Journal Article

First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish

Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J.

Record Number:
5208
Year:
2021
Journal:
Research Square Preprint
Notes:
This preprint is under consideration at BMC Ecology and Evolution
Abstract:
Background Loaches of the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth. The genus Oreonectes with 18 currently recognized species contains representatives for all three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwellingrelated traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable resource for research into the evolution of cavefishes. Results Here we assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. Based on in total 50.9 Gb of sequencing data, our genome assembly from Canu and Pilon spans approximately 515.64 Mb (estimated coverage of 100 ×), containing 803 contigs with N50 values of 5.58 Mb. 25,247 proteincoding genes were predicted, of which 95.65% have been functionally annotated. We also performed genome resequencing of three additional cave-dwelling Oreonectes fishes. Twenty-nine pseudogenes annotated using DAVID showed significant enrichment for the GO terms of “eye development” and “retina development in camera-type eye”. It is presumed that these pseudogenes might lead to eye degeneration of semi/complete cave-dwelling Oreonectes species. Furthermore, Mc1r (melanocortin-1 receptor) is a pseudogenization by a deletion in O. daqikongensis, likely blocking biosynthesis of melanin and leading to the albino phenotype. Conclusions We here report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. Pseudogenization of genes related to body color and eye development may be responsible for loss of pigmentation and vision deterioration in cave-dwelling species. This genome assembly will contribute to the study of the evolution and adaptation of fishes within Oreonectes and beyond (Cobitidea).
Times Cited:
4
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Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J. (2021)
First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish
Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J. (2021)
First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish
Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J. (2021)
First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish
Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J. (2021)
First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish