Schizothoracine fishes are distributed in the Nagqu region,which is the hinterland of the Tibetan Plateau.They have adapted to the cold and strongly ultraviolet environment of the plateau and show diverse morphologies...Schizothoracine fishes are distributed in the Nagqu region,which is the hinterland of the Tibetan Plateau.They have adapted to the cold and strongly ultraviolet environment of the plateau and show diverse morphologies,which makes them ideal for studying the relationship between phenotype and environment.However,traditional morphological measurements are time consuming and labor costly.In this study,we propose a deep-learningbased method for acquiring high-throughput phenotypic data of fishes,including image dataset construction of schizothoracine fishes(including front,side,and top views),fish keypoint detection based on the You Only Look Once(YOLO)model,and reconstruction of 2D and 3D keypoint coordinates based on multiple views.A total of 7050 phenotypic data points consisting of keypoint distances and angles were constructed for each fish and were highly correlated(>0.98)with the corresponding data measured manually.We obtained phenotypic data for a total of 525 fishes from three schizothoracine fish groups inhabiting riverine,lacustrine,and river–lake transitional environments using the proposed phenotypic data acquisition method.We employed a random forest algorithm to classify the groups,achieving a classification accuracy of 96%,and identified 15 morphometric indices that exhibited statistically significant differences.,of which 6 were related to head morphology,6 related to body shape,and 3 related to tail morphology,based on the random forest algorithm.Specifically,river-living schizothoracine fishes showed a blunt head,robust body,and elongated caudal peduncle which may reflect adaptations to the turbulence of the river,while the lake-living schizothoracine fishes have the opposite effect.Schizothoracine fishes at the river–lake transitional zones were phenotypically characterized as being in the middle of the two phenotypes,and these presumably reflect adaptations to their lake habitat.This study provides a methodological reference for obtaining high-throughput phenotypic data on fish and a theoretical basis for understanding the adaptation of very high-altitude schizothoracine fishes to their environment.展开更多
The Yarlung Tsangpo River on the Tibetan Plateau provides a unique natural environment for studying fish evolution and ecology.However,the genomes and genetic diversity of plateau fish species have been rarely reporte...The Yarlung Tsangpo River on the Tibetan Plateau provides a unique natural environment for studying fish evolution and ecology.However,the genomes and genetic diversity of plateau fish species have been rarely reported.Schizopygopsis younghusbandi,a highly specialized Schizothoracine species and economically important fish inhabiting the Yarlung Tsangpo River,is threatened by overfishing and biological invasion.Herein,we generated a chromosome-level genome of S.younghusbandi and whole-genome resequencing data for 59 individuals from six locations of the river.The results showed that the divergence time between S.younghusbandi and other primitive Schizothoracine species was~4.2 Mya,coinciding with the major phase of the Neogene Tibetan uplift.The expanded gene families enriched in DNA integration and replication,ion binding and transport,energy storage,and metabolism likely contribute to the adaption of this species.The S.younghusbandi may have diverged from other highly specialized Schizothoracine species in the Zanda basin during the Pliocene epoch,which underwent major population reduction possibly due to the drastic climate change during the last glacial period.Population analysis indicated that the ancient population might have originated upstream before gradually adapting to evolve into the populations inhabiting the mid-stream and downstream regions of the Yarlung Tsangpo River.In conclusion,the chromosome-level genome and population diversity of S.younghusbandi provide valuable genetic resources for the evolution,ecology,and conservation studies of endemic fishes on the Tibetan Plateau.展开更多
Gut microbiota play important roles in host health and diseases.Several factors,in particular antibiotics,affect the gut microbiota of pigs.Cross-fostering has been applied as a regular practice to equalize litter siz...Gut microbiota play important roles in host health and diseases.Several factors,in particular antibiotics,affect the gut microbiota of pigs.Cross-fostering has been applied as a regular practice to equalize litter size,reduce pre-weaning mortality and increase body weight.However,the effect of cross-fostering on cecal microbiota is unclear.In this study,we fostered three Jinhua pigs to a Yorkshire sow.The fostered Jinhua piglets grew significantly faster than their biological siblings.To explore whether the cecal microbiota of piglets will alter during fostering,we characterized the cecal microbiota of allpiglets by examining the V3 hypervariable region of 16S rDNA.We observed altered cecal microbiota in these piglets using the Illumina HiSeq 2000 platform,and this was accompanied with an increase in growth rate after fostering.The relative abundance of Bacteroidetes in the fostered Jinhua piglets was decreased compared with their biological siblings,although still higher in comparison with their new littermates.Beta-diversity analysis also showed that the cecal microbiota of the adopted Jinhua piglets differed from their biological siblings with a shift toward their step-siblings.Our data show that cecal microbiota of piglets were altered after cross-fostering while the growth rate increased.展开更多
基金funded by the National Natural Science Foundation of China(NSFC)Joint Fund Priority Support Program(U23A20249)the“Special fund for youth team of the Southwest University”(SWUXJPY202302)+3 种基金the“National Talent Research Grant for 2023”(5330500953)National Natural Science Foundation of China(32072980)Chongqing Innovation Program for Graduate Research(CYB240106)the National Key R&D Program of China(grant no.2024YFD1200703).
文摘Schizothoracine fishes are distributed in the Nagqu region,which is the hinterland of the Tibetan Plateau.They have adapted to the cold and strongly ultraviolet environment of the plateau and show diverse morphologies,which makes them ideal for studying the relationship between phenotype and environment.However,traditional morphological measurements are time consuming and labor costly.In this study,we propose a deep-learningbased method for acquiring high-throughput phenotypic data of fishes,including image dataset construction of schizothoracine fishes(including front,side,and top views),fish keypoint detection based on the You Only Look Once(YOLO)model,and reconstruction of 2D and 3D keypoint coordinates based on multiple views.A total of 7050 phenotypic data points consisting of keypoint distances and angles were constructed for each fish and were highly correlated(>0.98)with the corresponding data measured manually.We obtained phenotypic data for a total of 525 fishes from three schizothoracine fish groups inhabiting riverine,lacustrine,and river–lake transitional environments using the proposed phenotypic data acquisition method.We employed a random forest algorithm to classify the groups,achieving a classification accuracy of 96%,and identified 15 morphometric indices that exhibited statistically significant differences.,of which 6 were related to head morphology,6 related to body shape,and 3 related to tail morphology,based on the random forest algorithm.Specifically,river-living schizothoracine fishes showed a blunt head,robust body,and elongated caudal peduncle which may reflect adaptations to the turbulence of the river,while the lake-living schizothoracine fishes have the opposite effect.Schizothoracine fishes at the river–lake transitional zones were phenotypically characterized as being in the middle of the two phenotypes,and these presumably reflect adaptations to their lake habitat.This study provides a methodological reference for obtaining high-throughput phenotypic data on fish and a theoretical basis for understanding the adaptation of very high-altitude schizothoracine fishes to their environment.
基金supported by the National Natural Science Foundation of China[grant numbers 32160864,32072980]the National Natural Science Foundation of China(NSFC)Joint Fund Priority Support Program[grant number U23A20249]+1 种基金the National Talent Research Grant for 2023[grant number 5330500953]the Special Fund for Youth Team of the Southwest University[grant number SWUXJPY202302].
文摘The Yarlung Tsangpo River on the Tibetan Plateau provides a unique natural environment for studying fish evolution and ecology.However,the genomes and genetic diversity of plateau fish species have been rarely reported.Schizopygopsis younghusbandi,a highly specialized Schizothoracine species and economically important fish inhabiting the Yarlung Tsangpo River,is threatened by overfishing and biological invasion.Herein,we generated a chromosome-level genome of S.younghusbandi and whole-genome resequencing data for 59 individuals from six locations of the river.The results showed that the divergence time between S.younghusbandi and other primitive Schizothoracine species was~4.2 Mya,coinciding with the major phase of the Neogene Tibetan uplift.The expanded gene families enriched in DNA integration and replication,ion binding and transport,energy storage,and metabolism likely contribute to the adaption of this species.The S.younghusbandi may have diverged from other highly specialized Schizothoracine species in the Zanda basin during the Pliocene epoch,which underwent major population reduction possibly due to the drastic climate change during the last glacial period.Population analysis indicated that the ancient population might have originated upstream before gradually adapting to evolve into the populations inhabiting the mid-stream and downstream regions of the Yarlung Tsangpo River.In conclusion,the chromosome-level genome and population diversity of S.younghusbandi provide valuable genetic resources for the evolution,ecology,and conservation studies of endemic fishes on the Tibetan Plateau.
基金supported by the National Special Foundation for Transgenic Species of China(2014ZX0800950B,2011ZX08006-003)the Specialized Research Fund of Ministry of Agriculture of China(NYCYTX-009)+3 种基金the Fundof Fok Ying-Tung Education Foundation(141117)the Fund for Distinguished Young Scientists of Sichuan Province(2013JQ0013)the Program for Changjiang Scholars and Innovative Research Teamin University(IRT13083)to Mingzhou Li and Xuewei Lithe‘‘100-Talent Program’’in Sichuan Science Foundation for Youths of Sichuan Province to Ying Li
文摘Gut microbiota play important roles in host health and diseases.Several factors,in particular antibiotics,affect the gut microbiota of pigs.Cross-fostering has been applied as a regular practice to equalize litter size,reduce pre-weaning mortality and increase body weight.However,the effect of cross-fostering on cecal microbiota is unclear.In this study,we fostered three Jinhua pigs to a Yorkshire sow.The fostered Jinhua piglets grew significantly faster than their biological siblings.To explore whether the cecal microbiota of piglets will alter during fostering,we characterized the cecal microbiota of allpiglets by examining the V3 hypervariable region of 16S rDNA.We observed altered cecal microbiota in these piglets using the Illumina HiSeq 2000 platform,and this was accompanied with an increase in growth rate after fostering.The relative abundance of Bacteroidetes in the fostered Jinhua piglets was decreased compared with their biological siblings,although still higher in comparison with their new littermates.Beta-diversity analysis also showed that the cecal microbiota of the adopted Jinhua piglets differed from their biological siblings with a shift toward their step-siblings.Our data show that cecal microbiota of piglets were altered after cross-fostering while the growth rate increased.
