Cotton is a major crop that provides the most important renewable textile fibers in the world.Studies of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic va...Cotton is a major crop that provides the most important renewable textile fibers in the world.Studies of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin,evolution,and cultivation of polyploid species.Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation.Whereas,with only a few mitogenomes assembled in the cotton genus Gossypium,our knowledge about their roles in cotton evolution and speciation is still scarce.To close this gap,here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades(A–G,K,and AD genomes)and 5 cotton relatives using short and long sequencing reads.Systematic analyses uncovered a high level of mitochondrial gene sequence conservation,abundant sequence repeats and many insertions of foreign sequences,as well as extensive structural variations in cotton mitogenomes.The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general,while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content,RNA editing,and gene expression level.Interestingly,we further revealed the specific presence and expression of two novel mitochondrial open reading frames(ORFs)in lint-fiber cotton species.Finally,these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.展开更多
Members of the Malvaceae family,including Corchorus spp.,Gossypium spp.,Bombax spp.,and Ceiba spp.,are important sources of naturalfibers.In the past decade,the genomes of several Malvaceae species have been assembled...Members of the Malvaceae family,including Corchorus spp.,Gossypium spp.,Bombax spp.,and Ceiba spp.,are important sources of naturalfibers.In the past decade,the genomes of several Malvaceae species have been assembled;however,the evolutionary history of Malvaceae species and the differences in theirfiber development remain to be clarified.Here,we report the genome assembly and annotation of two nat-uralfiber plants from the Malvaceae,Bombax ceiba and Ceiba pentandra,whose assembled genome sizes are 783.56 Mb and 1575.47 Mb,respectively.Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number(2n=14 to 2n=96)and genome size(234 Mb to 2676 Mb)among Malvaceae species.We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromo-somes,providing new insights into the evolutionary trajectories of Malvaceae species.MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions infiber cell-fate determination in the epidermis.It appears to perform this function in any tissue where it is expressed,i.e.infibers on the endo-carp of B.ceiba and in ovulefibers of cotton.We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of thefiner,less spinnable,weakerfibers of B.ceiba.Our study provides two high-quality genomes of naturalfiber plants and offers insights into the evolution of Malvaceae species and differences in their naturalfiber formation and devel-opment through multi-omics analysis.展开更多
基金the Zhejiang Natural Science Foundation Outstanding Youth Grant(LR20C020002)the Zhejiang Provincial Natural Science Foundation of China(LZ23C020002)+4 种基金the National Natural Science Foundation of China(32200231)the National Key Research and Development Program of China(2022YFD1401600)the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang(2019R01002)Key Research Project of Zhejiang Lab(2021PE0AC04)the U.S.National Science Foundation(MCB 2148206).
文摘Cotton is a major crop that provides the most important renewable textile fibers in the world.Studies of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin,evolution,and cultivation of polyploid species.Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation.Whereas,with only a few mitogenomes assembled in the cotton genus Gossypium,our knowledge about their roles in cotton evolution and speciation is still scarce.To close this gap,here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades(A–G,K,and AD genomes)and 5 cotton relatives using short and long sequencing reads.Systematic analyses uncovered a high level of mitochondrial gene sequence conservation,abundant sequence repeats and many insertions of foreign sequences,as well as extensive structural variations in cotton mitogenomes.The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general,while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content,RNA editing,and gene expression level.Interestingly,we further revealed the specific presence and expression of two novel mitochondrial open reading frames(ORFs)in lint-fiber cotton species.Finally,these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.
基金supported by the National Key R&D Program of China (2022YFF1001400)the National Natural Science Foundation of China (32341024)+4 种基金the 2021 Research Program of Sanya Yazhou Bay Science and Technology City (SKJC-2021-02-001)the Hainan Provincial Natural Science Foundation of China (323CXTD385)the Major Science and Technology Plan of Hainan Province (ZDKJ2021018)Research Startup Funding from the Hainan Institute of Zhejiang University (0202-6602-A12201)the Distinguished Discipline Support Program of Zhejiang University (226-2022-00100).
文摘Members of the Malvaceae family,including Corchorus spp.,Gossypium spp.,Bombax spp.,and Ceiba spp.,are important sources of naturalfibers.In the past decade,the genomes of several Malvaceae species have been assembled;however,the evolutionary history of Malvaceae species and the differences in theirfiber development remain to be clarified.Here,we report the genome assembly and annotation of two nat-uralfiber plants from the Malvaceae,Bombax ceiba and Ceiba pentandra,whose assembled genome sizes are 783.56 Mb and 1575.47 Mb,respectively.Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number(2n=14 to 2n=96)and genome size(234 Mb to 2676 Mb)among Malvaceae species.We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromo-somes,providing new insights into the evolutionary trajectories of Malvaceae species.MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions infiber cell-fate determination in the epidermis.It appears to perform this function in any tissue where it is expressed,i.e.infibers on the endo-carp of B.ceiba and in ovulefibers of cotton.We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of thefiner,less spinnable,weakerfibers of B.ceiba.Our study provides two high-quality genomes of naturalfiber plants and offers insights into the evolution of Malvaceae species and differences in their naturalfiber formation and devel-opment through multi-omics analysis.
