“…For instance, the species in Clade III‐2, including the nominal subfamilies Hypophthalmichthyinae, Xenocyprinae, and Cultrinae and some species of Leuciscinae and Gobiobotinae, turned out to have similar numbers of total IBs, epineurals, and epipleurals (Figure ). Tinca tinca, a species previously placed in the Leuciscinae, has long been treated as incertae sedis in both morphological and molecular studies (see more discussion in Jiang et al, ). Here, this species had a similar IB composition to Acheilognathus , but distinct from most other Leuciscinae species (Figure ).…”

“…Among them, 88 individuals were fresh samples collected from Yunnan province of China, and the others were ethanol‐preserved samples deposited in the Kunming Institute of Zoology (KIZ), Chinese Academy of Sciences. We identified samples according to the 12‐subfamily classification system of Chen (), which is one of the most useful and popular systems for taxonomic studies involving Chinese cyprinids (Jiang et al, ). We selected samples for a large coverage of all the 12 subfamilies, and we ensured that each subfamily included at least one genus and two species.…”

Comprehensive Transcriptional Changes in the Liver of Kanglang White Minnow (Anabarilius grahami) in Response to the Infection of Parasite Ichthyophthirius multifiliis

“…Kanglang white minnow (KWM), Anabarilius grahami, is a typical fish species with "3E" (Endangered, Endemic, and Economic) status and priorities in the Yunnan-Guizhou Plateau of China [1]. It has been known as one of the "Four Famous Fishes" in Yunnan, with a restricted distribution in Fuxian Lake, the second deepest lake in China [2].…”