Gene_locus Report for: poptr-a0a2k1wv10

Other strains: Populus trichocarpa (Western balsam poplar) (Populus balsamifera subsp. trichocarpa); Populus alba (White poplar)

(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.)
> cellular organisms: N E > Eukaryota: N E > Viridiplantae: N E > Streptophyta: N E > Streptophytina: N E > Embryophyta: N E > Tracheophyta: N E > Euphyllophyta: N E > Spermatophyta: N E > Magnoliophyta: N E > Mesangiospermae: N E > eudicotyledons: N E > Gunneridae: N E > Pentapetalae: N E > rosids: N E > fabids: N E > Malpighiales: N E > Salicaceae: N E > Saliceae: N E > Populus: N E > Populus trichocarpa: N E

Title: De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China
Liu YJ, Wang XR, Zeng QY
Ref: Sci China Life Sciences, 62:609, 2019 : PubMed
Abstract


ESTHER: Liu_2019_Sci.China.Life.Sci_62_609
PubMedSearch: Liu 2019 Sci.China.Life.Sci 62 609
PubMedID: 30661181
Gene_locus related to this paper: poptr-a9pch4, poptr-a0a2k1wwt1, poptr-a0a2k1wv10, poptr-a0a2k2asj6, poptr-a0a2k1x6k1, poptr-u5fv96, popal-a0a4u5qy13, popal-a0a4u5mi39

Abstract

The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred ~5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (~ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170+/-0.014, which was lower than that in Italy (0.271+/-0.051) and Hungary (0.264+/-0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.



        

Title: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S and Rokhsar D <100 more author(s)> Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (- 100)
Ref: Science, 313:1596, 2006 : PubMed
Abstract


ESTHER: Tuskan_2006_Science_313_1596
PubMedSearch: Tuskan 2006 Science 313 1596
PubMedID: 16973872
Gene_locus related to this paper: burvg-a4jw31, delas-a9c1v9, poptr-a9pfp5, poptr-a9ph43, poptr-a9ph71, poptr-a9pha7, poptr-b9giq0, poptr-b9gjs0, poptr-b9gl72, poptr-b9gmx8, poptr-b9gnp9, poptr-b9gny4, poptr-b9grg2, poptr-b9gsc2, poptr-b9gvp3, poptr-b9gvs3, poptr-b9gwn9, poptr-b9gy32, poptr-b9gyq1, poptr-b9gys8, poptr-b9h0h0, poptr-b9h4j2, poptr-b9h6c2, poptr-b9h6c5, poptr-b9h6l8, poptr-b9h8c9, poptr-b9h301, poptr-b9h579, poptr-b9hbl2, poptr-b9hbw5, poptr-b9hcn9, poptr-b9hee0, poptr-b9hee2, poptr-b9hee5, poptr-b9hee6, poptr-b9hef3, poptr-b9hfa7, poptr-b9hfd3, poptr-b9hfi6, poptr-b9hft8, poptr-b9hg83, poptr-b9hif5, poptr-b9hll5, poptr-b9hmd0, poptr-b9hnv3, poptr-b9hqr6, poptr-b9hqr7, poptr-b9hrv7, poptr-b9hs66, poptr-b9huf0, poptr-b9hur3, poptr-b9hux1, poptr-b9hwp2, poptr-b9hxr7, poptr-b9hyk8, poptr-b9hyx2, poptr-b9i2q8, poptr-b9i5b8, poptr-b9i5j8, poptr-b9i5j9, poptr-b9i5k0, poptr-b9i6b6, poptr-b9i7b7, poptr-b9i9p8, poptr-b9i484, poptr-b9i994, poptr-b9ial3, poptr-b9ial4, poptr-b9ib28, poptr-b9ibr8, poptr-b9id97, poptr-b9idr4, poptr-b9iid9, poptr-b9iip0, poptr-b9ik80, poptr-b9ik90, poptr-b9il63, poptr-b9ink7, poptr-b9iqa0, poptr-b9iqd5, poptr-b9mwf1, poptr-b9mwi8, poptr-b9n0c6, poptr-b9n0n1, poptr-b9n0n4, poptr-b9n0z5, poptr-b9n1t8, poptr-b9n1z3, poptr-b9n3m7, poptr-b9n233, poptr-b9n236, poptr-b9n395, poptr-b9nd33, poptr-b9nd34, poptr-b9ndi6, poptr-b9ndj5, poptr-b9p9i8, poptr-a9pfa7, poptr-b9hdp2, poptr-b9inj0, poptr-b9n5g7, poptr-b9i8q4, poptr-u5g0r4, poptr-u5gf59, poptr-u7e1l9, poptr-b9hj61, poptr-b9hwd0, poptr-u5fz17, poptr-a0a2k2brq1, poptr-a0a2k2b9i6, poptr-a0a2k1x9y8, poptr-a9pch4, poptr-a0a2k1wwt1, poptr-a0a2k1wv10, poptr-a0a2k2a850, poptr-a0a2k2asj6, poptr-a0a2k1x6k1, poptr-u5fv96, poptr-a0a2k2blg2, poptr-a0a2k1xpi3, poptr-a0a2k1xpj0, poptr-a0a2k2b331, poptr-a0a2k2byl7, poptr-b9iek5, poptr-a9pfg4, poptr-a0a2k1xzs5, poptr-b9gga9, poptr-b9guw6, poptr-b9hff2

Abstract

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.