ultivated cotton is one of the most economically important crop plants in the world. The allotetraploid Upland cotton, G. hirsutum (n = 2x = 26, (AD) 1), currently dominates the world's cotton commerce 1,2. Hybridization between the Old World A-genome progenitor and a New World D-genome ancestor, followed by chromosome doubling, formed the allopolyploid cotton ~1−2 million years ago (Ma) 3,4. Uncertainty regarding the actual A-genome donor of the widely cultivated allotetraploid cotton G. hirsutum has persisted 5-13. A 1 (n = x = 13) and A 2 (n = x = 13), commonly known as African and Asiatic cotton, respectively, are the only two extant diploid A-genome species in the world 14. Stephens first proposed in Nature, using genetic and morphological evidence, that A 2 was the A-genome donor of present-day allopolyploid cottons 6. Gerstel argued via cytogenetic studies that A 1 was more closely related to the A-genome in the allopolyploids than A 2 (ref. 8). Despite recent efforts to sequence the cotton genomes, including Gossypium raimondii (D 5) 15,16 , A 2 (refs. 17,18), (AD) 1 (refs. 10,19-21) and Gossypium barbadense 10,21 ((AD) 2 , a much less cultivated tetraploid cotton), the origin history of the A-genome donor for the tetraploid (AD) 1-genome 5,11,13 and the extent of divergence between the A-genomes remain elusive 22,23. Abundant studies support a Gossypium species resembling D 5 as the D-genome donor 13 , but currently there is no solid evidence to suggest that the actual A-genome donor of tetraploid cottons is either A 2 (refs. 6,7,10,19) or A 1 (refs. 8,9,11-13) as has been suggested. In this study, we assembled A 1 variety africanum for the first time and reassembled high-quality A 2 cultivar Shixiya1 and (AD) 1 genetic standard Texas Marker-1 (TM-1) genomes on the basis of PacBio long reads, paired-end sequencing and high-throughput chromosome conformation capture (Hi-C) technologies. Upon assembling and updating cotton genomes, we revealed the origin of cotton A-genomes, the occurrence of several transposable element (TE) bursts and the genetic divergence of diploid A-genomes worldwide. Also, we identified abundant structural variations (SVs) that have affected the expression of neighboring genes and help explain phenotypic differences among the cotton species. Results Sequencing and assembly of three high-quality cotton genomes. Here we sequenced the A 1-genome var. africanum for the first time by generating ~225-gigabase (Gb) PacBio single-molecule real-time (SMRT) long reads (the N50 (minimum length to cover 50% of the total length) of these reads was 13 kilobases (kb)) with 138-fold genome coverage. We generated an assembly that captured 1,556 megabases (Mb) of genome sequences, consisting of 1,781 contigs with the N50 of these contigs reaching up to 1,915 kb (Table 1). The initial assemblies were then corrected by using highly accurate Illumina paired-end reads (Supplementary Table 1). Finally, 95.69% of total contigs spanning 1,489 Mb were categorized and ordered into 13 chromosome-scale scaffold...

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.

Yak domestication represents an important episode in the early human occupation of the high-altitude Qinghai-Tibet Plateau (QTP). The precise timing of domestication is debated and little is known about the underlying genetic changes that occurred during the process. Here we investigate genome variation of wild and domestic yaks. We detect signals of selection in 209 genes of domestic yaks, several of which relate to behaviour and tameness. We date yak domestication to 7,300 years before present (yr BP), most likely by nomadic people, and an estimated sixfold increase in yak population size by 3,600 yr BP. These dates coincide with two early human population expansions on the QTP during the early-Neolithic age and the late-Holocene, respectively. Our findings add to an understanding of yak domestication and its importance in the early human occupation of the QTP.

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