Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica)

Populus euphratica is well adapted to extreme desert environments and is an important model species for elucidating the mechanisms of abiotic stress resistance in trees. The current assembly of P. euphratica genome is highly fragmented with many gaps and errors, thereby impeding downstream applications. Here, we report an improved chromosome‐level reference genome of P. euphratica (v2.0) using single‐molecule sequencing and chromosome conformation capture (Hi‐C) technologies. Relative to the previous reference genome, our assembly represents a nearly 60‐fold improvement in contiguity, with a scaffold N50 size of 28.59 Mb. Using this genome, we have found that extensive expansion of Gypsy elements in P. euphratica led to its rapid increase in genome size compared to any other Salicaceae species studied to date, and potentially contributed to adaptive divergence driven by insertions near genes involved in stress tolerance. We also detected a wide range of unique structural rearrangements in P. euphratica, including 2,549 translocations, 454 inversions, 121 tandem and 14 segmental duplications. Several key genes likely to be involved in tolerance to abiotic stress were identified within these regions. This high‐quality genome represents a valuable resource for poplar breeding and genetic improvement in the future, as well as comparative genomic analysis with other Salicaceae species.     

钾素对药用植物短葶飞蓬生长和有效成分积累的影响

在不同钾素供应下对药用植物短葶飞蓬（Erigeronbreviscapus）进行了人工栽培试验,探讨了钾素对其生长和次生代谢产物积累的影响。结果显示：在0～0．372g／株钾素施用量范围内,钾素供应量与短葶飞蓬单株生物量以及总咖啡酸酯和灯盏乙素的产量呈极显著的正相关;但植株总咖啡酸酯和灯盏乙素的含量则随钾素供应量增加先升高后降低;总咖啡酸酯和灯盏乙素含量与植株N含量呈显著的线性负相关,与碳素／营养平衡假说一致。0～0．248g／株钾素施用量范围内,短葶飞蓬地上生物量和总生物量与总咖啡酸酯和灯盏乙素含量都呈现出极显著的正相关。研究表明：当钾供应量不十分丰富时,适当增施钾可促进植株酚类次生代谢产物的积累,但高钾供应量则抑制积累。并不是只有在生长胁迫生境中才能得到高的酚类次生代谢产物积累,生长与次生代谢产物积累间不存在权衡关系。     

Construction and comparison of three reference‐quality genome assemblies for soybean

We report reference‐quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan‐gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.     

灯盏花大小孢子形成与胚胎发育

用石蜡切片法对灯盏花从花原基分化到胚胎形成的全过程进行系统观察,结果表明:灯盏花从初孕花序至头状花序的直径(d)在2.8～3.1 mm时为花器官分化期,包括花原基分化期、花萼与花冠分化期、雌雄蕊分化期以及分化完成期4个阶段;灯盏花花药4室,药壁发育属双子叶型,绒毡层细胞属于变形绒毡层;小孢子母细胞减数分裂为同时型,成熟花粉为3-细胞型;子房下位,1室,单珠被,薄珠心,胚珠倒生,胚囊发育为蓼型;珠孔受精,属于有丝分裂前类型,胚乳发育为细胞型,胚胎发育应属紫菀型.     

Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding

Apolygus lucorum (Miridae) is an omnivorous pest that occurs worldwide and is notorious for the serious damage it causes to various crops and substantial economic losses. Although some studies have examined the biological characteristics of the mirid bug, no reference genome is available in Miridae, limiting in‐depth studies of this pest. Here, we present a chromosome‐scale reference genome of A. lucorum, the first sequenced Miridae species. The assembled genome size was 1.02 Gb with a contig N50 of 785 kb. With Hi‐C scaffolding, 1,016 Mb contig sequences were clustered, ordered and assembled into 17 large scaffolds with scaffold N50 length 68 Mb, each corresponding to a natural chromosome. Numerous transposable elements occur in this genome and contribute to the large genome size. Expansions of genes associated with omnivorousness and mesophyll feeding such as those related to digestion, chemosensory perception, and detoxification were observed in A. lucorum, suggesting that gene expansion contributed to its strong environmental adaptability and severe harm to crops. We clarified that a salivary enzyme polygalacturonase is unique in mirid bugs and has significantly expanded in A. lucorum, which may contribute to leaf damage from this pest. The reference genome of A. lucorum not only facilitates biological studies of Hemiptera as well as an understanding of the damage mechanism of mesophyll feeding, but also provides a basis on which to develop efficient control technologies for mirid bugs.     

三倍体短葶飞蓬的发现及其在育种上的意义

对云南省野生居群的短葶飞蓬有丝分裂的细胞学特征进行观察研究。在云南省大理苍山、腾冲杨家坪的二倍体野生居群中,发现有三倍体个体的存在。苍山居群的两种核型分别为2n=2x=18=4m 10sm 4st,2n=3x=27=6m 12sm 9st;杨家坪居群的两种核型分别为2n=2x=18=6m 10sm 2st,2n=3x=27=3m 15sm 9st。通过对其生物学特性及表型的分析,认为短葶飞蓬可以采取多倍体育种方式获得更优良的品种。     

Screening of free radical scavengers from Erigeron breviscapus using on-line HPLC-ABTS/DPPH based assay and mass spectrometer detection

Erigeron breviscapus is a well-known traditional Chinese herbal medicine. In this study, on-line HPLC-ABTS/DPPH assay coupled with MS detection were applied to screen and identify the free radical scavengers in 70% methanol extracts of E. breviscapus. Using on-line HPLC-ABTS-MS and HPLC-DPPH-MS assay, 13 radical scavengers (including 4-O-caffeoylquinic acid (4-CQA) (1), 9-caffeoyl-2,7-anhydro-2-octulosonic acid (9-COA) (2), 3-caffeoyl-2,7-anhydro-3-deoxy-2-octulopyranosonic acid (3-CDOA) (3), erigeside I (4), quercetin-3-O-glucuronide (5), eriodictyol-7-O-glucuronide (6), scutellarin (7), 1,4-di-O-caffeoylquinic acid (1,4-di-CQA) (8), 3,5-di-CQA (9), 1-malonyl-3,5-di-CQA (10), erigoster B (11), 4,5-di-CQA (12) and 4,9-di-CDOA (13)) and 9 radical scavengers (including 1, 4, 7, 8, 9, 10, 11, 12 and 13) were discovered, respectively. Furthermore, the anti-oxidative activities of 4 compounds, including 7, 9, 11 and 12 were evaluated. Reverse anti-oxidative activity order of scutellarin and 3,5-di-CQA was observed in on-line HPLC-ABTS assay and on-line HPLC-DPPH assay. To validate their anti-oxidative activities, the off-line ABTS and DPPH assays were performed. Given sufficient reaction time, 3,5-di-CQA showed higher activity than scutellarin, which was consistent with the order obtained in on-line HPLC-ABTS assay. These results revealed that on-line HPLC-ABTS assay is a more sensitive method for screening and determining free radical scavengers, especially more suitable for those compounds with slower reaction kinetics.     

Apomixis via recombination of genome regions for apomeiosis (diplospory) and parthenogenesis in Erigeron (daisy fleabane, Asteraceae)

Apomixis in daisy fleabanes (Erigeron annuus and E. strigosus) is controlled by two genetically unlinked loci that regulate, independently, the formation of unreduced female gametophytes (apomeiosis, diplospory) and autonomous seed formation (parthenogenesis). In this work, fully apomictic F2s were regenerated by crossing F1s bearing, separately, these two functional regions. Two triploid (3x = 2n = 27) highly diplosporous F1s served as seed parents to an aneuploid (2x + 1 = 2n = 19) meiotic pollen donor bearing four AFLP markers linked to parthenogenetic seed formation but producing only abortive embryos and endosperm. Of 408 hybrids, 21 (5.1%) produced seed. Nine of these putative apomicts were tetraploids (4x), likely combining an unreduced egg from the diplosporous seed parent and a haploid gamete from the pollen parent (3x + x). The other 12 hybrid apomicts were pentaploid, interpreted as arising from the fusion of an unreduced diplosporous egg with an unreduced sperm cell (3x + 2x). Analysis indicated that all but three of the 21 synthetic apomicts recombined markers linked to diplospory and parthenogenesis. In addition, three additional hybrids combined markers linked to the two functional regions but produced only aborted embryos. The apomicts varied in percentage of diplosporous ovules (4.7–95.3% of all ovules produced) and in percentage of ovules that developed into seed (3.8–58.0%). These results support the hypothesis that apomeiosis and autonomous seed formation are genetically distinct, and that the traits can be separated and recombined to create hybrids exhibiting apomixis at near wildtype levels.     

The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis

Chimonanthus salicifolius, a member of the Calycanthaceae of magnoliids, is one of the most famous medicinal plants in Eastern China. Here, we report a chromosome‐level genome assembly of C. salicifolius, comprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36 651 annotated protein‐coding genes. Phylogenetic analyses revealed that magnoliids were sister to the eudicots. Two rounds of ancient whole‐genome duplication were inferred in the C. salicifolious genome. One is shared by Calycanthaceae after its divergence with Lauraceae, and the other is in the ancestry of Magnoliales and Laurales. Notably, long genes with > 20 kb in length were much more prevalent in the magnoliid genomes compared with other angiosperms, which could be caused by the length expansion of introns inserted by transposon elements. Homologous genes within the flavonoid pathway for C. salicifolius were identified, and correlation of the gene expression and the contents of flavonoid metabolites revealed potential critical genes involved in flavonoids biosynthesis. This study not only provides an additional whole‐genome sequence from the magnoliids, but also opens the door to functional genomic research and molecular breeding of C. salicifolius.     

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring‐spot virus resistance locus

Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high‐quality 313.4‐Mb genome sequence of a bottle gourd inbred line, USVL1VR‐Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the assembled scaffolds are anchored to the 11 pseudomolecules. Our comparative genomic analysis identifies chromosome‐level syntenic relationships between bottle gourd and other cucurbits, as well as lineage‐specific gene family expansions in bottle gourd. We reconstructed the genome of the most recent common ancestor of Cucurbitaceae, which revealed that the ancestral Cucurbitaceae karyotypes consisted of 12 protochromosomes with 18 534 protogenes. The 12 protochromosomes are largely retained in the modern melon genome, while have undergone different degrees of shuffling events in other investigated cucurbit genomes. The 11 bottle gourd chromosomes derive from the ancestral Cucurbitaceae karyotypes followed by 19 chromosomal fissions and 20 fusions. The bottle gourd genome sequence has facilitated the mapping of a dominant monogenic locus, Prs, conferring Papaya ring‐spot virus (PRSV) resistance in bottle gourd, to a 317.8‐kb region on chromosome 1. We have developed a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus and demonstrated its potential application in marker‐assisted selection of PRSV resistance in bottle gourd. This study provides insights into the paleohistory of Cucurbitaceae genome evolution, and the high‐quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement.     

灯盏花种质资源群体表型多样性研究

以采集自云南和贵州的21份灯盏花种质资源为材料,观测了它们的群体表型性状特征,并分析了这些表型性状的遗传多样性.结果表明:灯盏花种质资源的表型质量性状在居群内外均有丰富变异,不同质量性状的频率不同,并以多叶型的植株、绿色的茎、疏的茎毛、倒披针型的基生叶、全缘叶、锐尖的叶尖、花色淡紫和黄色的管状花冠口等为代表性表型性状.居群内各数量性状间以单株基生叶数和单株分枝数变异系数较高(均超过50%),而花序直径变异系数最低(18.14%);居群间各表型性状以株高和单序管状花数变异系数较高(52.98%和41.98%),而单株基生叶数和基生叶长变异系数较低(<20%).地理类群间表型分化系数为26.58%,地理类群内表型分化系数为73.42%.灯盏花性状表型多样性指数以株高最高(2.243),以单株分枝数和单株基生叶数较低(1.723和1.874),总体平均表型多样性指数为2.028;不同地理类群的表型多样性指数为1.589~1.890,并以楚雄地区最高,曲靖地区最低.研究发现,灯盏花种质资源具有丰富的质量和数量性状变异,多数性状的地理类群内变异大于地理类群间,且表型多样性指数相对较高,对其地理类群内变异的保护和利用对灯盏花育种具有重要的意义.     

同源四倍体灯盏花离体再生及其倍性鉴定

以四倍体灯盏花的无菌苗叶柄为外植体进行离体培养,研究其再生体系,并对再生植株进行染色体倍性鉴定。结果表明:叶柄外植体在MS+0.05 mg·L-1NAA+0.5 mg·L-16-BA+0.65%琼脂+3%蔗糖的培养基上不定芽的再生频率可达87.3%;继代培养(MS+0.1 mg·L-1NAA+0.3 mg·L-16-BA+0.65%琼脂+3%蔗糖)增殖系数为7.8,诱导(1/2MS+1.0 mg·L-1NAA+1.0 mg·L-1IBA+0.65%琼脂+3%蔗糖)生根率100%,移栽成活率为90%。细胞学鉴定结果表明,再生植株的染色体数为2n=4x=36,而原二倍体的染色体数目为2n=2x=18,基数x=9,因此,再生植株为四倍体。     

短葶飞蓬总咖啡酸酯和灯盏乙素含量的空间变化

依据嵌套分层设计原理制定野外调查取样方案,以药用资源植物短葶飞蓬不同产地93个自然种群310份植株样品的灯盏乙素和咖啡酸酯含量的嵌套方差分析,探讨次生代谢有效成分含量在产区间的空间变化。结果表明:短葶飞蓬有效成分含量存在空间差异,最低含量产区的总咖啡酸酯和灯盏乙素含量分别只是最高含量产区的52.1%和41.8%,但不与产地间的空间距离远近完全一致;同一产地短葶飞蓬总咖啡酸酯和灯盏乙素含量有一定的年际差异,但高含量产地与低含量产地是相对稳定的;作为优质药材的基本产地单元,自然地理区划单元比行政区划单元更科学;短葶飞蓬总咖啡酸酯和灯盏乙素含量与植株含N量呈极显著负相关,符合"碳/氮营养平衡假说"的预测,但植株含N量的变化只能解释短葶飞蓬总咖啡酸酯和灯盏乙素含量不同产区间约30%的变异。植物药材有效成分含量的空间变化是药用植物地区间遗传变异和生长地环境生态因子变化共同作用的结果,用自然地理区划单元为产地单元更客观。确定药材的"优质产地"可作为保障药材有效性的科学管理途径之一。