REFERENCES
- Bairoch, A., & Apweiler, R. (2000). The SWISS-PROT protein sequence
database and its supplement TrEMBL in 2000. Nucleic Acids Res ,
28(1), 45–48.
- Baud, S., Guyon, V., Kronenberger, J., Wuillème, S., Miquel, M.,
Caboche, M., Lepiniec, L., & Rochat, C. (2003). Multifunctional
acetyl-CoA carboxylase 1 is essential for very long chain fatty acid
elongation and embryo development in Arabidopsis . Plant
J , 33(1), 75–86
- Bernard, A., Domergue, F., Pascal, S., Jetter, R., Renne, C., Faure,
J.D., Haslam, R.P., Napier, J.A., Lessire, R., & Joubès, J. (2012).
Reconstitution of plant alkane biosynthesis in yeast demonstrates thatArabidopsis ECERIFERUM1 and ECERIFERUM3 are core components of
a very-long-chain alkane syn- thesis complex. Plant Cell ,
24(7), 3106–3118.
- Birney, E., Clamp, M., & Durbin, R. (2004). GeneWise and genomewise.Genome Res , 14(5), 988–995.
- Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible
trimmer for Illumina sequence data. Bioinformatics , 30(15),
2114–2120.
- Bonaventure, G., Salas, J.J., Pollard, M.R., & Ohlrogge, J.B. (2003).
Disruption of the FATB gene in Arabidopsis demonstrates
an essential role of saturated fatty acids in plant growth.Plant Cell , 15(4), 1020–1033.
- Chen, C., Zheng, Z.L., Wu, D.D., Tan, L., Yang, C.R., Liu, S.Q., Lu,
J.L., Cheng, Y.R., Sha, L.N., Wang, Y., Kang, H.Y., Fan, X., Zhou,
Y.H., Zhang, C.B., & Zhang, H.Q. (2022). Morphological, cytological,
and molecular evidences for natural hybridization betweenRoegneria stricta and Roegneria turczaninovii(Triticeae: Poaceae). Ecol Evol , 12(1), e8517.
- Chen, N., Chen, W.J., Yan, H., Wang, Y., Kang, H.Y., Zhang, H.Q.,
Zhou, Y.H., Sun, G.L., Sha, L.N., & Fan, X. (2020). Evolutionary
patterns of plastome uncover diploid-polyploid maternal relationships
in Triticeae. Mol Phylogenet Evol , 149, 106838.
- Devos, K., Dubcovsky, J., Dvořák, J., Chinoy, C., & Gale, M. (1995).
Structural evolution of wheat chromosomes 4A, 5A, and 7B and its
impact on recombination. Theor. Appl Genet , 91, 282–288.
- Dewey, D.R. (1984). The genomic system of classification. A guide to
intergeneric hybridization with the perennial Triticeae. Gene
Manipulation in Plant Improvement. 209–279.
- Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high
accuracy and high throughput. Nucleic Acids Res , 32(5),
1792–1797.
- Fiebig, A., Mayfield, J.A., Miley, N., Chau, S., Fischer, R.L., &
Preuss, D. (2000). Alterations in CER6 , a gene identical toCUT1 , differentially affect long-chain lipid content on the
surface of pollen and stems. Plant Cell , 12(10), 2001–2008.
- Finn, R.D., Attwood, T.K., Babbitt, P.C., Bateman, A., Bork, P.,
Bridge, A.J., Chang, H.Y., Dosztányi, Z., El-Gebali, S., & Fraser, M.
(2017). InterPro in 2017—beyond protein family and domain
annotations. Nucleic Acids Res , 45(D1), 190–199.
- Finn, R.D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R.Y.,
Eddy, S.R., Heger, A., Hetherington, K., Holm, L., & Mistry, J.
(2014). Pfam: the protein families database. Nucleic Acids Res ,
42(D1), 222–230.
- Finn, R.D., Clements, J., Arndt, W., Miller, B.L., Wheeler, T.J.,
Schreiber, F., Bateman, A., and Eddy, S.R. (2015). HMMER web server:
2015 update. Nucleic Acids Res , 43(W1), 30–38.
- Fraser, L.H., Greenall, A., Carlyle, C., Turkington, R., & Friedman,
C.R. (2009). Adaptive phenotypic plasticity of Pseudoroegneria
spicata : response of stomatal density, leaf area and biomass to
changes in water supply and increased temperature. Ann Bot ,
103(5), 769–775.
- Gamache, J., & Sun, G.L. (2015). Phylogenetic analysis of the genusPseudoroegneria and the Triticeae tribe using the rbcLgene. Biochem Syst Ecol , 62, 73–81.
- Greer, S., Wen, M., Bird, D., Wu, X., Samuels, L., Kunst, L., &
Jetter, R. (2007). The cytochrome P450 enzyme CYP96A15 is the midchain
alkane hydroxylase responsible for formation of secondary alcohols and
ketones in stem cuticular wax of Arabidopsis . Plant
Physiol , 145(3), 653–667.
- Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis,
J., White, O., Buell, C.R., & Wortman, J.R. (2008). Automated
eukaryotic gene structure annotation using EVidenceModeler and the
program to assemble spliced alignments. Genome Biol , 9, 1–22.
- Haslam, T.M., & Kunst, L. (2021). ArabidopsisECERIFERUM2-LIKEs are mediators of condensing enzyme function.Plant Cell Physiol , 61(12), 2126–2138.
- Jetter, R., Kunst, L., & Samuels, A.L. (2006). Composition of plant
cuticular waxes. In: Riederer M, Muller C, eds. Biology of the
plant cuticle , Oxford: Blackwell 145–175.
- Joubès, J.M., Raffaele, S., Bourdenx, B., Garcia, C.,
Laroche-Traineau, J., Moreau, P., Domergue, F., & Lessire, R. (2008).
The VLCFA elongase gene family in Arabidopsis thaliana :
phylogenetic analysis, 3D modelling and ex- pression profiling.Plant Mol Biol , 67, 547–566.
- Kong, L., Song, X., Xiao, J., Sun, H., Dai, K., Lan, C., Singh, P.,
Yuan, C., Zhang, S., & Singh, R. (2018). Development and
characterization of a complete set of Triticum
aestivum–Roegneria ciliaris disomic addition lines. Theor Appl
Genet , 131, 1793–1806.
- Kosma, D.K., Molina, I., Ohlrogge, J.B., & Pollard, M. (2012).
Identification of an Arabidopsis fatty alcohol:
caffeoyl-Coenzyme A acyltransferase required for the synthesis of
alkyl hydroxycinnamates in root waxes. Plant Physiol , 160(1),
237–248.
- Larson, L., & Kiemnec, G. (2003). Seedling Growth and Interference of
Diffuse Knapweed (Centaurea diffusa ) and Bluebunch Wheatgrass
(Pseudoroegneria spicata ). Weed Technol , 17(1), 79–83.
- Lee, S.B., Jung, S.J., Go, Y.S., Kim, H.U., Kim, J.K., Cho, H.J.,
Park, O.K., & Suh, M.C. (2009). Two Arabidopsis 3-ketoacyl CoA
synthase genes, KCS20 and KCS2/DAISY , are functionally
redundant in cuticular wax and root suberin biosynthesis, but
differentially controlled by osmotic stress. Plant J , 60(3),
462–475.
- Lee, S.B., & Suh, M.C. (2022). Regulatory mechanisms underlying
cuticular wax biosynthesis. J Exp Bot , 73(9), 2799–2816.
- Lewandowska, M., Keyl, A., & Feussner, I. (2020). Wax biosynthesis in
response to danger: its regulation upon abiotic and biotic stress.New Phytol , 227(3), 698–713.
- Li, H., Mo, Y.L., Cui, Q., Yang, X.Z., Guo, Y.L., Wei, C.H., Yang, J.,
Zhang, Y., Ma, J.X., & Zhang, X. (2019). Transcriptomic and
physiological analyses reveal drought adaptation strategies in
drought-tolerant and -susceptible watermelon genotypes. Plant
Sci , 278, 32–43.
- Li, G., Wang, L., Yang, J., He, H., Jin, H., Li, X., Ren, T., Ren, Z.,
Li, F., & Han, X. (2021). A high-quality genome assembly highlights
rye genomic characteristics and agronomically important genes.Nat Genet , 53(4), 574–584.
- Li, H., & Durbin, R. (2010). Fast and accurate long-read alignment
with Burrows–Wheeler transform. Bioinformatics, 26(5), 589–595.
- Lieberman-Aiden, E., Van Berkum, N.L., Williams, L., Imakaev, M.,
Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., &
Dorschner, M.O. (2009). Comprehensive mapping of long-range
interactions reveals folding principles of the human genome.Science , 326(5950), 289–293.
- Liu, Z., Li, D., & Zhang, X. (2007). Genetic relationships among five
basic genomes St, E, A, B and D in Triticeae revealed by genomic
southern and in situ hybridization. J Integr Plant Biol , 49(7),
1080–1086.
- Liu, Z.W., & Wang, R.R.C. (1993). Genome analysis of Elytrigia
caespitosa , Lophopyrum nodosum , Pseudoroegneria
geniculata ssp. scythica , and Thinopyrum intermedium(Triticeae: Gramineae). Genome , 36(1), 102–111.
- Lu, X.W., Liu, B., Liu, R.J., & Dou, Q.W. (2019). Cytogenetic
identification on interspecific hybrids in genus Elymus L. of
Qinghai Plateau. Bull Bot Res , 39(6), 846–852.
- Luo, M.C., Gu, Y.Q., Puiu, D., Wang, H., Twardziok, S.O., Deal, K.R.,
Huo, N., Zhu, T., Wang, L., & Wang, Y. (2017). Genome sequence of the
progenitor of the wheat D genome Aegilops tauschii .Nature , 551(7681), 498–502.
- Miftahudin, K.R., Ma, X.F., Mahmoud, A., Layton, J., Milla, M.R.,
Chikmawati, T., Ramalingam, J., Feril, O., Pathan, M., Momirovic,
G.S., Kim, S., Chema, K., Fang, P., Haule, L., Struxness, H., Birkes,
J., Yaghoubian, C., Skinner, R., McAllister, J., Nguyen, V., Qi, L.L.,
Echalier, B., Gill, B.S., Linkiewicz, A.M., Dubcovsky, J., Akhunov,
E.D., Dvořák, J., Dilbirligi, M., Gill, K.S., Peng, J.H., Lapitan,
N.L.V., Bermudez-Kandianis, C.E., Sorrells, M.E., Hossain, K.G.,
Kalavacharla, V., Kianian, S.F., Lazo, G.R., Chao, S., Anderson, O.D.,
Gonzalez-Hernandez, J., Conley, E.J., Anderson, J.A., Choi, D.W.,
Fenton, R.D., Close, T.J., McGuire, P.E., Qualset, C.O., Nguyen, H.T.,
& Gustafson, J.P., (2004). Analysis of expressed sequence tag loci on
wheat chromosome group 4. Genetics , 168(2), 651–663.
- Mulder, N., & Apweiler, R. (2008). Interpro and interproscan.Comparative Genomics , 59–70.
- Parra, G., Bradnam, K., & Korf, I. (2007). CEGMA: a pipeline to
accurately annotate core genes in eukaryotic genomes.Bioinformatics , 23(9), 1061–1067.
- Pertea, M., Pertea, G.M., Antonescu, C.M., Chang, T.C., Mendell, J.T.,
& Salzberg, S.L. (2015). StringTie enables improved reconstruction of
a transcriptome from RNA-seq reads. Nat Biotechnol , 33(3),
290–295.
- Roesler, K., Shintani, D., Savage, L., Boddupalli, S., & Ohlrogge, J.
(1997). Targeting of the Arabidopsis homomeric acetyl-coenzyme
A carboxylase to plastids of rapeseeds. Plant Physiol , 113(1),
75–81.
- Roudier, F., Gissot, L., Beaudoin, F., Haslam, R., Michaelson, L.,
Marion, J., Molino, D., Lima, A., Bach, L., Morin, H., Tellier, F.,
Palauqui, J., Bellec, Y., Renne, C., Miquel, M., DaCosta, M., Vignard,
J., Rochat, C., Markham, J.E., Moreau, P., Napier, J., & Faure, J.D.
(2010). Very-long-chain fatty acids are involved in polar auxin
transport and developmental patterning in Arabidopsis .Plant Cell , 22(2), 364–375.
- Seo, P.J., Lee, S.B., Suh, M.C., Park, M.-J., Go, Y.S., & Park, C.M.
(2011). The MYB96 transcription factor regulates cuticular wax
biosynthesis under drought conditions in Arabidopsis .Plant Cell , 23(3), 1138–1152.
- Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., &
Zdobnov, E.M. (2015). BUSCO: assessing genome assembly and annotation
completeness with single-copy orthologs. Bioinformatics ,
31(19), 3210–3212.
- Sun, J.M., Sheykh, M., Ahmadi, N., Cao, M.M., Zhang, Z.L., Tian, S.C.,
Sha, J., Jian, Z.M., Windley, B.F., & Talebian, M. (2021). Permanent
closure of the Tethyan Seaway in the northwestern Iranian Plateau
driven by cyclic sea-level fluctuations in the late Middle Miocene.Palaeogeogr Palaeocl , 564, 110172.
- Trapnell, C., Pachter, L., & Salzberg, S.L. (2009). TopHat:
discovering splice junctions with RNA-Seq. Bioinformatics ,
25(9), 1105–1111.
- Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley,
D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., & Pachter, L. (2012).
Differential gene and transcript expression analysis of RNA-seq
experiments with TopHat and Cufflinks. Nat Protoc , 7(3),
562–578.
- Trenkamp, S., Martin, W., & Tietjen, K. (2004). Specific and
differential inhibition of very-long-chain fatty acid elongases fromArabidopsis thaliana by different herbicides. Proc Natl
Acad , Sci. 101(32), 11903–11908
- Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A.,
Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., & Young, S.K.
(2014). Pilon: an integrated tool for comprehensive microbial variant
detection and genome assembly improvement. PLoS One , 9(11),
e112963.
- Wang, H., Sun, S., Ge, W., Zhao, L., Hou, B., Wang, K., Lyu, Z., Chen,
L., Xu, S., & Guo, J. (2020). Horizontal gene transfer of Fhb7from fungus underlies Fusarium head blight resistance in wheat.Science , 368(6493), eaba5435.
- Wang, R.R.C., Li, X.F., Robbins, M.D., Larson, S.R., Bushman, S.,
Jones, T.A., & Thomas, A. (2020). DNA sequence-based mapping and
comparative genomics of the St genome of Pseudoroegneria
spicata (Pursh) Á. Löve versus wheat (Triticum aestivum L.)
and barley (Hordeum vulgare L.). Genome , 63(9),
445–457.
- Wang, X., Yan, X., Hu, Y., Qin, L., Wang, D., Jia, J., & Jiao, Y.
(2022). A recent burst of gene duplications in Triticeae. Plant
Communications , 3(2), 100268.
- Wu, D.D., Yang, N.M,, Xiang, Q., Zhu, M.K., Fang, Z.Y., Zheng, W., Lu,
J.L., Sha, L.N., Fan, X., Cheng, Y.R., Wang, Y., Kang, H.Y., Zhang,
H.Q., & Zhou, Y.H. (2022). Pseudorogneria libanoticaintraspecific genetic polymorphism revealed by fluorescence in situ
hybridization with newly identified tandem repeats and wheat
single-copy gene probes. Int J Mol Sci . 23(23), 14818.
- Wu, D.D., Liu, X.Y., Yu, Z.H., Tan, L., Lu, J.L., Cheng, Y.R., Sha,
L.N., Fan, X., Kang, H.Y., & Wang, Y., Zhou, Y.H., Zhang, C.B., &
Zhang, H.Q. (2023). Recent natural hybridization in Elymus andCampeiostachys of Triticeae: evidence from morphological,
cytological and molecular analyses. Bo. J Linn Soc , 201(4),
428–442.
- Xue, D., Zhang, X., Lu, X., Chen, G., & Chen, Z.H. (2017). Molecular
and evolutionary mechanisms of cuticular wax for plant drought
tolerance. Front Plant Sci , 8, 621.
- Yan, C., & Sun, G.L. (2011). Nucleotide divergence and genetic
relationships of Pseudoroegneria species. Biochem Syst
Ecol , 39(4-6), 309–319.
- Yang, G.T., Boshoff, W.H.P., Li, H.W., Pretorius, Z.A., Luo, Q.L., Li,
B., Li, Z.S., & Zheng, Q. (2021). Chromosomal composition analysis
and molecular marker development for the novel Ug99 -resistant
wheat–Thinopyrum ponticum translocation line WTT34.Theor Appl Genet , 134, 1587–1599.
- Yen, C., & Yang, J.L. (2011). Triticeae biosystematics, vol. 4,
Chinese Agricultural Press, Beijing.
- Zaharia, M., Bolosky, W.J., Curtis, K., Fox, A., Patterson, D.,
Shenker, S., Stoica, I., Karp, R.M., & Sittler, T. (2011). Faster and
more accurate sequence alignment with SNAP. ArXiv , 1111.5572.
- Zeng, J., Fan, X., Zhang, H.Q., Sha, L.N., Kang, H.Y., Zhang, L.,
Yang, R.W., Ding, C.B., & Zhou, Y.H. (2012). Molecular and
cytological evidences for the natural wheat grass hybrids occurrence
and origin in west China. Genes Genom , 34(5), 499–507.
- Zhang, D., Yang, H., Wang, X., Qiu, Y., Tian, L., Qi, X., & Qu, L.Q.
(2020). Cytochrome P450 family member CYP96B5 hydroxylates
alkanes to primary alcohols and is involved in rice leaf cuticular wax
synthesis. New Phytol , 225(5), 2094–2107.
- Zhang, L., Zhu, X., Zhao, Y., Guo, J., Zhang, T., Huang, W., Huang,
J., Hu, Y., Huang, C.H., & Ma, H. (2022). Phylotranscriptomics
resolves the phylogeny of pooideae and uncovers factors for their
adaptive evolution. Mol Biol Evol , 39(2), msac026.
- Zhao, L., Haslam, T.M., Sonntag, A., Molina, I., & Kunst, L. (2019).
Functional overlap of long-chain acyl-CoA synthetases inArabidopsis . Plant Cell Physiol , 60(5), 1041–1054.
- Zhu, X., & Xiong, L. (2013). Putative megaenzyme DWA1 plays
essential roles in drought resistance by regulating stress-induced wax
deposition in rice. PANS , 110(44), 17790–17795.