On October 5, BGI Ocean and the Kunming Institute of Zoology of the Chinese Academy of Sciences jointly published the first high-quality map of the genome of the wheat field river golden herring (Figure 1) in the latest issue of Frontiers in Genetics.
Through a comparative genomic analysis of five species of gilt, the paper details the position of the genus Hypercycle in the historical evolution and the changes in the number of copies of immune and apoptosis-related genes[1].
This research result provides a valuable reference for in-depth study of the historical process of cave bream and the molecular mechanism of cave adaptation.
Figure 1. The wheat field river catfish genome paper was published in Frontiers in Genetics
Cave dwellers live in dark underground environments. Over time, they adapt to the lightless and starved cave environment through various characteristic changes in morphology, behavior, and physiology.
Compared with surface fish, cave fish have gradually degenerated eyes, decreased body pigmentation, decreased immunity, and weakened circadian rhythms.
Sinocyclocheilus maitianheensis is a carp of the cyprinid family, living in the surface waters of the Wheat River in Kunming, Yunnan Province, and is closely related to the eyeless golden herring (a cave fish living in the same region).
The genus May share the evolutionary origins of tetraploidy, with 48 pairs of chromosomes, twice as many as most teleost fish.[2]
The genomic diversity of giltfish makes it a good model for studying cave adaptability and phylogenetics.
In this study, whole genome sequencing, assembly and annotation were performed on Wheat field river nasturtium, and genomic analysis and immune-related gene surveys were compared with four other species of nasturtium (surface species Dianchi nasturt, semi-burrowing species rhinoceros goldenrod, burrowing species phyllonorycter and anhydrite).
The catfish is a national second-level protected animal, and this study also provides a reference for the comprehensive conservation and economic value development of these endemic rare species.
Figure 2. Wheat field river golden thread catfish
Genome assembly results, gene family clustering and phylogenetic tree construction
After de novo assembly, the final obtained wheat field golden herring genome size was 1.7 Gb, scaffold N50 and contig N50 were 1.4 Mb and 24.7 kb, respectively, and the GC content was 37.6%.
Busco assessed a genome integrity of 97.1% and was highly complete. Repeat sequences account for 39.4% of the genome.
A total of 39,977 protein-coding genes were predicted, with an average length of 15.9 kb. A total of 38,677 predicted genes were comparable to public functional databases, accounting for 96.8% of the annotated genes.
Using genomic data from five species of clematis and six other representative vertebrate species, a total of 26,875 gene families were predicted in this study, of which 191 were common single-copy gene families.
There are 32,150 protein-coding genes clustered into 15,617 gene families in wheat field catfish; the number of multi-copy, single-copy, and endemic gene families is 15,400, 2,508, and 981, respectively (Figure 3A). Figure 3B summarizes the number of genes shared among the five species of goldenrod.
Based on genomic and transcriptome data, the team used 191 common single-copy gene families to construct a phylogenetic tree, revealing novel evolutionary relationships between five species of golden herring (Figure 3C).
This topology is consistent with earlier phylogenetic trees based on a small number of genomes[2] and mitochondrial genes[3], but differs from evolutionary trees based on eye morphological characteristics[4].
Therefore, this study is based on the genome level, using the latest species evolutionary topology to support new insights into the phylogenesis of gilts.
The Wheat Field River Bream is closestly related to the Eyeless Bream and lives geographically closest, separating about 2.7 million years ago.
This may be due to the continuous uplift of the Yunnan-Guizhou Plateau after the Himalayan orogeny, and the ancestors of the anthropocene swim along the wheat field river into the surrounding caves, thus forming geographical isolation and species differentiation.
Figure 3. Gene family clustering and evolutionary analysis
Temporal estimation of genome-wide replication (WGD) events in the genus Goldenrod
Some species of carps experienced a special WGD event in bony fish after the third genome-wide replication event (3R WGD).
In this study, 4dTv analysis was used to estimate the timing of specific genome-wide replication events of the gilt lineage. The results of the study found that the self-comparison peaks of the homologous gene pairs of 5 species of golden ray and carp were close (between 0.04-0.06, Figure 3D).
This suggests that these science fish may have had recent specific genome-wide replication events; they were expected to occur 18.1 million years ago, earlier than the time of differentiation between giltfish and carp.
Analysis of the copy number of immune-related genes reveals trends in immunity change in cave fish
In this study, copies of 15 immune and apoptosis-related genes in P38 and mitochondrial pathways in Anchovy were investigated and counted.
Overall, the gene copy number of the gilt and carp is twice that of other diploid bony fish. But in cave fish, the number of some genes has undergone interesting changes.
In anthocular goldfish, one copy of ask1 (a regulatory kinase associated with apoptotic signaling) is predicted to be a pseudogene, with multiple copies of the bcl-2a gene and no mkk4a gene.
At the same time, compared with the wheat field river nasturt with 2 copies, only one copy of bcl2l1 (encoding the BCL-2 family apoptosis regulator) was retained in the eyeless bream.
In addition, for most of the genes studied by this team, another cave fish, the Mexican fat carp, also has a smaller number of gene copies.
These differences in gene copy number suggest that cave fish may have been less immune and apoptosis activity, which is consistent with previous reports by researchers that cave fish are less immune.[5]
summary
This paper is the first to report the genome assembly results of the wheat field river nasturt, and based on the relevant data, a close relationship between the wheat field golden herring and the eyeless golden ray is established.
A decrease in the number of copies of immune and apoptosis-related genes may reflect a decrease in immune and apoptosis activity in cave fish.
The results of this study will provide valuable genetic resources for comparative study of the actual farming of such endemic economic fish, the biology of supporting cave fish and species conservation.
About the author
Li Ruihan, phD student of BGI Oceanographic Research Institute, Wang Xiaoai, associate researcher of Kunming Institute of Zoology, and Bian Chao, associate researcher of BGI Oceanographic Research Institute, are the co-first authors of the paper.
Professor Shi Qiong, President of BGI Ocean research institute, and Professor Yang Junxing of Kunming Institute of Zoology are co-corresponding authors.
bibliography
[1] Li R,et al. Frontiers in Genetics, 2021, 12:736500.
[2] Yang J, et al. BMC Biology, 2016, 14:1.
[3] Zhang R,et al. Genes & Genomics, 2018, 40(10):1033-1040.
[4] Mao TR,et al. BMC Ecology and Evolution, 2021, 21(1):45.
[5] Qiu Y,et al. Communicative & Integrative Biology, 2016, 9(6):e1255833.